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Tomasello, Salvatore, and Günther Heubl. "Phylogenetic Analysis and Molecular Characterization of Xanthium sibiricum Using DNA Barcoding, PCR-RFLP, and Specific Primers." Planta Medica 83, no. 11 (April 10, 2017): 946–53. http://dx.doi.org/10.1055/s-0043-106585.
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AbstractThe fruits of Xanthium sibiricum have been widely used in traditional Chinese medicine for the treatment of nasal sinusitis and headaches. The genus Xanthium (cocklebur) is a taxonomically complex genus. Different taxonomic concepts have been proposed, some including several species, others lumping the different taxa in a few extremely polymorphic species. Due to the morphological similarities between species, the correct authentication of X. sibiricum is very difficult. Therefore, we established a polymerase chain reaction-restriction fragment length polymorphism method and diagnostic PCR based on nuclear internal transcribed spacer and chloroplast trnQ-rps16 barcodes to differentiate X. sibirium from related species.Results from the phylogenetic analyses based on sequence information from four marker regions (plastidal psbA-trnH and trnQ-rps16 and nuclear ITS and D35) support those taxonomic concepts accepting a reduced number of species, as four to five major clades are revealed in the phylogenetic reconstructions. X. sibiricum, together with some accessions from closely related taxa, is always supported as monophyletic, constituting a well-defined genetic entity. Allele-specific primer pairs for ITS and trnQ-rps16 were designed to amplify diagnostic products from the genomic DNA of X. sibiricum. Specific PCR in combination with digestion using the restriction enzyme MseI allowed for the identification of X. sibiricum by producing specific restriction patterns. The results demonstrate that the applied techniques provide effective and accurate authentication of X. sibiricum.
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Byrne, M., and M. Hankinson. "Testing the variability of chloroplast sequences for plant phylogeography." Australian Journal of Botany 60, no. 7 (2012): 569. http://dx.doi.org/10.1071/bt12146.
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Phylogeography in plants is hampered by lack of DNA-sequence regions that detect sufficient variation in intra-specific lineages to reveal historical patterns. We tested 13 putatively highly variable non-coding chloroplast regions in six species complexes, from four different angiosperm families, where phylogeographic patterns have previously been identified using restriction fragment length polymorphism analysis of the chloroplast genome. All regions tested amplified in most of the species. The intergenic spacer regions trnQ–rps16, trnS–trnG, psbA–trnH, psbD–trnT and ndhC–trnV were the five most promising regions for phylogeographic analysis in terms of variability, and petB and rpl16 were variable, given the utility of being amplified in a single reaction. The trnQ–rps16 and psbA–trnH intergenic spacer regions and the rpl16 D4-loop intron showed variation between known lineages in all species. The psbA–trnH intergenic spacer that has been suggested as a suitable barcoding gene for plants, generally showed a level of variation similar to that in other variable regions in the species investigated here, suggesting that some caution is required in the use of this region for barcoding applications. The present analysis identified a set of seven chloroplast regions that are a useful basis for informed selection of sequences for assessment of phylogeographic structure in plants.
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ÖZÜDOĞRU, Barış. "Thlaspiceras sensu Meyer Tür Kompleksinin Plastidik trnQ-5'rps16 Bölgesine Dayalı Filogenisi." Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi 22, no. 1 (June 6, 2017): 186. http://dx.doi.org/10.19113/sdufbed.86695.
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Chen, Tao, Xiao-rong Wang, Hao-ru Tang, Qing Chen, Xiao-jiao Huang, and Jiao Chen. "Genetic diversity and population structure of Chinese Cherry revealed by chloroplast DNA trnQ-rps16 intergenic spacers variation." Genetic Resources and Crop Evolution 60, no. 6 (February 9, 2013): 1859–71. http://dx.doi.org/10.1007/s10722-013-9960-9.
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Powell, Robyn F., Anthony R. Magee, and James S. Boatwright. "Decoding ice plants: challenges associated with barcoding and phylogenetics in the diverse succulent family Aizoaceae." Genome 61, no. 11 (November 2018): 815–21. http://dx.doi.org/10.1139/gen-2018-0055.
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Aizoaceae is the largest succulent plant family in the world, including in excess of 1800 species. Despite its richness, a large proportion of its taxa are listed as data deficient and as such, has been identified as the top priority for taxonomic research in South Africa. Limitations to accurate taxonomic identification of taxa in the family may be partly attributed to the degree of technical knowledge required to identify taxa in the Aizoaceae. DNA barcoding may provide an alternative method of identification; however, the suitability of commonly used gene regions has not been tested in the family. Here, we analyse variable and parsimony informative characters (PIC), as well as the barcoding gap, in commonly used plastid regions (atpB-rbcL, matK, psbA-trnH, psbJ-petA, rpl16, rps16, trnD-trnT, trnL-trnF, trnQ-rps16, and trnS-trnG) and the nuclear region ITS (for Aizooideae only) across two subfamilies and two expanded clades within the Aizoaceae. The relative percentage of PIC was much greater in subfamilies Aizooideae and Mesembryanthemoideae than in Ruschioideae. Although nrITS had the highest percentage of PIC, barcoding gap analyses identified neither ITS nor any chloroplast region as suitable for barcoding of the family. From the results, it is evident that novel barcoding regions need to be explored within the Aizoaceae.
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Prieto, José Antonio Fernández, Joaquín Molero Mesa, Marta Pérez Suárez, Mauro Sanna, José Miguel Muñoz Díaz, and Eduardo Cires. "Are they different species or vicariant elevational races of the same species? The case of an Iberian endemic plant, Ranunculus bupleuroides (Ranunculaceae)." Phytotaxa 239, no. 3 (December 24, 2015): 242. http://dx.doi.org/10.11646/phytotaxa.239.3.5.
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The infrageneric taxonomy and evolution of Ranunculus are still not well understood. In this regard, we investigated the origin and genetic diversity of the Iberian endemic plant Ranunculus bupleuroides s.l. by analysis of nuclear internal transcribed spacers (ITS) and plastid (rpl32-trnL, rps16-trnQ, trnK-matK, ycf6-psbM) sequence data. Phylogenetic analysis reveals two geographically well supported subclades: one formed by high mountain plants and another by more typical samples of Ranunculus bupleuroides from the lowlands of the western Iberian Peninsula. The subclade of montane plants includes both plants originating in Gredos and Béjar (Ranunculus cherubicus subsp. cherubicus) and those from Sierra Nevada (R. cherubicus subsp. girelai). In the light of the new molecular results obtained, combined with an assessment of morphological, geographical and ecological characters, a new systematic treatment is proposed.
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Downie, Stephen R., Deborah S. Katz-Downie, Feng-Jie Sun, and Chang-Shook Lee. "Phylogeny and biogeography of Apiaceae tribe Oenantheae inferred from nuclear rDNA ITS and cpDNA psbI–5′trnK(UUU) sequences, with emphasis on the North American Endemics clade." Botany 86, no. 9 (September 2008): 1039–64. http://dx.doi.org/10.1139/b08-055.
