Academic literature on the topic 'TrnL-trnF'

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.

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.

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.

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.

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.

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.

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.

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.

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.

Mentha (Nepetoideae, Lamiaceae) is a taxonomically complex genus that includes economically important members such as spearmint and peppermint and species of global conservation interest. Mentha is considered challenging systematically due to its high incidence of polyploidy, diverse morphology, variation in base chromosome number, and frequent interspecific hybridization. Our objectives were to test the monophyly of Mentha and each of its traditionally recognized sections, assess phylogenetic relationships of the Mentha species, test hypotheses of hybridization for the putative stabilized allopolyploids (M spicata and M. canadensis), and determine the ancestral base chromosome number using DNA sequence data from the chloroplast trnL-trnF and nuclear ribosomal internal transcribed spacer (ITS) regions. Based on trnL-trnF data, Mentha appears monophyletic. However, ITS data place the Mentha species into two distinct clades that include 12 other Mentheae genera. None of the sections with more than one species sampled form monophyletic groups based on either data set, and are therefore inconsistent with traditional classification. Cloned ITS sequences of M. canadensis and M. spicata support the hypothesis of hybridization as evidenced by nucleotide site polymorphism in ITS direct sequences and divergent clones cluster with different species. Moreover, our data indicate that M. spicata, rather than M. longifolia, may be a parent of M. canadensis. Character optimization of base chromosome number on to the molecular phylogenies shows that x = 12 may be ancestral based on trnL-trnF data or possibly x = 9 or x = 10 based on ITS data.

Thesis (MSc)--Stellenbosch University, 2003.
ENGLISH ABSTRACT: The phylogenetic relationships and taxonomic status of South African Oxalis L. species are highly unresolved, both regionally and with regard to precise placement within the genus as a whole. Studies based exclusively on morphological and palynological characteristics have hitherto proved only partially successful in resolving natural groupings among the indigenous taxa of the region. Recent studies involving a few native taxa have indicated the plastid trnL-trnF non-coding DNA region as useful for the purposes of reconstructing phylogenetic relationships within the genus. The present study addressed the taxonomic monophyly and relationships of the highly unresolved section Angustatae subsection Lineares, using DNA sequence data. The phylogenetic reconstruction of southern African Oxalis species renders five of the subsections of section Angustatae sensu Salter (1944) polyphyletic, three of them conclusively so. The members of subsection Lineares are split between three clades, two of them with strong bootstrap support. None of these three clades consists exclusively of species of subsection Lineares. Likewise four of the seven assemblages of related taxa within subsection Lineares sensu Salter (1944) are not retrieved as monophyletic. Pollen data sensu Dreyer (1996) supports the clades retrieved in this study, whereas very few morphological characters could be plotted as potential synapomorphies for these clades. The resultant phylogenetic reconstruction thus supports palynological data of this subsection, and indicates the urgent need for a revision of the current morphological classification of Salter (1944).
AFRIKAANSE OPSOMMING: Die filogenetiese verwantskappe en taksonomiese klassifikasie van Suid Afrikaanse Oxalis L. spesies is nog baie onduidelik, beide binne die gebied en ten opsigte van die presiese plasing binne die genus as 'n geheel. Vorige werk, uitsluitlik gebaseer op morfologiese en palinologiese kenmerke, was tot dusver nog net gedeeltelik suksesvol in die identifikasie van natuurlike groepe binne die inheemse taksa van die gebied. Onlangse studies op 'n paar inheemse spesies het die nut van die plastied trnL-trnF nie-koderende DNA area bevestig vir die rekonstruksie van filogenetiese verwantskappe in die genus. Hierdie studie is gerig op die taksonomiese monofilie en verwantskappe van die onnatuurlike seksie Angustatae subseksie Lineares, deur gebruik te maak van DNA basis-volgorde data. Die filogenetiese rekonstruksie van Suid Afrikaanse Oxalis spesies dui aan dat vyf van die subseksies van seksie Angustatae sensu Salter (1944) polifileties is, met sterk steun daarvoor dat drie van hulle onnatuurlik is. Die lede van subseksie Lineares is tussen drie verskillende groepe versprei; twee van dié groepe het sterk ondersteuning. Nie een van die drie groepe bestaan uitsluitlik uit spesies van subseksie Lineares nie. So ook is vier van die sewe groepe van verwante spesies binne subseksie Lineares sensu Salter (1944) polifileties. Stuifmeel data volgens Dreyer (1996) ondersteun die groepe wat deur die DNA volgordes uitgewys is, terwyl baie min morfologiese kenmerke gebruik kan word as potensiële sinapomorfe/kenmerke. Die filogenetiese rekonstruksie ondersteun dus die palinologiese data van die subseksie, en dui op die dringende behoefte aan 'n hersiening van die huidige morfologiese klassifikasie van Salter (1944).

Thesis (M.Sc.(Systematics and Biodiversity Science))-- Stellenbosch University, 2001.
ENGLISH ABSTRACT: Sequence data from the intron and the spacer of the trnL-F chloroplast DNA region were used to study the phylogenetic relationships of the genus Zygophyllum L. (Zygophylloideae: Zygophyllaceae) in the southern African region. The chloroplast DNA was extracted from both herbarium and silica-gel dried material. Closely related genera, i.e. Augea Thunb., Fagonia L. and Tetraena Maxim. within the subfamily Zygophylloideae and more distantly related genera Seetzenia R.Br. ex Decne and Tribulus L. were used as outgroups. Sequences revealed length variation mainly due to the presence of indels (insertions and deletions). Phylogenetic analysis using parsimony revealed two distinct lineages for southern African members of Zygophyllum, corresponding to the proposed subgeneric classification (Van Huysteen 1937; Van Zyl 2000). There is a strong monophyly support for the sections within the subgenus Agrophyllum (Neck.) Endl. However, the transference of the monotypic section Grandifolia Engl. from subgenus Zygophyllum to Agrophyllum is not confirmed, because material of Z. stapffii Schinz. was not available. Despite the morphological evidence for the subdivision of the subgenus Zygophyllum, the molecular data did not confirm the monophyly for its sections. This could be the result of biased sampling, since all the species used in the analyses, except Z. cordifolium L.f. and Z. morgsana L., belong to section Capensia Engl. The trnL region data support the transfer of the mono typic section Morgsana Huysst. from subgenus Agrophyllum to subgenus Zygophyllum. The molecular data also seem to have implications for the biogeography of Zygophyllum. The southern African Agrophyllum representatives are related to East African and Middle East Zygophyllum species, whereas the southern African subgenus Zygophyllum members are closely related to Australian Zygophyllum species.
AFRIKAANSE OPSOMMING: Die volgorde-data van die trnL-F chloroplas-DNA gebied is gebruik om die filogenetiese verwantskappe van die genus Zygophyllum L. (Zygophylloideae: Zygophyllaceae) in suider Afrika te bestudeer. Die chloroplas-DNA is geëkstraheer van beide herbaria en silica-gel gedroogde materiaal. Naverwante genera binne die subfamilie Zygophylloideae bv. Augea Thunb., Fagonia L. en Tetraena Maxim., sowel as verder verwante genera, soos Seetzenia R.Br. ex Decne en Tribulus L., was as buite-groepe gebruik. Die lengte-variasie in die volgorde-data kan toegeskryf word aan indels (insertions and deletions). Filogenetiese analise deur die gebruik van parsimonie het twee duidelike ontwikkelingslyne vir suider-Afrikaanse Zygophyllum taksa aangedui. Dit stem goed ooreen met die voorgestelde subgeneriese klassifikasiesisteem vir die genus (Van Huysteen1937; Van Zyl 2000). Daar is 'n sterk ondersteuning vir monofilie van die seksies binne die subgenus Agrophyllum (Neck.) Endl. Die oorplasing van die monotipiese seksie Grandifolia Engl. vanaf subgenus Zygophyllum na subgenus Agrophyllum is nie bevestig nie, want materiaal van Z. stapffii Schinz. was nie beskikbaar nie. Ten spyte van morfologiese bewyse vir die subdivisie van die subgenus Zygophyllum het die molekulêre data nie die monofilie van die seksies bevestig nie. