Journal articles: 'TrnL-trnF'

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Sedláková, V., P. Sedlák, D. Zeka, J. Domkářová, P. Doležal, and P. Vejl. "Evaluation of variations in plastid DNA non-coding regions in selected species of the genus Solanum." Czech Journal of Genetics and Plant Breeding 53, No. 3 (September 13, 2017): 127–31. http://dx.doi.org/10.17221/76/2015-cjgpb.

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The diversity of three non-coding plastid DNA loci (trnL/trnF spacer, trnV/16SrRNA spacer, trnL/trnL intron) was assessed in 16 Solanum L. species (135 individuals). Polymorphisms were detected by denaturing gradient gel electrophoresis (DGGE) and verified by direct sequencing. No intraspecific diversity and only poor interspecific diversity was detected. Unique S. mochiquense Ochoa specific length polymorphism at the trnL/trnL locus represented by duplication of an 18 bp segment was discovered. The detected DGGE interspecific trnL/trnF locus polymorphism did not specifically associate with single point mutations in the sequence confirmed by sequencing. The DGGE method was found to be a simple and cheap pre-exploring tool for mutation detection in compared DNA regions. Some identified polymorphisms can be used in the management of genetic resources.

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Tüyel, Abdurrahman Umut, Ezgi Çabuk Şahin, Funda Şentürk Akfirat, Yıldız Aydin, and Ahu Altınkut Uncuoğlu. "Phylogenetic analysis of Colchicum (Colchicaceae) genus by molecular markers from nuclear and chloroplast genome." Genetics & Applications 4, no. 1 (June 23, 2020): 1. http://dx.doi.org/10.31383/ga.vol4iss1pp1-11.

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We evaluated the patterns of genetic variation of 16 Colchicum species, including 37 different genotypes, using RAPD marker and trnL–trnF chloroplast DNA sequence. A total of 861 polymorphic alleles through RAPDs showed a mean of 33.88 ± 3.80 alleles per primer, while mean major allele frequency was 0.067 ± 0.05. The sequence length of trnL–trnF ranged from 1022 bp to 1081 bp. The phylogenetic tree was constructed to understand the relationship between Colchicum species and the discrimination power of the nuclear and chloroplast genome for species. The results showed that trnL–trnF gene region grouped Colchicum species well in comparison with RAPD analysis. This data was also supported by haplotype network analysis, structure analysis and PCA (Principle Component Analysis). This study showed that there is a need for a characterization that contains more molecular and morphological methods to correctly distinguish Colchicum species.

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Jarret, Robert L. "DNA Barcoding in a Crop Genebank: The Capsicum annuum Species Complex." Open Biology Journal 1, no. 1 (October 28, 2008): 35–42. http://dx.doi.org/10.2174/1874196700801010035.

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Variability within eight cpDNA introns including trnS-trnfM, trnL-trnT, trnH-psbA, trnF-trnL, trnD-trnT, trnCrpoB, rps16 and matK, and the nuclear waxy introns was examined in seven species of Capsicum (C. annuum, C. baccatum, C. chinense, C. frutescens, C. pubescens, C. chacoense and C. rhomboideum) in order to evaluate the feasibility of utilizing these loci for DNA barcoding within the C. annuum complex. Numerous insertions/deletions (indels) and substitutions were detected in all cpDNA introns. However, none was sufficient to differentiate the individual members of the C. annuum complex (C. annuum, C. chinense and C. frutescens). Variation within trnL-trnT, trnF-trnL and trnH-psbA enabled the differentiation of the complex from the other taxa examined. In contrast, single base indels and substitutions within the waxy introns permitted the differentiation of all taxa within the plant materials examined. The use of trnH-psbA or trnL-trnT, and the waxy introns is proposed for barcoding members of the C. annuum complex.

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ZHANG, WEI, JIAO QIN, RUI YANG, YI YANG, and SHI-BAO ZHANG. "Two new natural hybrids in the genus Pleione (Orchidaceae) from China." Phytotaxa 350, no. 3 (May 23, 2018): 247. http://dx.doi.org/10.11646/phytotaxa.350.3.4.

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Several species in the genus Pleione (Orchidaceae) have same or overlapping geographical distribution in China. In this study, two new natural hybrids, Pleione × baoshanensis and Pleione × maoershanensis, were described and illustrated. The parentage for these two hybrids was confirmed using molecular data from ITS of the nuclear ribosomal, trnT-trnL spacer and trnL-trnF region (trnL intron and trnL-trnF spacer) of the plastid DNA. Pleione × baoshanensis is intermediate between P. albiflora and P. yunnanensis, and characterized by its erose lamellae on the lip. Meanwhile, Pleione × maoershanensis is intermediate between P. hookeriana (P. chunii) and P. pleionoides, and characterized by its deep lacerate lamellae on the lip. For the individuals tested, molecular data suggest that P. albiflora is the maternal parent of Pleione × baoshanensis, and P. hookeriana (P. chunii) is the maternal parent of Pleione × maoershanensis. The history and taxonomic status of P. chunii is also discussed.

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Yingzhi, Li, Cheng Yunjiang, Tao Nengguo, and Deng Xiuxin. "Phylogenetic Analysis of Mandarin Landraces, Wild Mandarins, and Related Species in China Using Nuclear LEAFY Second Intron and Plastid trnL-trnF Sequence." Journal of the American Society for Horticultural Science 132, no. 6 (November 2007): 796–806. http://dx.doi.org/10.21273/jashs.132.6.796.

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Nucleotide sequences of the second intron of the nuclear LEAFY gene (FLint2) and trnL-trnF region of the chloroplast genome were used to analyze the phylogenetic relationships among eight wild mandarins (Citrus reticulata Blanco), 19 mandarin landraces, and 19 related species of Citrus L. Forty-six trnL-trnF sequences and 111 FLint2 sequences were obtained from 46 ingroup accessions, with an average length of 1059.7 and 776.7 bp respectively. Phylogeny reconstructions were conducted separately for these two data sets using maximum parsimony and maximum likelihood criteria. Monophyly of mandarins was supported by both of these data sets, and in this clade, most mandarin landraces formed an unresolved polytomy, whereas ‘Jiangyong 1’, ‘Chongyi A2’, ‘Chongyi A1’ (or ‘Jiangyong 4’ in FLint2 data), and ‘Daoxian 1’ wild mandarins formed a subclade. ‘Mangshan A1’ and ‘Daoxian 5’ wild mandarins were sisters to this mandarin clade. A hybrid origin of five mandarin landraces and several mandarin-related species was suggested as a plausible hypothesis to explain the incongruence between the FLint2 and trnL-trnF data sets.

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Mustapha, S. B., H. Ben Tamarzizt, G. Baraket, D. Abdallah, and A. Salhi-Hannachi. "Cytoplasmic polymorphism and evolutionary history of plum cultivars: Insights from chloroplast DNA sequence variation of trnL-trnF spacer and aggregated trnL intron & trnL-trnF spacer." Genetics and Molecular Research 14, no. 2 (2015): 3964–79. http://dx.doi.org/10.4238/2015.april.27.11.

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Feng, Tingting, Qiwei Li, Yesheng Wang, Simin Qiu, Mengling He, Weimin Zhang, Jun Dong, and Shuang Zhu. "Phylogenetic analysis of Aquilaria Lam. (Thymelaeaceae) based on DNA barcoding." Holzforschung 73, no. 6 (June 26, 2019): 517–23. http://dx.doi.org/10.1515/hf-2018-0127.

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AbstractAquilariaLam. is an important group of trees that produce agarwood, which is widely used for manufacturing medicine, perfumes and incense. The members of the genusAquilariaare close to being extinct due to illegal harvesting and are now protected in many countries. In this study, five DNA barcodes [internal transcribed spacer (ITS), maturase K (matK),psbA-trnH, ribulose bisphosphate carboxylase (rbcL) andtrnL-trnF] and their combinations were evaluated for the discrimination of the major (16 out of 21) species ofAquilariabased on three criteria: sequence variation, genetic distances and the discrimination ability. In addition, we attempted to determine the phylogenetic relationship betweenAquilariaandGyrinopsspecies using three phylogenetic analysis methods. We observed that the combination barcode ITS+trnL-trnF had a good discrimination ability based on the best match and best close match methods, provided more genetic information, and clearly indicated the comprehensive phylogenetic relationship between mostAquilariaandGyrinopsspecies. Considering the overall performance of these barcodes, the ITS+trnL-trnF is a suitable barcode for the identification ofAquilariaspecies.

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Murphy, Daniel J., Frank Udovicic, and Pauline Y. Ladiges. "Phylogenetic analysis of Australian Acacia (Leguminosae: Mimosoideae) by using sequence variations of an intron and two intergenic spacers of chloroplast DNA." Australian Systematic Botany 13, no. 5 (2000): 745. http://dx.doi.org/10.1071/sb99027.

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Three regions of chloroplast DNA are assessed for their utility for phylogenetic analysis of Acacia subgenus Phyllodineae: psbA–trnH intergenic spacer, the trnL intron and the trnL–trnF intergenic spacer. There are large differences in the lengths of the psbA–trnH spacer (155–440 bp) and trnL–trnF intergenic spacer (101–422 bp) regions, and large multi-residue indels were coded as multistate characters. Overall information content in these regions is relatively low, but the total evidence tree has 12 nodes resolved, five with jackknife support. By using Parkia timoriana as the outgroup, Acacia subgenus Acacia (A. farnesiana) is basal and Acacia subgenus Aculeiferum (A. senegal) is the sister taxon to subgenus Phyllodineae. Although based on a small sample size, within subgenus Phyllodineae, the results of this study have shown that section Alatae is not monophyletic, section Lycopodiifoliae is monophyletic and Botrycephalae is related to members of section Phyllodineae with racemose inflorescences.

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Meagher, David A., and Michael J. Bayly. "Morphological and molecular data support reinstatement of Spiridens muelleri Hampe (Bryophyta: Hypnodendraceae), a Lord Howe Island endemic." Australian Systematic Botany 27, no. 2 (2014): 95. http://dx.doi.org/10.1071/sb14001.

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For more than 75 years, the Lord Howe Island moss Spiridens muelleri Hampe has been considered conspecific with Spiridens vieillardii Schimp., originally described from New Caledonia. A comparison of morphological characters not previously considered, along with DNA sequences from three chloroplast loci (trnL–trnF, rps4–trnS, rpl32–trnL) and ITS-2 of nuclear rDNA, supports their recognition as separate species.

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Nosov, N. N., A. A. Gnutikov, E. O. Punina, E. M. Machs, G. Yu Konechnaya, and A. V. Rodionov. "On distinction of the reed species (Phragmites, Poaceae) according to the molecular phylogenetic data." Проблемы ботаники Южной Сибири и Монголии 19, no. 1 (June 1, 2020): 8–13. http://dx.doi.org/10.14258/pbssm.2020002.

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Molecular phylogenetic analysis of the marker sequences ITS and trnL–trnF of the Phragmites australis,P. altissimus, some putative hybrids between them and the sample of P. australis s. l. from Republic of Tuva was performed.ITS1 sequences of the sample from Tuva were studied by the New-generation sequencing method (NGS) revealingintragenomic polymorphism of the ITS sequences in allopolyploid species. We showed good differences betweenP. australis and P. altissimus in the ITS1-5.8S rDNA-ITS2 sequences by many single-nucleotide substitutions anddeletions, in particular, there is a 12 b.p. deletion. P. australis s. l. sample from Tuva (Hemchik river) demonstrates aseparate position on the phylogenetic tree. All reed species studied by us do not have significant differences between eachother according to the chloroplast sequences trnL–trnF.

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Beghalem, Hamida, Khadidja Aliliche, and Ahmed Landoulsi. "Phylogeny and Sequence Analysis of Sulla species Based on Intergenic Spacers trnL-trnF." South Asian Journal of Experimental Biology 11, no. 3 (May 24, 2021): 321–26. http://dx.doi.org/10.38150/sajeb.11(3).p321-326.

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Chloroplast DNA (cpDNA) sequence variations are broadly used to investi-gate interspecific relationships among plants. The trnL-trnF spacer is located in the large single-copy region of the chloroplast genome. The objective of this study was to evaluate the level of genetic variability between the Algeri-an and Tunisian species Hedysarum pallidum (North African endemic spe-cies) and H. capitatum. The phylogenetic relationships among the studied species were investigated by means of maximum Likehood analysis of se-quence polymorphism from chloroplast trnL-trnF spacer DNA; the tree parti-tioned the studied species in two clades. In addition, some specific variations loci- were identified between the species. The observed variations suggest considerable differentiation among cpDNA which could be useful to identify species.

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Hue, Huynh Thi Thu, Nguyen Thi Thanh Hoa, Le Thi Thu Hien, and Nguyen Đang Ton. "Analyzing the plastid trnL-trnF sequences of Vietnamese Solanum procumbens Lour. plants." Vietnam Journal of Biotechnology 19, no. 2 (August 2, 2021): 309–19. http://dx.doi.org/10.15625/1811-4989/15361.

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Solanum is a genus which belongs to Solanaceae family, includes many species of cropsor medicinal plants as eggplant, tomato, potato, twoleaf nightshade, etc. Number of species are used as medicinal herbs of Solanum genus in Vietnam is up to 41, one of those is Solanum procumbens Lour., which is often used to treat hepatitis or cirrhosis. The needs of planting this plant is rising up, but it still lacks of studies based on DNA barcode of Solanum, in order to prevent the confusion of the raw materials in dry form of medicinal plants. This study provides sequencing and analysis the DNA barcode region trnL-trnF, in order to support further researches about identification, classification and evolution of Solanum procumbens species. The DNA covering the trnL-trnF region was amplified, sequenced and the nucleotide sequences from 10 samples of dry leaves Solanum procumbens species were analyzed with the reference sequences from GenBank. The results show that the similarity between these samples and others in previous publications of Solanum procumbens Lour. is 100%. Moreover, the estimated genetic distance on trnL-trnF region of the Vietnamese samples compared to few other species in Solanum genera varies between 0,0082 to 0,0399. The data from this research provides more information for any further studies about genome biodiversity of the Solanum genus as well as Vietnamese medicinal plants.

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Wangiyana, I. Gde Adi Suryawan. "DNA BARCODING LIBRARY DATABASE OF AQUILARIA MEMBER AND GYRINOPS MEMBER." Jurnal Silva Samalas 3, no. 2 (December 29, 2020): 68. http://dx.doi.org/10.33394/jss.v3i2.3693.

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Aquilaria and Gyrinops are the primary agarwood producer on international trade. For authentication and standardization purposes, it is essential to carry DNA barcoding studies of these genera. DNA barcoding studies on plants need a database of several regions on the plant genome that could act as a barcoding marker. These DNA barcoding markers could be divided into Chloroplasts barcoding and Nuclear barcoding. Several markers have been used for DNA barcoding study of agarwood producer species, including trnL-trnF, matK, rbcL, rpoC1, ycf1 (Chloroplast barcoding), and ITS (Nuclear barcoding). This review breakdown the availability of those DNA barcoding markers on the online genebank database for Aquilaria and Gyrinops. Aquilaria genus has 12 species members, while Gyrinops genus has six species members. The sequence of region trnL-trnF is the only barcoding marker covering all 12 species members of Aquilaria and six species members of Gyrinops. Both ITS and matK have covered nine species among 12 total species members of Aquilaria. The rbcL, rpoC1, and ycf1, respectively, have covered eight, five, and four species members of Aquilaria. Most of the barcoding markers have covered three species members of Gyrinops except for ITS (5 species) and rpoC1 (1 species). However, Gyrinops members have no ycf1 sequence on genebank database. Based on sequence availability on the genebank database, it could be concluded that the trnL-trnF region is the most promising DNA barcoding marker for the Aquilaria and Gyrinops members especially for the phylogenetic analysis purpose.

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Saadati, Nasim, Maryam Khoshsokhan Mozaffar, Mahboubeh Sherafati, and Shahrokh Kazempour Osaloo. "Pseudoheterocaryum, a new genus segregated from Heterocaryum (Boraginaceae) on the basis of molecular data." Australian Systematic Botany 30, no. 1 (2017): 105. http://dx.doi.org/10.1071/sb16022.

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The phylogeny of Heterocaryum and Suchtelenia was examined using sequence data from the internal transcribed spacer region of the nuclear rDNA (ITS) and plastid trnL intron and trnL–trnF intergenic spacer (trnL–F) regions. Results indicated that Heterocaryum is non-monophyletic because of the inclusion of Suchtelenia calycina (C.A.Mey.) A.DC. Heterocaryum laevigatum (Kar. & Kir.) A.DC. formed a distinct branch sister to S. calycina and remaining Heterocaryum species. Hence, all species of Heterocaryum except H. laevigatum (type species of the genus) are transferred to a new genus, Pseudoheterocaryum. Taxonomic descriptions are presented for Pseudoheterocaryum and Heterocaryum, as well as a diagnostic key to the three genera included in the present study.

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Mast, Austin R. "Molecular systematics of subtribe Banksiinae (Banksia and Dryandra; Proteaceae) Based on cpDNA and nrDNA sequence data: Implications for taxonomy and biogeography." Australian Systematic Botany 11, no. 4 (1998): 321. http://dx.doi.org/10.1071/sb97026.

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Despite considerable research interest in the subtribe Banksiinae (Banksia L.f. and Dryandra R.Br.), no strongly supported phylogenetic hypothesis for the relationship between the genera exists, nor have molecular characters been sampled for phylogenetic reconstruction at any level. In this study, DNA sequence characters were sampled from chloroplast DNA (cpDNA; the trnL intron, the trnL 3′ exon, and the spacer between the trnL 3′ exon and trnF) and nuclear ribosomal DNA (nrDNA; both internal transcribed spacers) of 18 species of Banksia and five of Dryandra, with six outgroup taxa from the subfamily Grevilleoideae. The molecular characters provided the opportunity to code taxa outside of Banksia for cladistic comparison with the genus—an opportunity not previously provided by morphological characters. Cladistic analyses, using parsimony, explored the effects of various weightings of transition to transversion events and base substitution to insertion and deletion events to determine which relationships in the cladograms were robust. The trnL/trnF and ITS characters strongly supported a paraphyletic Banksia with respect to a monophyletic Dryandra. The molecular results supported a single root for Thiele and Ladiges’(1996) unrooted morphological cladogram along the branch between the Isotylis to B. fuscolutea clade and the Grandes to B. tricuspis clade. George’s (1981) subgenus Banksia and section Banksia appeared dramatically non-monophyletic. The distribution of eastern taxa at derived positions on the molecular cladograms suggested considerable cladogenesis in the the genus prior to the formation of the Nullarbor Plain during the Tertiary.

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JIANG, MING-TAO, SHA-SHA WU, ZHONG-JIAN LIU, and SI-REN LAN. "Pleione jinhuana (Arethuseae; Epidendroideae; Orchidaceae), a new species from China based on morphological and DNA evidence." Phytotaxa 345, no. 1 (March 20, 2018): 43. http://dx.doi.org/10.11646/phytotaxa.345.1.5.

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Pleione jinhuana, a new orchid from China, is illustrated and described based on morphological and phylogenetic evidence. Detailed morphological comparisons between the new species and other members of Pleione indicate that P. jinhuana is similar to P. bulbocodioides and P. formosana but differs in having a lip with an erose apical margin and lateral lobes not enfolding the column. To explore the phylogenetic position of this species, nuclear ribosomal ITS and plastid DNA (matK exon, trnT-trnL spacer, trnL exon and trnL-trnF spacer) were sequenced for P. jinhuana and individuals of P. formosana collected in Taiwan, Fujian and Zhejiang Provinces. The morphological and molecular evidence support the hypothesis that P. jinhuana is a new species.

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YURTSEVA, OLGA V., ELENA E. SEVEROVA, ANDREY G. DEVIATOV, MARINA V. OLONOVA, and TAHIR H. SAMIGULLIN. "Polygonum schischkinii is a member of Atraphaxis (Polygonaceae, Polygoneae): evidences from morphological and molecular analyses." Phytotaxa 491, no. 3 (March 23, 2021): 193–216. http://dx.doi.org/10.11646/phytotaxa.491.3.1.

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The Chinese endemic Polygonum schischkinii was studied from both morphological and molecular points of view. On the basis of the structure of ocreas and ocreolas, P. schischkinii appears to be a member of the genus Atraphaxis. The results of Maximum Likelihood and Bayesian analyses of combined data of the plastid [rpl32-trnL(UAG) IGS, trnL(UAA) intron, trnL-trnF IGS] and nuclear rDNA ITS1–2 regions, carried out on 61 members of tribe Polygoneae, confirmed position of P. schischkinii in the Atraphaxis clade. A new combination—Atraphaxis glareosa—based on P. glareosum, which has nomenclatural priority over P. schischkinii, is proposed. Ecological notes and a detailed distributional map of the species are also provided.

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Huh, Man-Kyu, Hye-Jeong Yoon, and Joo-Soo Choi. "Phylogenic Study of Genus Citrus and Two Relative Genera in Korea by trnL-trnF Sequence." Journal of Life Science 21, no. 10 (October 30, 2011): 1452–59. http://dx.doi.org/10.5352/jls.2011.21.10.1452.

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Amundsen, Keenan, and Scott Warnke. "Agrostis Species Relationships Based on trnL-trnF and atpI-atpH Intergenic Spacer Regions." HortScience 47, no. 1 (January 2012): 18–24. http://dx.doi.org/10.21273/hortsci.47.1.18.

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The bentgrasses (Agrostis spp.) are among the most important species to the turfgrass industry. They have complex genomes resulting from polyploidization and high rates of interspecific hybridization. An understanding of species relationships would improve the efficiency of developing improved bentgrass cultivars. To elucidate the evolutionary relationships among Agrostis species, phylogenetic analyses were performed on sequences of two chloroplast-encoded intergenic spacer regions. A 298-bp region of the trnL-trnF intergenic spacer and a 451-bp region of the atpI-atpH intergenic spacer were included in the analyses. A total of 47 Agrostis accessions were included with both cultivated and unimproved material from the National Plant Germplasm System. Of these 47 Agrostis collections, there were 10 unique trnL-trnF haplotypes and eight distinct atpI-atpH haplotypes, indicating a high degree of shared sequence identity within these chloroplast intergenic regions. These findings suggest that the chloroplast genomes of A. canina and A. stolonifera are more closely related to each other than either species is to A. capillaris, incongruent with our previous understanding of genome relationships in the genus.

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Tineo, Daniel, Danilo E. Bustamante, Martha S. Calderon, Jani E. Mendoza, Eyner Huaman, and Manuel Oliva. "An integrative approach reveals five new species of highland papayas (Caricaceae, Vasconcellea) from northern Peru." PLOS ONE 15, no. 12 (December 10, 2020): e0242469. http://dx.doi.org/10.1371/journal.pone.0242469.

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The assignment of accurate species names is crucial, especially for those with confirmed agronomic potential such as highland papayas. The use of additional methodologies and data sets is recommended to establish well-supported boundaries among species of Vasconcellea. Accordingly, six chloroplast (trnL-trnF, rpl20-rps12, psbA-trnH intergenic spacers, matK and rbcL genes) and nuclear (ITS) markers were used to delimit species in the genus Vasconcellea using phylogeny and four DNA-based methods. Our results demonstrated congruence among different methodologies applied in this integrative study (i.e., morphology, multilocus phylogeny, genetic distance, coalescence methods). Genetic distance (ABGD, SPN), a coalescence method (BPP), and the multilocus phylogeny supported 22–25 different species of Vasconcellea, including the following five new species from northern Peru: V. badilloi sp. nov., V. carvalhoae sp. nov., V. chachapoyensis sp. nov., V. pentalobis sp. nov., and V. peruviensis sp. nov. Genetic markers that gave better resolution for distinguishing species were ITS and trnL-trnF. Phylogenetic diversity and DNA-species delimitation methods could be used to discover taxa within traditionally defined species.

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Perrie, Leon R., Daniel J. Ohlsen, Lara D. Shepherd, Michael Garrett, Patrick J. Brownsey, and Michael J. Bayly. "Tasmanian and Victorian populations of the fern Asplenium hookerianum result from independent dispersals from New Zealand." Australian Systematic Botany 23, no. 6 (2010): 387. http://dx.doi.org/10.1071/sb10028.

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The fern Asplenium hookerianum Colenso (Aspleniaceae) is indigenous to New Zealand and Australia. In New Zealand, it is widespread and genetically diverse, with 26 haplotypes previously identified for the chloroplast trnL–trnF locus. In Australia, A. hookerianum is currently known only from two small populations in Victoria and two in Tasmania. The present study assessed the diversity, relationships and biogeographic history of the Australian populations. A single trnL–trnF haplotype was identified in Tasmanian populations, and it was shared with populations in south-western New Zealand. The single haplotype found in Victorian populations was unique and most similar to a haplotype found in populations from central and eastern North Island, New Zealand. Relationships among haplotypes suggest that the two Australian haplotypes are derived within the group (not close to the root of the haplotype network) and only distantly related. This pattern is consistent with two independent dispersals of A. hookerianum from New Zealand to Australia. These findings are unique in providing evidence for more than one trans-Tasman dispersal event in a species of vascular plant.

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Medvedeva, Svetlana, Olga Cherepanova, Olga Tolkach, Vasiliy Ponomarev, and Galina Malosieva. "TrnL-trnfF cpDNA polymorphism in some representatives of the genus Betula." BIO Web of Conferences 35 (2021): 00017. http://dx.doi.org/10.1051/bioconf/20213500017.

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We present preliminary results of the trnL-trnF cpDNA region analysis for some representatives of the g. Betula, out of which B. procurva can be considered the most interesting. The disjunctive range of this species is confined to the mountain system in southeast Central Asia (Pamir-Alai). The occurrence of the birch is isolated from the main range in the mountainous part of the Urals, in the boreal forests zone and in the Trans-Ural forest-steppe. Due to high interspecific hybridization and population variability of the g. Betula, doubts were raised about the correct identification of the representatives of B. procurva. The studied genetic variability and population structure of B. procurva, B. nana, B. pubescens, B. turkestanica, B. tianshanica and B. pendula species indicate active introgression and hybridization processes. Polymorphism in all groups is significantly reduced, increasing slightly when comparing the most distant groups. The matching of the B. procurva cpDNA haplotypes (GBS) with B. pendula, B. nana, and B. pubescens shows that this trnL-trnF cpDNA site cannot be used for molecular identification of birch species by barcoding as a single marker, but this marker use is possible for determination of certain B. procurva population. Based on the studied cpDNA region (trnL-F) we found a clear geographic subdivision in B. procurva populations of the Trans-Urals and Central Asia,.

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Inglis, Peter, Lorena Mata, Marcos da Silva, Roberto Vieira, Rosa de B. N. Alves, Dijalma Silva, and Vânia Azevedo. "DNA Barcoding for the Identification of Phyllanthus Taxa Used Medicinally in Brazil." Planta Medica 84, no. 17 (June 21, 2018): 1300–1310. http://dx.doi.org/10.1055/a-0644-2688.

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AbstractPlants of the genus Phyllanthus, principally Phyllanthus amarus, Phyllanthus urinaria, Phyllanthus niruri, and Phyllanthus tenellus, are used in Brazilian folk medicine to treat kidney stones as well as other ailments, where the latter two species are listed in the Brazilian Pharmacopeia as quebra-pedra (stone-breaker). However, only P. niruri has been shown to be effective in a clinical setting. Nuclear ribosomal internal transcribed spacer (ITS1 – 5.8S rRNA-ITS2), internal transcribed spacer 2, and chloroplasts rbcL, matK, psbA-trnH, trnL, and trnL-trnF were screened for their potential as DNA barcodes for the identification of 48 Phyllanthus taxa in Brazilian medicinal plant germplasm banks and in “living pharmacies”. The markers were also tested for their ability to validate four commercial herbal teas labelled as quebra-pedra. Using the criterion of high clade posterior probability in Bayesian phylogenetic analysis, the internal transcribed spacer, internal transcribed spacer 2, and chloroplast matK, psbA-trnH, trnL, and trnL-trnF markers all reliably differentiated the four Phyllanthus species, with the internal transcribed spacer and matK possessing the additional advantage that the genus is well represented for these markers in the Genbank database. However, in the case of rbcL, posterior probability for some clades was low and while P. amarus and P. tenellus formed monophyletic groups, P. niruri and P. urinaria accessions could not be reliably distinguished with this marker. Packaged dried quebra-pedra herb from three Brazilian commercial suppliers comprised P. tenellus, but one sample was also found to be mixed with alfalfa (Medicago sativa). An herb marketed as quebra-pedra from a fourth supplier was found to be composed of a mixture of Desmodium barbatum and P. niruri.

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YURTSEVA, OLGA V., OXANA I. KUZNETSOVA, and EVGENY V. MAVRODIEV. "A broadly sampled 3-loci plastid phylogeny of Atraphaxis (Polygoneae, Polygonoideae, Polygonaceae) reveals new taxa: I. Atraphaxis kamelinii spec. nov. from Mongolia." Phytotaxa 268, no. 1 (July 15, 2016): 1. http://dx.doi.org/10.11646/phytotaxa.268.1.1.

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Maximum Likelihood (ML) and Bayesian analyses (BI) applied for 3-plastid loci (cpDNA trnL(UAA) intron, trnL–trnF IGS, and rpl32–trnL(UAG) IGS regions) / 65 tips matrix resulted in preliminary phylogenetic reconstruction of the genus Atraphaxis. In combination with the morphological data the obtained phylogeny appears sufficient for recognition of challenging taxonomic entities. We found that a collection of Atraphaxis from the Dzungarian Gobi, which appears to be phylogenetically related to A. pungens, is morphologically different from the latter by the predominantly dimerous perianth and gynoecium, shorter outer perianth segments, and the absence of the spiny shoots. It also differs from all other species of Atraphaxis that occur in Mongolia and neighboring countries. As a result, we described the novel endemic species Atraphaxis kamelinii O.V.Yurtseva sp. nov. More investigations are necessary to fully understand the origin of the newly described species.

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Lukhanina, Natalia V., Marina G. Sinyavskaya, Inessa M. Goloenko, and Oleg G. Davydenko. "Chloroplast microsatellites in barley: the reduction of variability spectrum in cultivated forms." Ecological genetics 4, no. 1 (March 15, 2006): 17–21. http://dx.doi.org/10.17816/ecogen4117-21.

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The chloroplast genomes of 67 accessions of Hordeum vulgare L were surveyed for simple sequence repeat polymorphism. Seven SSR loci were investigated, trnL/trnF and psbI-trnS intergenic regions, as well as two regions 3' trnS genes were polymorphic. The rare variants of these loci were revealed and five rare accessions were found. Our results show an extremely low level of cpDNA polymorphism of cultivated barley.

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MAMONTOV, YURIY S., NADEZHDA A. KONSTANTINOVA, and ANNA A. VILNET. "One more species in the genus Jungermannia (Marchantiophyta: Jungermanniaceae)." Bryophyte Diversity and Evolution 40, no. 2 (December 27, 2018): 79. http://dx.doi.org/10.11646/bde.40.2.6.

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Jungermannia afoninae is described from the mountains of South Siberia based on a complex taxonomical approach exploring critical reinvestigation of morphological features and analyses of newly obtained trnL–trnF and trnG-intron cpDNA sequences from six Jungermannia specimens incorporated into a previously published dataset. Description and illustrations of the new species are provided with notes on its differentiation from allied species, ecology and distribution.

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Xie, Dong Mei, DAI-YIN PENG, CHENG-WU FANG, MIN-JIAN QIN, DE-QUN WANG, and LU-QI HUANG. "Sedum spiralifolium (Crassulaceae): a new species from Anhui Province, China." Phytotaxa 183, no. 3 (October 22, 2014): 171. http://dx.doi.org/10.11646/phytotaxa.183.3.4.

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A new species of Sedum, S. spiralifolium from Anhui Province, eastern China is described and illustrated. Our molecular systematics results (based on nuclear ITS and plastid trnL-trnF) and morphological analyses indicate that this new species is closest to S. sarmentosum. It differs from S. sarmentosum by having linear-lanceolate leaves, earlier flowering and twisted upper leaves at the top of its sterile shoots.

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Stoneberg Holt, S. D., L. Horová, P. Bureš, J. Janeček, and V. Černoch. "The trnL-F plastid DNA characters of three Poa pratensis (Kentucky bluegrass) varieties." Plant, Soil and Environment 51, No. 2 (November 19, 2011): 94–99. http://dx.doi.org/10.17221/3561-pse.

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The characterization of crop cultivars (varieties) will come to depend increasingly on molecular characters in addition to traditional morphological and agronomic characters. Three cultivars of Kentucky bluegrass (Poa pratensis L.), developed by the Plant Breeding Station Hladké Životice (PBHŽ), were characterized using sequences and PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism) patterns from the non-coding plastid trnL-F region (trnL intron, 549 bp, and trnL-trnF intergenic spacer [IGS], 344 to 364 bp). These characters could be readily and repeatably determined not only for mature plants, but also for seedlings (less than 12 weeks old), which are difficult to distinguish morphologically. The method is quick and sensitive. When restricted with a combination of BsaJ I and Bsm I, cultivar Slezanka has one major band, Moravanka has two, and Harmonie has three. When restricted with Alu I, the heaviest band migrates most slowly for Slezanka. It is expected that many Kentucky bluegrass cultivars will share the same trnL-F sequence, so these characters alone are not sufficient for variety identification.

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Bakker, Freek T., Alastair Culham, Rosalba Gomez-Martinez*, Jose Carvalho, James Compton, Richard Dawtrey, and Mary Gibby. "Patterns of Nucleotide Substitution in Angiosperm cpDNA trnL (UAA)–trnF (GAA) Regions." Molecular Biology and Evolution 17, no. 8 (August 1, 2000): 1146–55. http://dx.doi.org/10.1093/oxfordjournals.molbev.a026397.

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Schneider, J. V., U. Swenson, R. Samuel, T. Stuessy, and G. Zizka. "Phylogenetics of Quiinaceae (Malpighiales): evidence from trnL-trnF sequence data and morphology." Plant Systematics and Evolution 257, no. 3-4 (February 16, 2006): 189–203. http://dx.doi.org/10.1007/s00606-005-0386-5.

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PATIL, SACHIN M., RONAK N. KACHHIYAPATEL, RAVI S. PATEL, and KISHORE S. RAJPUT. "Ophioglossum gujaratense, a new species from Gujarat State, India." Phytotaxa 351, no. 4 (June 7, 2018): 273. http://dx.doi.org/10.11646/phytotaxa.351.4.3.

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A new species, Ophioglossum gujaratense, is described from Gujarat state (India). It resembles O. polyphyllum in the presence of sheathing rhizomorph and 1–4 (rarely 5) trophophylls. On the other hand, rhizomorph morphology, common stalk, trophophyll arrangement, leaf lamina and leaf base make it distinct from O. polyphyllum. Stoloniferous roots, trophophyll number and their arrangement of the new species also resemble O. parvifolium and O. nudicaule. However, both these species lack a sheath around the leaf-stem base. A comparative account of morphologically similar species, viz. O. gujaratense, O. polyphyllum, O. parvifolium and O. nudicaule is provided. The distinctness of the new taxon has been confirmed using molecular data from chloroplast genome markers viz rbcL, trnH-psbA, trnF-trnE and trnL-trnF.

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32

Safaei Chaei Kar, S., F. Ghanavati, M. R. Naghavi, H. Amirabadi-zade, and R. Rabiee. "Molecular phylogenetics of the Onobrychis genus (Fabaceae: Papilionoideae) using ITS and trnL–trnF DNA sequence data." Australian Journal of Botany 62, no. 3 (2014): 235. http://dx.doi.org/10.1071/bt13279.

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Onobrychis, comprising more than 130 species, is a genus of the family Fabaceae. At this time, the interspecies relationship of this biologically important genus is still a subject of great discussion and debate. To help resolve this disagreement, we used molecular phylogeny to analyse internal transcribed spacer (ITS) and trnL–trnF sequences of 76 species of Onobrychis. Bayesian interference, maximum parsimony and maximum likelihood analyses of nuclear ITS and plastid trnL–trnF DNA sequence data generated trees with strong posterior probability for two groups: Onobrychis subgen. Sisyrosema (including: Heliobrychis, Hymenobrychis, Afghanicae and Anthyllium sections) along with Laxiflorae section in Group I and Onobrychis subgen. Onobrychis (except Laxiflorae section) in the other (Group II). The Laxiflorae section roots back to the ancestral node for Sisyrosema subgen. O. viciifolia (cultivated species), which is closely associated with O. cyri var. cyri, suggesting that the latter may be a wild progenitor of O. viciifolia. The present study supported the paraphyly of subgenera Onobrychis and Sisyrosema. The study proposed the paraphyletic nature of the sections Onobrychis, Dendrobrychis, Heliobrychis and Hymenobrychis. Together with our molecular phylogenetic analyses we present a review of Onobrychis morphology and discuss and compare our results with those of earlier morphological and molecular phylogenetic analyses.

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Drábková, Lenka, Jan Kirschner, Čestmír Vlček, and Václav Pačes. "TrnL–trnF Intergenic Spacer and trnL Intron Define Major Clades Within Luzula and Juncus (Juncaceae): Importance of Structural Mutations." Journal of Molecular Evolution 59, no. 1 (July 2004): 1–10. http://dx.doi.org/10.1007/s00239-004-2598-7.

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KOÇYIĞIT, MINE, ALEXEY P. SEREGIN, NERIMAN ÖZHATAY, and NIKOLAI FRIESEN. "Allium urusakiorum (Amaryllidaceae), a new member of the Balkan clade of the section Oreiprason from European Turkey." Phytotaxa 275, no. 3 (September 21, 2016): 228. http://dx.doi.org/10.11646/phytotaxa.275.3.2.

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The taxonomy of the Allium saxatile group (sect. Oreiprason) has been studied recently upon morphological and molecular data. New specimens collected from the European part of Turkey near the Istranca Mountains and identified as ‘A. saxatile’ proved to be a new species confirmed by sequences of internal transcribed spacer (ITS) and two plastid DNA regions (rpl32–trnL and trnL–trnF) and supported by morphological characters. Allium urusakiorum, a new species from the A. saxatile group, is described here through living and herbarium specimens. It is the only species of the sect. Oreiprason in the country and seems to be an endemic species of the Turkish flora. Characteristics of the species include morphological description, identification key, molecular dataset, and karyotype (2n = 16).

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35

KONSTANTINOVA, NADEZDA A. A., and ANNA A. VILNET. "A new species of the genus Jungermannia (Jungermanniales, Marchantiophyta) from the Caucasus with notes on taxa delimitation and taxonomy of Jungermannia s. str." Phytotaxa 255, no. 3 (April 11, 2016): 227. http://dx.doi.org/10.11646/phytotaxa.255.3.4.

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The new species Jungermannia calcicola Konstant. et Vilnet, is described based on a critical reinvestigation of morphological features and molecular analyses of trnL–trnF and trnG intron cpDNA sequences of forty samples of Jungermannia s. str. The new species is described and illustrated as well as noting its differentiation from allied species and distribution patterns. New data on some taxonomical ambiguities and on the taxa delimitation in the Jungermannia s. str. are discussed.

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Mitchell, A. D., P. B. Heenan, B. G. Murray, B. P. J. Molloy, and P. J. de Lange. "Evolution of the south-western Pacific genus Melicytus (Violaceae): evidence from DNA sequence data, cytology and sex expression." Australian Systematic Botany 22, no. 3 (2009): 143. http://dx.doi.org/10.1071/sb08042.

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Phylogenetic analyses of nuclear DNA external transcribed spacer (ETS) and chloroplast DNA trnL–trnF markers were undertaken to reconstruct the evolutionary history of the South Pacific genus Melicytus. Bayesian analyses of the ETS sequence data produced a phylogenetic tree with several well supported groups, including clades comprising: (1) species from Australia, Tasmania and Lord Howe Island; (2) the Norfolk Island M. latifolius and New Zealand off-shore island M. novae-zelandiae subsp. novae-zelandiae; (3) the large-leaved M. ramiflorus complex; (4) M. fasciger and M. micranthus; and (5) M. obovatus and allies from the Cook Strait region. Phylogenetic analysis of trnL–trnF sequence data also retrieved some of these groups although, in general, was not as well resolved. The relationships of M. lanceolatus are equivocal, as in the ETS phylogeny it is sister to a clade comprising the large-leaved tree species M. fasciger and M. ramiflorus complex and the small-leaved M. micranthus, whereas in the trnL–trnF phylogeny it is sister to a clade of small-leaved shrub species such as M. alpinus and M. crassifolius. Several biogeographic patterns are evident, with dispersal to the west from New Zealand, to Australia, involving small-leaved shrub species. Dispersal to the north from New Zealand, to Norfolk Island and Fiji, involves large-leaved tree species. The sex expression is documented for all named species and undescribed entities, with these being either hermaphroditic or dioecious. When sex expression is mapped onto the phylogeny, the hermaphroditic system is inferred to have evolved from the dioecious system. New chromosome counts are presented for M. angustifolius (2n = 64) and M. dentatus (2n = 32), and earlier counts of 2n = 64 are confirmed for M. crassifolius and M. alpinus. An additional 17 counts are provided for two natural hybrids and several undescribed entities from Australia and New Zealand. The polyploid chromosome number of 2n = 64 occurs most frequently in small-leaved divariate plants with hermaphroditic flowers. When chromosome numbers are plotted onto the phylogeny it is inferred that high polyploids (e.g. 2n = 64) and small-leaved shrubs have evolved from large-leaved trees with functional diploid (e.g. 2n = 32) chromosome numbers.

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Prishnivskaya, Ya, E. Nassonova, Yu Vasileva, and S. Boronnikova. "Selecting of Polymorphic Loci of Genome for Identification of Populations of Pinus sylvestris L. on East-Europe Plain." Bulletin of Science and Practice 5, no. 5 (May 15, 2019): 25–30. http://dx.doi.org/10.33619/2414-2948/42/03.

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10 pairs of primers from 8 related Pinus sylvestris L. populations collected on East-European plain to 10 genes and 4 primer’s pairs to 4 loci of uncoding clDNA regions. 2 loci of uncoding clDNA regions (psbA-trnH, trnL-trnF) were selected from tested 14 primer’s pairs. These two loci are most polymorphic and has homologous consistencies in data bases. Therefore, these loci is recommended for molecular–genetic identification of related Pinus sylvestris L. populations on East–European plain.

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38

NGAMRIABSAKUL, C., M. F. NEWMAN, and Q. C. B. CRONK. "THE PHYLOGENY OF TRIBE ZINGIBEREAE (ZINGIBERACEAE) BASED ON ITS (nrDNA) AND trnL–F (cpDNA) SEQUENCES." Edinburgh Journal of Botany 60, no. 3 (November 2003): 483–507. http://dx.doi.org/10.1017/s0960428603000362.

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A phylogenetic analysis of the tribe Zingibereae (Zingiberaceae) was performed using nuclear ribosomal DNA (ITS1, 5.8S and ITS2) and chloroplast DNA (trnL (UAA) 5′ exon to trnF (GAA)). The tribe is monophyletic with two major clades, the Curcuma clade and the Hedychium clade. Paracautleya, sampled for the first time, comes out as predicted while Caulokaempferia comes out in a different position from that found in another recent study. The genera Boesenbergia and Curcuma are apparently not monophyletic.

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39

JONGSOOK, HATHAICHANOK, KITTIPAN SAMERPITAK, ANISSARA DAMTHONGDEE, and Tanawat Chaowasku. "The non-monophyly of Dasymaschalon dasymaschalum (Annonaceae) revealed by a plastid DNA phylogeny, with D. halabalanum sp. nov. from Thailand and D. argenteum comb. nov." Phytotaxa 449, no. 3 (June 23, 2020): 265–78. http://dx.doi.org/10.11646/phytotaxa.449.3.5.

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An extended molecular phylogeny of the genus Dasymaschalon (Annonaceae) has been reconstructed using up to six plastid DNA regions (matK, ndhF, rbcL exons; trnL intron; psbA-trnH, trnL-trnF intergenic spacers). The results unraveled the non-monophyly of a widely distributed D. dasymaschalum. A lineage of D. dasymaschalum native to Java and cultivated at Bogor Botanical Garden represents the true D. dasymaschalum, whereas the name Pelticalyx argentea is applicable to a distantly related clade of D. dasymaschalum from mainland Asia. Dasymaschalon argenteum comb. nov. is accordingly made. Additionally, the true D. dasymaschalum has been retrieved as the sister group of D. halabalanum, a new species from Narathiwat Province, southern Thailand herein described. Pedicel length, petal size and color, and the number of stamens per flower principally distinguish the new species from its sister group.

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SMIRNOV, SERGEI, MIKHAIL SKAPTSOV, ALEXANDER SHMAKOV, REINHARD M. FRITSCH, and NIKOLAI FRIESEN. "Spontaneous hybridization among Allium tulipifolium and A. robustum (Allium subg. Melanocrommyum, Amaryllidaceae) under cultivation." Phytotaxa 303, no. 2 (April 11, 2017): 155. http://dx.doi.org/10.11646/phytotaxa.303.2.5.

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In the living Allium collection of the South Siberian Botanical Garden of the Altai State University, Barnaul (Russia), among the species Allium tulipifolium and A. robustum (A. subg. Melanocrommyum sect. Decipientia), several morphologically intermediate plants grown from seeds were found. We assumed they could result from spontaneous hybridization. To confirm our assumption we studied the hybrids and their alleged parents cytologically (chromosome and genome size) and compared the sequences of the nuclear DNA (ITS) and three plastid DNA fragments (trnL-trnF and rpl32-trnL spacers and rps16 intron). Our data confirmed the hybrid nature of these plants and also showed that the hybridization between the two species (A. tulipifolium and A. robustum) is possible in both directions. This opens up opportunities for targeted hybridization and breeding of new ornamental varieties.

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Jung, Yong-Hwan, Eun Young Song, Seung Jong Chun, Ki Chang Jang, Misun Kim, Sang Heon Kang, and Seong Cheol Kim. "Phylogenetic analysis of plastid trnL-trnF sequences from Arisaema species (Araceae) in Korea." Euphytica 138, no. 1 (2004): 81–88. http://dx.doi.org/10.1023/b:euph.0000047078.20546.b6.

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Kojoma, Mareshige, Kogo Kurihara, Kazuya Yamada, Setsuko Sekita, Motoyoshi Satake, and Osamu Iida. "Genetic Identification of Cinnamon (Cinnamomum spp.) Based on the trnL-trnF Chloroplast DNA." Planta Medica 68, no. 1 (January 2002): 94–96. http://dx.doi.org/10.1055/s-2002-20051.

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43

Bayer, Randall J., and Julian R. Starr. "Tribal Phylogeny of the Asteraceae Based on Two Non-Coding Chloroplast Sequences, the trnL Intron and trnL/trnF Intergenic Spacer." Annals of the Missouri Botanical Garden 85, no. 2 (1998): 242. http://dx.doi.org/10.2307/2992008.

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44

Zhang, Xiufu, Adam Marchant, Karen L. Wilson, and Jeremy J. Bruhl. "Phylogenetic relationships of Carpha and its relatives (Schoeneae, Cyperaceae) inferred from chloroplast trnL intron and trnL–trnF intergenic spacer sequences." Molecular Phylogenetics and Evolution 31, no. 2 (May 2004): 647–57. http://dx.doi.org/10.1016/j.ympev.2003.09.004.

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CHEN, YAN-QIONG, YA-TING ZHU, HUI ZHONG, ZE-XIN LI, ZHONG-JIAN LIU, JUN-WEN ZHAI, and SI-REN LAN. "Calanthe tsiana, a new orchid species from China (Epidendroideae: Collabieae): evidence from morphological and molecular analyses." Phytotaxa 428, no. 1 (January 6, 2020): 67–72. http://dx.doi.org/10.11646/phytotaxa.428.1.7.

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A new orchid, Calanthe tsiana, is described from southeastern Yunnan, China, based on morphological and DNA evidence. In morphological comparisons, C. tsiana is similar to C. arisanensis, but it differs in having subspatulate petals and falcate-obovate lateral lobes of lip with one ridge on the disk. The phylogenetic analyses based on nuclear ribosomal ITS and plastid DNA (rbcL, matK and trnL-trnF) place C. tsiana with C. arisanensis as sister species and support C. tsiana as a new species.

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46

Czumay, Aleksandra, Shanshan Dong, Armin Scheben, Alfons Schäfer-Verwimp, Kathrin Feldberg, and Jochen Heinrichs. "Transfer of Lejeunea huctumalcensis to Physantholejeunea (Lejeuneaceae, Porellales)." Australian Systematic Botany 26, no. 5 (2013): 386. http://dx.doi.org/10.1071/sb13039.

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Phylogenetic analyses of a three-marker dataset of Lejeuneaceae (chloroplast genome rbcL gene and trnL–trnF region, and nuclear ribosomal ITS1–5.8S-ITS2 region) resolve Lejeunea huctumalcensis (synonym Ceratolejeunea dussiana) in a well supported lineage with Physantholejeunea portoricensis. Representatives of Lejeunea and Ceratolejeunea form independent lineages. Physantholejeunea and L. huctumalcensis share the presence of ocelli, pycnolejeuneoid innovations and keeled perianths, with keels forming horn-like projections. On the basis of the molecular phylogenetic and morphological evidence, we transfer L. huctumalcensis to Physantholejeunea.

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MAMONTOV, YURIY S., ANNA A. VILNET, and ALEXEY D. POTEMKIN. "Scapania marsupelloides sp. nov. (Scapaniaceae, Marchantiophyta), a remarkable new species near the base of Scapania phylogeny." Phytotaxa 385, no. 2 (December 28, 2018): 55. http://dx.doi.org/10.11646/phytotaxa.385.2.1.

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Scapania marsupelloides is described as new to science based on collection from Yunnan, China. The species looks different from the other known Scapania species and similar to Marsupella sphacelata. Molecular phylogenic analyses of ITS1-2 and trnL–trnF sequences suggested the close affinity of Scapania marsupelloides to S. contorta of the subgenus Ascapania. Description, line drawings, color and SEM images, and keys for differentiation of S. marsupelloides from S. cuspiduligera, S. contorta, S. pseudocontorta, S. hians and Marsupella sphacelata are provided.

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VANZARA, AKASH G., ILESH KATARA, and PADAMNABHI S. NAGAR. "Alternanthera kanhae (Amaranthaceae), a new species from Sabarmati Estuary of India." Phytotaxa 500, no. 1 (May 7, 2021): 21–28. http://dx.doi.org/10.11646/phytotaxa.500.1.3.

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A new species of Amaranthaceae, Alternanthera kanhae, is described and illustrated from the bank of Sabarmati estuary in the state of Gujarat of Peninsular India. The new species is closely allied with A. caracasana and A. pungens but differs in many attributes. The identity of the newly proposed species is confirmed by molecular analysis of three chloroplast DNA (cpDNA) regions viz., rbcL, psbA–trnH and trnL–trnF. The sequences showed that A. kanhae has an independent lineage to that of its sister clade.

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YURTSEVA, OLGA V., N. K. BADMAEVA, and EVGENY V. MAVRODIEV. "A broadly sampled 3-loci plastid phylogeny of Atraphaxis (Polygoneae, Polygonoideae, Polygonaceae) reveals new taxa: II. Atraphaxis selengensis spec. nov., and A. davurica Jaub. & Spach from Russian Transbaikalia." Phytotaxa 484, no. 1 (February 15, 2021): 44–74. http://dx.doi.org/10.11646/phytotaxa.484.1.2.

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Maximum Likelihood (ML) and Bayesian analyses (BI) applied for 3-plastid loci (cpDNA trnL(UAA) intron, trnL–trnF IGS, and rpl32–trnL(UAG) IGS regions) / 55 tips of Atraphaxis revealed a subclade of two endemics from Transbaikalia (Dahuria) which are often mistaken for A. pungens and A. frutescens but phylogenetically distant from both. Atraphaxis selengensis is a species new to science which inhabits dune sands along the Selenga and Chikoy rivers and has specific morphology of perianth, fruits, ochreas, leaf blades, and pollen. Atraphaxis davurica inhabits stony mountain steppe in Buryatia and Chita region and differs from A. pungens and A. frutescens by longer ochreas, fruits, styles and stigmas extended to ends. Two varieties recognized by Ledebour in plants from Russian Transbaikalia have no clear morphological and molecular distinctions, but the plants from Khentei-Chikoy Highlands subtly differ in leaf ratio (length/width), bark colour, and a single-nucleotide substitution in trnL–F region. These plants are described as A. davurica var. chikoensis var. nov. Morphological descriptions of A. selengensis and A. davurica are supplied with LM and SEM images and a distributional map. Atraphaxis frutescens and A. pungens are absent from Russian Transbaikalia but distributed in Altai, Tuva, Khakassia, Mongolia and China.

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COSTA, SUZANA M., ROSEMERI MOROKAWA, VOLKER BITTRICH, WILLIAM W. THOMAS, and MARIA DO CARMO E. AMARAL. "What about Cryptangieae (Cyperaceae)—a molecular hypothesis about its tribal status and circumscription." Phytotaxa 347, no. 2 (April 13, 2018): 127. http://dx.doi.org/10.11646/phytotaxa.347.2.2.

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Abstract:

We endorse the tribal status of Cryptangieae and discuss its most probable sister-group based on phylogenetic analyses using rbcL, trnL-trnL-trnF and ITS sequences. Cryptangieae were poorly sampled in previous molecular phylogenies of Cyperaceae: only three of about 50 species were sampled and all of them are currently included in the genus Lagenocarpus. We gathered more data about the tribe to verify its monophyletic status and to clarify the relationships among the tribes of subfamily Cyperoideae. Here we present a phylogeny with 18 species of Cryptangieae including all three currently recognized genera. Cryptangieae appears as monophyletic with great support in our Maximum Parsimony and Bayesian Inference analyses based on single and combined matrices. We emphasize the need for morphological, molecular and biogeographical data to achieve a broadly supported interpretation of the early divergent taxa of subfamily Cyperoideae.

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Journal articles on the topic 'TrnL-trnF'

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