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Intergeneric phylogenetic relationships within Apiaceae tribe Oenantheae were investigated using sequence data from the chloroplast DNA psbI–5′trnK(UUU) and nuclear ribosomal DNA internal transcribed spacer regions. One hundred and thirty-one accessions were examined, representing all 17 genera of the tribe and approximately one-half of its species. The cpDNA region includes four intergenic spacers and the rps16 intron and these noncoding loci were analyzed separately to assess their relative utility for resolving relationships. Separate maximum parsimony analyses of the entire psbI–5′trnK(UUU) and ITS regions, each with and without scored indels, yielded concordant trees. Phylogenies derived from maximum parsimony, Bayesian, or maximum likelihood analyses of combined chloroplast and nuclear DNA sequences for 82 accessions were highly resolved, well supported, and consistent. Among the five noncoding loci examined, the trnQ(UUG)–5′rps16 and 3′rps16–5′trnK(UUU) intergenic spacers are the most variable, with the latter contributing the greatest total number of parsimony informative characters relative to its size. The North American genera Atrema , Cynosciadium , Daucosma , Limnosciadium , Neogoezia , Oxypolis , Ptilimnium , and Trepocarpus ally with the western hemispheric and Australasian genus Lilaeopsis in a strongly supported North American Endemics clade that is a sister group to a clade composed primarily of Old World taxa ( Berula sensu lato, Cryptotaenia , Helosciadium , and Sium ). Oxypolis and Ptilimnium are not monophyletic, with the rachis-leaved members of each comprising a clade separate from their compound-leaved congeners. Dispersal-vicariance analysis suggests that the ancestors of the North American Endemics clade probably originated in Canada and the USA or in a broader ancestral area including Mexico and South America.
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SMIDT, ERIC DE CAMARGO, A. L. V. TOSCANO DE BRITO, ANNA VICTORIA SILVÉRIO R. MAUAD, and NICOLÁS GUTIÉRREZ MORALES. "An expanded concept of Madisonia including miscellaneous species of Pleurothallidinae (Orchidaceae): evidence from molecular analysis." Phytotaxa 505, no. 1 (May 28, 2021): 71–84. http://dx.doi.org/10.11646/phytotaxa.505.1.5.
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Prior taxonomic studies in subtribe Pleurothallidinae have suggested a close relationship between miscellaneous species featuring long-repent, segmented rhizomes, abbreviated ramicauls, few-flowered inflorescences, and flowers with partially connate sepals and trilobed lip. The lack of phylogenetic information for most species has prevented further conclusions or changes in their taxonomy; and as a result, they are currently assigned to several unrelated genera: Anathallis, Madisonia, Pabstiella, Pleurothallis, Sansonia and Specklinia. We performed phylogenetic analyses using nuclear (nrITS) and five plastid (matK, psbD-trnT, rps16-trnQ, trnH-psbA and trnS-trnG) markers and demonstrated that these species form an isolated clade which requires generic recognition. The name Madisonia, previously a monotypic genus endemic of the Amazon basin, is re-circumscribed and expanded to include nine species distributed in the Atlantic Rainforest and the Caribbean. Eight new nomenclatural combinations are proposed.
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Vinícius-Silva, Ronaldo, Lynn G. Clark, Jéferson Nunes Fregonezi, and Ana Paula Santos-Gonçalves. "Morphological evolution and molecular phylogenetics of the Merostachys clade (Poaceae: Bambusoideae: Bambuseae: Arthrostylidiinae) based on multi-locus plastid sequences." Botanical Journal of the Linnean Society 195, no. 1 (September 3, 2020): 53–76. http://dx.doi.org/10.1093/botlinnean/boaa057.
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Abstract Merostachys is a Neotropical woody bamboo genus that occurs in the understory and along forest borders. Our taxonomic studies of its species and morphological analyses have allowed us to recognize morphological groups in the genus. Previous molecular analyses, which included relatively few species, supported Merostachys as monophyletic and sister to Actinocladum or Athroostachys. We here provide a phylogenetic estimation for Merostachys based on a broader taxon sampling and seven plastid markers (one coding: ndhF 3′ end; four intergenic spacers: rps16-trnQ, trnC-rpoB, trnD-trnT and trnT-trnL; and two introns: rpl16 and rps16). We aimed to test the monophyly of the genus, to verify its relationship with other genera of Arthrostylidiinae, mainly Athroostachys and Actinocladum, and to test whether the previously identified morphological groups were congruent with the molecular data. The monophyly of the genus was confirmed, as was its sister relationship with Athroostachys, although alternate hypothesis testing could not reject a sister relationship with Actinocladum. Two well-supported clades in Merostachys were recovered, one of which encompasses a polytomy. These clades did not exhibit consistent morphological synapomorphies and were not congruent with the morphological groups; however, floret surface (shiny vs. dull) was correlated with the two clades. The lack of resolution in Merostachys, as exemplified by the polytomy, can be attributed mainly to incomplete lineage sorting, suggesting a recent radiation in this group.
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FRIESEN, NIKOLAI, POLINA VESSELOVA, BEKTEMIR OSMONALY, GULNARA SITPAYEVA, ALEXANDER LUFEROV, and ALEXANDER SHMAKOV. "Allium toksanbaicum (Amaryllidaceae), a new species from Southeast Kazakhstan." Phytotaxa 494, no. 3 (April 7, 2021): 251–67. http://dx.doi.org/10.11646/phytotaxa.494.3.1.
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Allium toksanbaicum from South East Kazakhstan is described as a new species. Molecular markers reveal a close relationship to A. obliquum and some other central Asian species of the section Oreiprason. We investigated the phylogenetic relationship of the new species based on sequences of two chloroplast spacers (rpl32-trnL and trnQ-rps16) and the nuclear ribosomal DNA internal transcribed spacer (ITS) region. The new species is diploid with a chromosome number of 2n = 2x = 16. A detailed morphological description, illustrations and karyotype features of the new species are given. With its falcate leaves, the new species is very similar to A. carolinianum from the section Falcatifolia, but in the shape of the inflorescence and flowers it is very different from it. From A. obliquum it differs for the purple colour of flowers and filaments, as well as the presence of teeth at the base of inner stamens.
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Sun, Jianying, Xiaofeng Dong, Qinghe Cao, Tao Xu, Mingku Zhu, Jian Sun, Tingting Dong, Daifu Ma, Yonghua Han, and Zongyun Li. "A systematic comparison of eight new plastome sequences from Ipomoea L." PeerJ 7 (March 11, 2019): e6563. http://dx.doi.org/10.7717/peerj.6563.
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Background Ipomoea is the largest genus in the family Convolvulaceae. The species in this genus have been widely used in many fields, such as agriculture, nutrition, and medicine. With the development of next-generation sequencing, more than 50 chloroplast genomes of Ipomoea species have been sequenced. However, the repeats and divergence regions in Ipomoea have not been well investigated. In the present study, we sequenced and assembled eight chloroplast genomes from sweet potato’s close wild relatives. By combining these with 32 published chloroplast genomes, we conducted a detailed comparative analysis of a broad range of Ipomoea species. Methods Eight chloroplast genomes were assembled using short DNA sequences generated by next-generation sequencing technology. By combining these chloroplast genomes with 32 other published Ipomoea chloroplast genomes downloaded from GenBank and the Oxford Research Archive, we conducted a comparative analysis of the repeat sequences and divergence regions across the Ipomoea genus. In addition, separate analyses of the Batatas group and Quamoclit group were also performed. Results The eight newly sequenced chloroplast genomes ranged from 161,225 to 161,721 bp in length and displayed the typical circular quadripartite structure, consisting of a pair of inverted repeat (IR) regions (30,798–30,910 bp each) separated by a large single copy (LSC) region (87,575–88,004 bp) and a small single copy (SSC) region (12,018–12,051 bp). The average guanine-cytosine (GC) content was approximately 40.5% in the IR region, 36.1% in the LSC region, 32.2% in the SSC regions, and 37.5% in complete sequence for all the generated plastomes. The eight chloroplast genome sequences from this study included 80 protein-coding genes, four rRNAs (rrn23, rrn16, rrn5, and rrn4.5), and 37 tRNAs. The boundaries of single copy regions and IR regions were highly conserved in the eight chloroplast genomes. In Ipomoea, 57–89 pairs of repetitive sequences and 39–64 simple sequence repeats were found. By conducting a sliding window analysis, we found six relatively high variable regions (ndhA intron, ndhH-ndhF, ndhF-rpl32, rpl32-trnL, rps16-trnQ, and ndhF) in the Ipomoea genus, eight (trnG, rpl32-trnL, ndhA intron, ndhF-rpl32, ndhH-ndhF, ccsA-ndhD, trnG-trnR, and pasA-ycf3) in the Batatas group, and eight (ndhA intron, petN-psbM, rpl32-trnL, trnG-trnR, trnK-rps16, ndhC-trnV, rps16-trnQ, and trnG) in the Quamoclit group. Our maximum-likelihood tree based on whole chloroplast genomes confirmed the phylogenetic topology reported in previous studies. Conclusions The chloroplast genome sequence and structure were highly conserved in the eight newly-sequenced Ipomoea species. Our comparative analysis included a broad range of Ipomoea chloroplast genomes, providing valuable information for Ipomoea species identification and enhancing the understanding of Ipomoea genetic resources.
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Islam, Melissa Bauer, and Robert P. Guralnick. "Generic Placement of the Former Condaliopsis (Rhamnaceae) species." Phytotaxa 236, no. 1 (November 25, 2015): 25. http://dx.doi.org/10.11646/phytotaxa.236.1.2.
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Condaliopsis is a genus of eight thorny shrub species. Previous morphological research shed doubt on the validity of Condaliopsis as a distinct genus in Rhamnaceae. Condaliopsis species were transferred to one of two genera, Ziziphus or Condalia, but some authors continue to recognize Condaliopsis. A recent phylogenetic study did not support Condaliopsis as monophyletic and placement of Condaliopsis species in either Ziziphus or Condalia was not straightforward. To clarify the generic placement of these eight species, we conducted phylogenetic analyses based on two nuclear loci (nrITS and 26S), two chloroplast loci (trnL-F and trnQ-rps16) and morphological characters. We present evidence that five of the Condaliopsis species should remain in Ziziphus, one should remain in Condalia, and two should be transferred from Ziziphus to Condalia. One of these species had an existing binomial within Condalia, Condalia parryi, and one required a new combination, Condalia celata. Condalia celata is a federally listed endangered species with a limited range in Florida.
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LI, HUAI-CHENG, XUE-LI ZHAO, XIN-FEN GAO, and BO XU. "Molecular phylogeny of the genus Hylodesmum (Fabaceae)." Phytotaxa 403, no. 3 (May 13, 2019): 221. http://dx.doi.org/10.11646/phytotaxa.403.3.6.
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The phylogenetic relationships of 12 Hylodesmum species and closely related genera were reconstructed using maximum parsimony, maximum likelihood, and Bayesian analyses based on two chloroplast DNA regions (rps16-trnQ and trnL-F) and one nuclear marker (internal transcribed spacer, ITS). All analyses yielded reliable relationships among the major lineages within Hylodesmum, suggesting that Hylodesmum is monophyletic. Neither the traditionally defined Desmodium sect. Podocarpium nor D. sect. Repanda within the genus was supported as being monophyletic based on the ITS analyses and the combined ITS and chloroplast dataset analyses. The phylogenetic topologies indicated that the three species included in D. sect. Repanda were separated into different clades, which suggested that D. sect. Repanda is paraphyletic. Generally, the clades retrieved by phylogenetic analyses within D. sect. Podocarpium were consistent with traditionally defined groups except for the American group. The molecular analysis provides information regarding the revision of the traditional taxonomic system of Hylodesmum and for the evaluation of the systematic positions of each species within the genus Hylodesmum.
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Solórzano, Chincoya, Sanchez-Flores, Estrada, Díaz-Velásquez, González-Rodríguez, Vaca-Paniagua, Dávila, and Arias. "De Novo Assembly Discovered Novel Structures in Genome of Plastids and Revealed Divergent Inverted Repeats in Mammillaria (Cactaceae, Caryophyllales)." Plants 8, no. 10 (October 1, 2019): 392. http://dx.doi.org/10.3390/plants8100392.
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The complete sequence of chloroplast genome (cpDNA) has been documented for single large columnar species of Cactaceae, lacking inverted repeats (IRs). We sequenced cpDNA for seven species of the short-globose cacti of Mammillaria and de novo assembly revealed three novel structures in land plants. These structures have a large single copy (LSC) that is 2.5 to 10 times larger than the small single copy (SSC), and two IRs that contain strong differences in length and gene composition. Structure 1 is distinguished by short IRs of <1 kb composed by rpl23-trnI-CAU-ycf2; with a total length of 110,189 bp and 113 genes. In structure 2, each IR is approximately 7.2 kb and is composed of 11 genes and one Intergenic Spacer-(psbK-trnQ)-trnQ-UUG-rps16-trnK-UUU-matK-trnK-UUU-psbA-trnH-GUG-rpl2-rpl23-trnI-CAU-ycf2; with a total size of 116,175 bp and 120 genes. Structure 3 has divergent IRs of approximately 14.1 kb, where IRA is composed of 20 genes: psbA-trnH-GUG-rpl23-trnI-CAU-ycf2-ndhB-rps7-rps12-trnV-GAC-rrn16-ycf68-trnI-GAU-trnA-AGC-rrn23-rrn4.5-rrn5-trnR-ACG-trnN-GUU-ndhF-rpl32; and IRB is identical to the IRA, but lacks rpl23. This structure has 131 genes and, by pseudogenization, it is shown to have the shortest cpDNA, of just 107,343 bp. Our findings show that Mammillaria bears an unusual structural diversity of cpDNA, which supports the elucidation of the evolutionary processes involved in cacti lineages.
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CHEN, Tao, Xiao-Rong WANG, Hua LUO, Chun-Tao WANG, Jia-Zhi ZHANG, and Ming-Min LUO. "Chloroplast DNA trnQ-rps16 variation and genetic structure of nine wild Chinese cherry (Cerasus pseudocerasus Lindl.) populations." Hereditas (Beijing) 34, no. 11 (November 20, 2012): 1475–83. http://dx.doi.org/10.3724/sp.j.1005.2012.01475.
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Attigala, Lakshmi, Jimmy K. Triplett, Hashendra-Suvini Kathriarachchi, and Lynn G. Clark. "A new genus and a major temperate bamboo lineage of the Arundinarieae (Poaceae: Bambusoideae) from Sri Lanka based on a multi-locus plastid phylogeny." Phytotaxa 174, no. 4 (July 16, 2014): 187. http://dx.doi.org/10.11646/phytotaxa.174.4.1.
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Kuruna, a new temperate woody bamboo (Poaceae, Bambusoideae, Arundinarieae) genus from Sri Lanka, is recognized based on chloroplast sequence data from five markers (coding: ndhF 3’ end; non-coding: rps16-trnQ, trnC-rpoB, trnD-trnT, trnT-trnL). This genus represents the twelfth major lineage of temperate woody bamboos and is characterized by pachymorph culm bases with short necks, unicaespitose clumps, culm leaf girdles ca. 1 mm wide, usually abaxially hispid culm leaves with non-irritating hairs, persistent foliage leaf sheaths, complete branch sheathing and acute to biapiculate palea apices. Maximum Parsimony, Bayesian Inference and Maximum Likelihood analyses of a combined data set consistently strongly supported the monophyly of this Sri Lankan temperate woody bamboo clade. Although the Kishino-Hasegawa test is unable to reject the alternative hypothesis of monophyly of the Sri Lankan clade plus Bergbambos tessellata from South Africa, Kuruna and Bergbambos are distinguishable by a combination of morphological characters. A few additional cpDNA markers not previously used in phylogenetic analyses of Arundinarieae were tested to evaluate their utility in this taxonomically difficult tribe.
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MILJKOVIĆ, MILICA, VLADIMIR RANĐELOVIĆ, and DÖRTE HARPKE. "A new species of Crocus (Iridaceae) from southern Albania (SW Balkan Peninsula)." Phytotaxa 265, no. 1 (June 9, 2016): 39. http://dx.doi.org/10.11646/phytotaxa.265.1.3.
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A new Crocus species (Iridaceae) for southern Albania, Crocus novicii sp. nov. (Iridaceae), is described and illustrated. We here provide diagnostic morphological characteristics, results of molecular analyses, detailed descriptions and illustrations of this new species and compare it with its relatives C. jablanicensis, C. cvijicii and C. veluchensis. Our molecular analysis is based on two chloroplast (matK–trnK, rps16–trnQ) and three nuclear markers (nrETS, nrITS, TOPO6B exon3–exon6) and includes representatives of all related species (C. cvijicii, C. dalmaticus, C. jablanicensis, C. rujanensis, C. sieberi subsp. atticus, and C. veluchensis). Morphologically, C. novicii can be distinguished from its relatives by its white flower with lilac coloring at the base of the perigone and its higher number of leaves (> 3). Although it is morphologically close to C. jablanicensis, molecular analysis has revealed a close affiliation to C. veluchensis. Crocus novicii is diploid with 2n = 20 chromosomes. The new species is named after the Serbian botanist Novica Ranđelović to honor his important work on the genus Crocus on the Balkan Peninsula.
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Niu, Erli, Chengying Jiang, Wei Wang, Yu Zhang, and Shenlong Zhu. "Chloroplast Genome Variation and Evolutionary Analysis of Olea europaea L." Genes 11, no. 8 (August 3, 2020): 879. http://dx.doi.org/10.3390/genes11080879.
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Olive (Olea europaea L.) is a very important woody tree and favored by consumers because of the fruit’s high-quality olive oil. Chloroplast genome analysis will provide insights into the chloroplast variation and genetic evolution of olives. The complete chloroplast genomes of three accessions (O. europaea subsp. cuspidata isolate Yunnan, O. europaea subsp. europaea var. sylvestris, and O. europaea subsp. europaea var. frantoio) were obtained by next-generation sequencing technology. A total of 133 coding regions were identified in the three chloroplast genomes without rearrangement. O. europaea subsp. europaea var. sylvestris and O. europaea subsp. europaea var. frantoio had the same sequences (155,886 bp), while O. europaea subsp. cuspidata isolate Yunnan (155,531 bp) presented a large gap between rps16 and trnQ-UUG genes with six small gaps and fewer microsatellites. The whole chloroplast genomes of 11 O. europaea were divided into two main groups by a phylogenetic tree and O. europaea subsp. cuspidata formed a separate group (Cuspidata group) with the other subspecies (Mediterranean/North African group). Identification of consistency and diversity among O. europaea subspecies will benefit the exploration of domestication events and facilitate molecular-assisted breeding for O. europaea.
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Song, Yun, Yan Chen, Jizhou Lv, Jin Xu, Shuifang Zhu, and MingFu Li. "Comparative Chloroplast Genomes of Sorghum Species: Sequence Divergence and Phylogenetic Relationships." BioMed Research International 2019 (March 19, 2019): 1–11. http://dx.doi.org/10.1155/2019/5046958.
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Sorghum comprises 31 species that exhibit considerable morphological and ecological diversity. The phylogenetic relationships among Sorghum species still remain unresolved due to lower information on the traditional DNA markers, which provides a limited resolution for identifying Sorghum species. In this study, we sequenced the complete chloroplast genomes of Sorghum sudanense and S. propinquum and analyzed the published chloroplast genomes of S. bicolor and S. timorense to retrieve valuable chloroplast molecular resources for Sorghum. The chloroplast genomes ranged in length from 140,629 to 140,755 bp, and their gene contents, gene orders, and GC contents were similar to those for other Poaceae species but were slightly different in the number of SSRs. Comparative analyses among the four chloroplast genomes revealed 651 variable sites, 137 indels, and nine small inversions. Four highly divergent DNA regions (rps16-trnQ, trnG-trnM, rbcL-psaI, and rps15-ndhF), which were suitable for phylogenetic and species identification, were detected in the Sorghum chloroplast genomes. A phylogenetic analysis strongly supported that Sorghum is a monophyletic group in the tribe Andropogoneae. Overall, the genomic resources in this study could provide potential molecular markers for phylogeny and species identification in Sorghum.
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Yik, Mavis Hong-Yu, Bobby Lim-Ho Kong, Tin-Yan Siu, David Tai-Wai Lau, Hui Cao, and Pang-Chui Shaw. "Differentiation of Hedyotis diffusa and Common Adulterants Based on Chloroplast Genome Sequencing and DNA Barcoding Markers." Plants 10, no. 1 (January 15, 2021): 161. http://dx.doi.org/10.3390/plants10010161.
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Chinese herbal tea, also known as Liang Cha or cooling beverage, is popular in South China. It is regarded as a quick-fix remedy to relieve minor health problems. Hedyotis diffusa Willd. (colloquially Baihuasheshecao) is a common ingredient of cooling beverages. H. diffusa is also used to treat cancer and bacterial infections. Owing to the high demand for H. diffusa, two common adulterants, Hedyotis brachypoda (DC.) Sivar and Biju (colloquially Nidingjingcao) and Hedyotis corymbosa (L.) Lam. (colloquially Shuixiancao), are commonly encountered in the market. Owing to the close similarity of their morphological characteristics, it is difficult to differentiate them. Here, we sequenced the complete chloroplast genomes of the three species of Hedyotis using next-generation sequencing (NGS). By comparing the complete chloroplast genomes, we found that they are closely related in the subfamily Rubioideae. We also discovered that there are significant differences in the number and repeating motifs of microsatellites and complex repeats and revealed three divergent hotspots, rps16-trnQ intergenic spacer, ndhD and ycf1. By using these species-specific sequences, we propose new DNA barcoding markers for the authentication of H. diffusa and its two common adulterants.
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Sexton, Tineke Berends, Jennifer T. Jones, and John E. Mullet. "Sequence and transcriptional analysis of the barley ctDNA region upstream of psbD-psbC encoding trnK(UUU), rps16, trnQ(UUG), psbK, psbI, and trnS(GCU)." Current Genetics 17, no. 5 (May 1990): 445–54. http://dx.doi.org/10.1007/bf00334526.
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Cui, Nie, Sun, Xu, Wang, Yu, Song, and Yao. "Comparative and Phylogenetic Analyses of Ginger (Zingiber officinale) in the Family Zingiberaceae Based on the Complete Chloroplast Genome." Plants 8, no. 8 (August 12, 2019): 283. http://dx.doi.org/10.3390/plants8080283.
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Zingiber officinale, commonly known as ginger, is an important plant of the family Zingiberaceae and is widely used as an herbal medicine and condiment. The lack of chloroplast genomic information hinders molecular research and phylogenetic analysis on ginger. We introduced the complete chloroplast genome of Z. officinale and identified its phylogenetic position in Zingiberaceae. The chloroplast genome of Z. officinale is 162,621 bp with a four-part circular structure and 36.1% GC content. All 113 unique genes were annotated. A total of 78 simple sequence repeats (SSRs) and 42 long repeat sequences, which are potential areas for species authentication, were found. Comparative analysis revealed some highly variable regions, including rps16-trnQ-UUG, atpH-atpI, trnT-UGU-trnL-UAA, ycf1, and psaC-ndhE. Moreover, the small single-copy (SSC) region was the most variable region in all four shared regions, indicating that it may be undergoing rapid nucleotide substitution in the family Zingiberaceae. Phylogenetic analysis based on all available chloroplasts of Zingiberales in the National Center for Biotechnology Information indicated that Zingiber is a sister branch to Kaempferia species. The availability of the Z. officinale chloroplast genome provided invaluable data for species-level authentication and phylogenetic analysis and can thus benefit further investigations on species in the family Zingiberaceae.
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Huang, Jiao, Yan Yu, Yan-Mei Liu, Deng-Feng Xie, Xing-Jin He, and Song-Dong Zhou. "Comparative Chloroplast Genomics of Fritillaria (Liliaceae), Inferences for Phylogenetic Relationships between Fritillaria and Lilium and Plastome Evolution." Plants 9, no. 2 (January 21, 2020): 133. http://dx.doi.org/10.3390/plants9020133.
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Fritillaria is a genus that has important medicinal and horticultural values. The study involved the most comprehensive chloroplast genome samples referring to Old and New World clades of Fritillaria for marker selection and phylogenetic studies. We reported and compared eleven newly sequenced whole-plastome sequences of Fritillaria which proved highly similar in overall size (151,652–152,434 bp), genome structure, gene content, and order. Comparing them with other species of Liliales (6 out of 10 families) indicated the same similarity but showed some structural variations due to the contraction or expansion of the inverted repeat (IR) regions. A/T mononucleotides, palindromic, and forward repeats were the most common types. Six hypervariable regions (rps16-trnQ, rbcL-accD, accD-psaI, psaJ-rpl33, petD-rpoA, and rpl32-trnL) were discovered based on 26 Fritillaria whole-plastomes to be potential molecular markers. Based on the plastome data that were collected from 26 Fritillaria and 21 Lilium species, a phylogenomic study was carried out with three Cardiocrinum species as outgroups. Fritillaria was sister to Lilium with a high support value, and the interspecies relationships within subgenus Fritillaria were resolved very well. The six hypervariable regions can be used as candidate DNA barcodes of Fritillaria and the phylogenomic framework can guide extensive genomic sampling for further phylogenetic analyses.
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Zhang, Qing-Ying, Yu-Juan Zhao, and Xun Gong. "Genetic variation and phylogeography of Psammosilene tunicoides (Caryophyllaceae), a narrowly distributed and endemic species in south-western China." Australian Journal of Botany 59, no. 5 (2011): 450. http://dx.doi.org/10.1071/bt11024.
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Psammosilene tunicoides is a narrowly distributed and endemic species in south-western China. An investigation of sequence variation at two chloroplast DNA (cpDNA) regions (rpL16, trnQ-5′rps16) and one nuclear DNA (nDNA) locus (GPA1) were carried out to survey the population structure and population history of the species. Among the 22 populations across its geographical range, nine chloroplast haplotypes and 17 nuclear alleles were identified. Both cpDNA and nDNA consistently revealed high levels of population differentiation (GST = 0.604 and 0.540, respectively), suggesting a distinct phylogeographic structure (NST > GST, P < 0.01). This high genetic differentiation might be a combined effect of breeding system, limited pollen and seed dispersal and geographic isolation of populations. The level of haplotype diversities (cpDNA, hT = 0.575; nDNA, hT = 0.724) were high, but the nucleotide diversities (cpDNA, π = 0.00099; nDNA, π = 0.00105) were low. These results together with the star-like phylogenetic pattern and neutrality tests indicate that P. tunicoides has experienced a population expansion event in its evolution. Limited genetic exchange after population expansion was supported by the pronounced genetic differentiation among populations as well as evidence for ‘isolation-by-distance’ revealed by cpDNA. Due to high population subdivision and complex landscape, as many populations as possible should be considered for genetic conservation.
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Özgişi, Kurtuluş, Burcu Tarıkahya-Hacıoğlu, and Atilla Ocak. "Species delimitation in Noccaea densiflora species complex (Brassicaceae) based on morphological and molecular data." Botany 99, no. 7 (July 2021): 389–402. http://dx.doi.org/10.1139/cjb-2020-0184.
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The accurate identification of an organism is the basis of all biological disciplines. Although there have been many different species concepts and methods proposed, researchers generally choose the most appropriate concept according to their interests. However, each species concept has both advantages and disadvantages. In such cases, an integrated concept based on evidence obtained from different species concepts and methods is suitable for the accurate delimitation of a species. The biggest dilemma of integrated species delimitation methods is the inconsistency between species concepts and methods. Herein, the congruency of the different concepts and methods was tested to reveal the relationship of the Noccaea densiflora species complex. Nuclear ribosomal internal transcribed spacer, chloroplast trnL-F, and trnQ-5′rps16 regions were used for species delimitation using the multispecies coalescent model as implemented in two developed Bayesian methods. Internal transcribed spacer and trnL-F regions were also used for Templeton, Crandall, and Singh haplotype network analyses. In addition to morphological measurements from different populations and vouchers, specific bioclimatic data values were also used for the principal component analysis. Based on the analyses, it was determined that only one population of N. densiflora (Boiss. & Kotschy) F.K. Mey. and one of Noccaea microstyla (Boiss.) F.K. Mey. were clearly distinct, whereas the rest of the specimens remain taxonomically uncertain.
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Gu, Li, Ting Su, Ming-Tai An, and Guo-Xiong Hu. "The Complete Chloroplast Genome of the Vulnerable Oreocharis esquirolii (Gesneriaceae): Structural Features, Comparative and Phylogenetic Analysis." Plants 9, no. 12 (December 2, 2020): 1692. http://dx.doi.org/10.3390/plants9121692.
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Oreocharis esquirolii, a member of Gesneriaceae, is known as Thamnocharis esquirolii, which has been regarded a synonym of the former. The species is endemic to Guizhou, southwestern China, and is evaluated as vulnerable (VU) under the International Union for Conservation of Nature (IUCN) criteria. Until now, the sequence and genome information of O. esquirolii remains unknown. In this study, we assembled and characterized the complete chloroplast (cp) genome of O. esquirolii using Illumina sequencing data for the first time. The total length of the cp genome was 154,069 bp with a typical quadripartite structure consisting of a pair of inverted repeats (IRs) of 25,392 bp separated by a large single copy region (LSC) of 85,156 bp and a small single copy region (SSC) of18,129 bp. The genome comprised 114 unique genes with 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Thirty-one repeat sequences and 74 simple sequence repeats (SSRs) were identified. Genome alignment across five plastid genomes of Gesneriaceae indicated a high sequence similarity. Four highly variable sites (rps16-trnQ, trnS-trnG, ndhF-rpl32, and ycf 1) were identified. Phylogenetic analysis indicated that O. esquirolii grouped together with O. mileensis, supporting resurrection of the name Oreocharis esquirolii from Thamnocharisesquirolii. The complete cp genome sequence will contribute to further studies in molecular identification, genetic diversity, and phylogeny.
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Tsudzuki, Junko, Keiko Nakashima, Takahiko Tsudzuki, Junzou Hiratsuka, Masaru Shibata, Tatsuya Wakasugi, and Masahiro Sugiura. "Chloroplast DNA of black pine retains a residual inverted repeat lacking rRNA genes: nucleotide sequences of trnQ, trnK, psbA, trnI and trnH and the absence of rps16." Molecular and General Genetics MGG 232, no. 2 (March 1992): 206–14. http://dx.doi.org/10.1007/bf00279998.
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Liu, Tong-Jian, Cai-Yun Zhang, Hai-Fei Yan, Lu Zhang, Xue-Jun Ge, and Gang Hao. "Complete plastid genome sequence ofPrimula sinensis(Primulaceae): structure comparison, sequence variation and evidence foraccDtransfer to nucleus." PeerJ 4 (June 28, 2016): e2101. http://dx.doi.org/10.7717/peerj.2101.
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Species-rich genusPrimulaL. is a typical plant group with which to understand genetic variance between species in different levels of relationships. Chloroplast genome sequences are used to be the information resource for quantifying this difference and reconstructing evolutionary history. In this study, we reported the complete chloroplast genome sequence ofPrimula sinensisand compared it with other related species. This genome of chloroplast showed a typical circular quadripartite structure with 150,859 bp in sequence length consisting of 37.2% GC base. Two inverted repeated regions (25,535 bp) were separated by a large single-copy region (82,064 bp) and a small single-copy region (17,725 bp). The genome consists of 112 genes, including 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Among them, seven coding genes, seven tRNA genes and four rRNA genes have two copies due to their locations in the IR regions. TheaccDandinfAgenes lacking intact open reading frames (ORF) were identified as pseudogenes. SSR and sequence variation analyses were also performed on the plastome ofPrimula sinensis, comparing with another available plastome ofP. poissonii. The four most variable regions,rpl36–rps8,rps16–trnQ,trnH–psbAandndhC–trnV, were identified. Phylogenetic relationship estimates using three sub-datasets extracted from a matrix of 57 protein-coding gene sequences showed the identical result that was consistent with previous studies. A transcript found fromP. sinensistranscriptome showed a high similarity to plastidaccDfunctional region and was identified as a putative plastid transit peptide at the N-terminal region. The result strongly suggested that plastidaccDhas been functionally transferred to the nucleus inP. sinensis.
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Holmes, Gareth D., Trisha L. Downing, Elizabeth A. James, Mark J. Blacket, Ary A. Hoffmann, and Michael J. Bayly. "Phylogeny of the holly grevilleas (Proteaceae) based on nuclear ribosomal and chloroplast DNA." Australian Systematic Botany 27, no. 1 (2014): 56. http://dx.doi.org/10.1071/sb13045.
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The holly grevilleas are an informal grouping of 15 species (19 taxa) of woody shrubs from south-eastern Australia, with a centre of distribution in central to western Victoria. Many of the species are narrowly endemic. The present study is the first molecular-phylogenetic analysis of the group, with the aim of providing an evolutionary framework for assessing species-level taxonomy and conservation priorities. Analyses using the nrDNA internal transcribed spacer (ITS) regions were complicated by the presence of divergent paralogues, including inferred pseudogenes; analyses restricted to presumed orthologous, functional ITS sequences were uninformative. Combined analyses of three chloroplast intergenic spacers (trnQ–5′rps16, trnL–trnF and rpoB–trnC) strongly support the monophyly of a core group of 16 taxa (the ‘southern holly grevilleas’) from Victoria and South Australia. However, nodes outside this group are poorly resolved and poorly supported, and the relationships of taxa from New South Wales and eastern Victoria (the ‘northern holly grevilleas’) are unclear. Among the southern holly grevilleas, the following four distinct and partly sympatric cpDNA clades are identified: the ‘Grevillea ilicifolia’, ‘G. aquifolium’, ‘G. dryophylla’ and ‘G. repens’ clades, among which the earliest and most strongly supported divergence is that of the western-most ‘G. ilicifolia’ clade. Variation in cpDNA is incongruent with current species-level taxonomy, especially for G. aquifolium (polyphyletic), G. montis-cole (polyphyletic, but the two subspecies each monophyletic) and G. microstegia (nested in G. aquifolium). The effects of incomplete chloroplast lineage sorting, gene flow through hybridisation or introgression, and inappropriate taxonomy are possible explanations for this incongruence. The formal conservation listing for some species within the holly grevillea group requires re-evaluation.
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Wang, Liqiang, Hui Zhang, Mei Jiang, Haimei Chen, Linfang Huang, and Chang Liu. "Complete plastome sequence of Iodes cirrhosa Turcz., the first in the Icacinaceae, comparative genomic analyses and possible split of Idoes species in response to climate changes." PeerJ 7 (April 1, 2019): e6663. http://dx.doi.org/10.7717/peerj.6663.
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Plastome-based phylogenetic study has largely resolved the phylogeny of Icacinaceae. However, no single complete plastome sequence is available for Icacinaceae species, thereby limiting the further phylogenomics analysis of the members of this family. Here, we obtained the complete plastome sequence of Iodes cirrhosa Turcz., which is the first in Icacinaceae, by using the next-generation sequencing technology. The genome was annotated and compared with other closely related plastomes by using mVISTA. The divergence time of six Iodes species was analyzed using the BEAST software. The plastome of I. cirrhosa was 151,994 bp long, with a pair of inverted repeats (IRs, 24,973 bp) separated by a large single-copy (LSC, 84,527 bp) region and a small single-copy (SSC, 17,521 bp) region. The plastome encoded 112 unique genes, including 80 protein-coding, 28 tRNA, and four rRNA genes. Approximately 59 repeat sequences and 188 simple sequence repeats were identified. Four pairs of partially overlapped genes, namely, psbD/psbC, ndhF/Ψycf1, atpB/atpE, and rpl22/rps3, were observed. A comparison of the boundaries of the LSC, SSC, and IR regions with four other plastomes from Aquifoliales and Sapindales exhibited a high overall degree of sequence similarity. Four most highly variable regions, namely, trnH-GUG/psbA, psbM/trnD-GUC, petA/psbJ, and rps16/trnQ-UUG, were found. Using the plastome of I. cirrhosa as reference, we reassembled the plastomes of five Iodes species. Ka/Ks ratio analyses revealed that 27 genes and 52 amino acid residue sites from 11 genes had undergone strong positive selection in the Iodes branch, with the most abundant proteins being the NDH and ribosomal proteins. Divergence-time analysis indicated that Iodes species were first formed 34.40 million years ago. Results revealed that the ancestor of the six species was likely to have split in the late Eocene epoch. In summary, the first complete plastome sequence of I. cirrhosa provided valuable information regarding the evolutionary processes of Iodes species.
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Yang, JiYoung, Yu-Chung Chiang, Tsai-Wen Hsu, Seon-Hee Kim, Jae-Hong Pak, and Seung-Chul Kim. "Characterization and comparative analysis among plastome sequences of eight endemic Rubus (Rosaceae) species in Taiwan." Scientific Reports 11, no. 1 (January 13, 2021). http://dx.doi.org/10.1038/s41598-020-80143-1.
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AbstractGenus Rubus represents the second largest genus of the family Rosaceae in Taiwan, with 41 currently recognized species across three subgenera (Chamaebatus, Idaoeobatus, and Malochobatus). Despite previous morphological and cytological studies, little is known regarding the overall phylogenetic relationships among the Rubus species in Taiwan, and their relationships to congeneric species in continental China. We characterized eight complete plastomes of Taiwan endemic Rubus species: subg. Idaeobatus (R. glandulosopunctatus, R. incanus, R. parviaraliifolius, R rubroangustifolius, R. taitoensis, and R. taiwanicolus) and subg. Malachobatus (R. kawakamii and R. laciniastostipulatus) to determine their phylogenetic relationships. The plastomes were highly conserved and the size of the complete plastome sequences ranged from 155,566 to 156,236 bp. The overall GC content ranged from 37.0 to 37.3%. The frequency of codon usage showed similar patterns among species, and 29 of the 73 common protein-coding genes were positively selected. The comparative phylogenomic analysis identified four highly variable intergenic regions (rps16/trnQ, petA/psbJ, rpl32/trnL-UAG, and trnT-UGU/trnL-UAA). Phylogenetic analysis of 31 representative complete plastomes within the family Rosaceae revealed three major lineages within Rubus in Taiwan. However, overall phylogenetic relationships among endemic species require broader taxon sampling to gain new insights into infrageneric relationships and their plastome evolution.
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Kong, Bobby Lim-Ho, Hyun-Seung Park, Tai-Wai David Lau, Zhixiu Lin, Tae-Jin Yang, and Pang-Chui Shaw. "Comparative analysis and phylogenetic investigation of Hong Kong Ilex chloroplast genomes." Scientific Reports 11, no. 1 (March 4, 2021). http://dx.doi.org/10.1038/s41598-021-84705-9.
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AbstractIlex is a monogeneric plant group (containing approximately 600 species) in the Aquifoliaceae family and one of the most commonly used medicinal herbs. However, its taxonomy and phylogenetic relationships at the species level are debatable. Herein, we obtained the complete chloroplast genomes of all 19 Ilex types that are native to Hong Kong. The genomes are conserved in structure, gene content and arrangement. The chloroplast genomes range in size from 157,119 bp in Ilex graciliflora to 158,020 bp in Ilex kwangtungensis. All these genomes contain 125 genes, of which 88 are protein-coding and 37 are tRNA genes. Four highly varied sequences (rps16-trnQ, rpl32-trnL, ndhD-psaC and ycf1) were found. The number of repeats in the Ilex genomes is mostly conserved, but the number of repeating motifs varies. The phylogenetic relationship among the 19 Ilex genomes, together with eight other available genomes in other studies, was investigated. Most of the species could be correctly assigned to the section or even series level, consistent with previous taxonomy, except Ilex rotunda var. microcarpa, Ilex asprella var. tapuensis and Ilex chapaensis. These species were reclassified; I. rotunda was placed in the section Micrococca, while the other two were grouped with the section Pseudoaquifolium. These studies provide a better understanding of Ilex phylogeny and refine its classification.
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Wang, Zhi, Caihong Zhong, Dawei Li, Chunlin Yan, Xiaohong Yao, and Zuozhou Li. "Cytotype distribution and chloroplast phylogeography of the Actinidia chinensis complex." BMC Plant Biology 21, no. 1 (July 6, 2021). http://dx.doi.org/10.1186/s12870-021-03099-y.
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Abstract Background Plant phylogeographic studies of species in subtropical China have mainly focused on rare and endangered species, whereas few studies have been conducted on taxa with relatively wide distribution, especially polyploid species. We investigated the cytotype and haplotype distribution pattern of the Actinidia chinensis complex, a widespread geographically woody liana with variable ploidy in subtropical China comprising two varieties, with three chloroplast fragments DNA (ndhF-rpl132, rps16-trnQ and trnE-trnT). Macroevolutionary, microevolutionary and niche modeling tools were also combined to disentangle the origin and the demographic history of the species or cytotypes. Results The ploidy levels of 3338 individuals from 128 populations sampled throughout the species distribution range were estimated with flow cytometry. The widespread cytotypes were diploids followed by tetraploids and hexaploids, whereas triploids and octoploids occurred in a few populations. Thirty-one chloroplast haplotypes were detected. The genetic diversity and genetic structure were found to be high between varieties (or ploidy races) chinensis and deliciosa. Our results revealed that these two varieties inhabit significantly different climatic niche spaces. Ecological niche models (ENMs) indicate that all varieties’ ranges contracted during the Last Inter Glacial (LIG), and expanded eastward or northward during the Last Glacial Maximum (LGM). Conclusions Pliocene and Plio-Pleistocene climatic fluctuations and vicariance appear to have played key roles in shaping current population structure and historical demography in the A. chinensis complex. The polyploidization process also appears to have played an important role in the historical demography of the complex through improving their adaptability to environmental changes.
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Zhang, Wen, Yuzhe Sun, Jia Liu, Chao Xu, Xinhui Zou, Xun Chen, Yanlei Liu, Ping Wu, Xueying Yang, and Shiliang Zhou. "DNA barcoding of Oryza: conventional, specific, and super barcodes." Plant Molecular Biology, September 3, 2020. http://dx.doi.org/10.1007/s11103-020-01054-3.
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Abstract Key message We applied the phylogenomics to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity. Abstract Rice (genus Oryza) is one of the most important crops in the world, supporting half of the world’s population. Breeding of high-yielding and quality cultivars relies on genetic resources from both cultivated and wild species, which are collected and maintained in seed banks. Unfortunately, numerous seeds are mislabeled due to taxonomic issues or misidentifications. Here, we applied the phylogenomics of 58 complete chloroplast genomes and two hypervariable nuclear genes to determine species identity in rice seeds. Twenty-one Oryza species were identified. Conspecific relationships were determined between O. glaberrima and O. barthii, O. glumipatula and O. longistaminata, O. grandiglumis and O. alta, O. meyeriana and O. granulata, O. minuta and O. malampuzhaensis, O. nivara and O. sativa subsp. indica, and O. sativa subsp. japonica and O. rufipogon.D and L genome types were not found and the H genome type was extinct. Importantly, we evaluated the performance of four conventional plant DNA barcodes (matK, rbcL, psbA-trnH, and ITS), six rice-specific chloroplast DNA barcodes (psaJ-rpl33, trnC-rpoB, rps16-trnQ, rpl22-rps19, trnK-matK, and ndhC-trnV), two rice-specific nuclear DNA barcodes (NP78 and R22), and a chloroplast genome super DNA barcode. The latter was the most reliable marker. The six rice-specific chloroplast barcodes revealed that 17% of the 53 seed accessions from rice seed banks or field collections were mislabeled. These results are expected to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity.
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Zheng, Hong-Yi, Xian-Lin Guo, Megan Price, Xing-Jin He, and Song-Dong Zhou. "Effects of Mountain Uplift and Climatic Oscillations on Phylogeography and Species Divergence of Chamaesium (Apiaceae)." Frontiers in Plant Science 12 (May 24, 2021). http://dx.doi.org/10.3389/fpls.2021.673200.
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Exploring the effects of orographic events and climatic shifts on the geographic distribution of organisms in the Himalayas-Hengduan Mountains (HHM) region and Qinghai-Tibetan Plateau (QTP) is crucial to understand the impact of environmental changes on organism evolution. To gain further insight into these processes, we reconstructed the evolutionary history of nine Chamaesium species distributed across the HHM and QTP regions. In total, 525 individuals from 56 populations of the nine species were analyzed based on three maternally inherited chloroplast fragments (rpl16, trnT-trnL, and trnQ-rps16) and one nuclear DNA region (internal transcribed spacer, ITS). Fifty-two chloroplast DNA (cpDNA) and 47 ITS haplotypes were identified in nine species. All of the cpDNA and ITS haplotypes were species-specific. Phylogenetic analysis suggested that all nine species form a monophyletic clade with high support. Dating analysis and ancestral area reconstruction revealed that the ancestral group of Chamaesium originated in the southern Himalayan region at the beginning of the Paleogene (60.85 Ma). The nine species of Chamaesium then separated well during the last 25 million years started in Miocene. Our maxent modeling indicated the broad-scale distributions of all nine species remained fairly stable from LIG to the present and predicted that it will remain stable into the future. The initial split of Chamaesium was triggered by climate changes following the collision of the Indian plate with the Eurasia plate during the Eocene. Subsequently, divergences within Chamaesium may have been induced by the intense uplift of the QTP, the onset of the monsoon system, and Central Asian aridification. Long evolutionary history, sexual reproduction, and habitat fragmentation could contribute to the high level of genetic diversity of Chamaesium. The higher genetic differentiation among Chamaesium populations may be related to the drastic changes of the external environment in this region and limited seed/pollen dispersal capacity.
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Namgung, Ju, Hoang Dang Khoa Do, Changkyun Kim, Hyeok Jae Choi, and Joo‑Hwan Kim. "Complete chloroplast genomes shed light on phylogenetic relationships, divergence time, and biogeography of Allioideae (Amaryllidaceae)." Scientific Reports 11, no. 1 (February 5, 2021). http://dx.doi.org/10.1038/s41598-021-82692-5.
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AbstractAllioideae includes economically important bulb crops such as garlic, onion, leeks, and some ornamental plants in Amaryllidaceae. Here, we reported the complete chloroplast genome (cpDNA) sequences of 17 species of Allioideae, five of Amaryllidoideae, and one of Agapanthoideae. These cpDNA sequences represent 80 protein-coding, 30 tRNA, and four rRNA genes, and range from 151,808 to 159,998 bp in length. Loss and pseudogenization of multiple genes (i.e., rps2, infA, and rpl22) appear to have occurred multiple times during the evolution of Alloideae. Additionally, eight mutation hotspots, including rps15-ycf1, rps16-trnQ-UUG, petG-trnW-CCA, psbA upstream, rpl32-trnL-UAG, ycf1, rpl22, matK, and ndhF, were identified in the studied Allium species. Additionally, we present the first phylogenomic analysis among the four tribes of Allioideae based on 74 cpDNA coding regions of 21 species of Allioideae, five species of Amaryllidoideae, one species of Agapanthoideae, and five species representing selected members of Asparagales. Our molecular phylogenomic results strongly support the monophyly of Allioideae, which is sister to Amaryllioideae. Within Allioideae, Tulbaghieae was sister to Gilliesieae-Leucocoryneae whereas Allieae was sister to the clade of Tulbaghieae- Gilliesieae-Leucocoryneae. Molecular dating analyses revealed the crown age of Allioideae in the Eocene (40.1 mya) followed by differentiation of Allieae in the early Miocene (21.3 mya). The split of Gilliesieae from Leucocoryneae was estimated at 16.5 mya. Biogeographic reconstruction suggests an African origin for Allioideae and subsequent spread to Eurasia during the middle Eocene. Cool and arid conditions during the late Eocene led to isolation between African and Eurasian species. African Allioideae may have diverged to South American taxa in the late Oligocene. Rather than vicariance, long-distance dispersal is the most likely explanation for intercontinental distribution of African and South American Allioideae species.
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Luo, Chao, Wulue Huang, Huayu Sun, Huseyin Yer, Xinyi Li, Yang Li, Bo Yan, et al. "Comparative chloroplast genome analysis of Impatiens species (Balsaminaceae) in the karst area of China: insights into genome evolution and phylogenomic implications." BMC Genomics 22, no. 1 (July 24, 2021). http://dx.doi.org/10.1186/s12864-021-07807-8.
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Abstract Background Impatiens L. is a genus of complex taxonomy that belongs to the family Balsaminaceae (Ericales) and contains approximately 1000 species. The genus is well known for its economic, medicinal, ornamental, and horticultural value. However, knowledge about its germplasm identification, molecular phylogeny, and chloroplast genomics is limited, and taxonomic uncertainties still exist due to overlapping morphological features and insufficient genomic resources. Results We sequenced the chloroplast genomes of six different species (Impatiens chlorosepala, Impatiens fanjingshanica, Impatiens guizhouensis, Impatiens linearisepala, Impatiens loulanensis, and Impatiens stenosepala) in the karst area of China and compared them with those of six previously published Balsaminaceae species. We contrasted genomic features and repeat sequences, assessed sequence divergence and constructed phylogenetic relationships. Except for those of I. alpicola, I. pritzelii and I. glandulifera, the complete chloroplast genomes ranging in size from 151,366 bp (I. alpicola) to 154,189 bp (Hydrocera triflora) encoded 115 distinct genes [81 protein-coding, 30 transfer RNA (tRNA), and 4 ribosomal RNA (rRNA) genes]. Moreover, the characteristics of the long repeat sequences and simple sequence repeats (SSRs) were determined. psbK-psbI, trnT-GGU-psbD, rpl36-rps8, rpoB-trnC-GCA, trnK-UUU-rps16, trnQ-UUG, trnP-UGG-psaJ, trnT-UGU-trnL-UAA, and ycf4-cemA were identified as divergence hotspot regions and thus might be suitable for species identification and phylogenetic studies. Additionally, the phylogenetic relationships based on Maximum likelihood (ML) and Bayesian inference (BI) of the whole chloroplast genomes showed that the chloroplast genome structure of I. guizhouensis represents the ancestral state of the Balsaminaceae family. Conclusion Our study provided detailed information about nucleotide diversity hotspots and the types of repeats, which can be used to develop molecular markers applicable to Balsaminaceae species. We also reconstructed and analyzed the relationships of some Impatiens species and assessed their taxonomic statuses based on the complete chloroplast genomes. Together, the findings of the current study might provide valuable genomic resources for systematic evolution of the Balsaminaceae species.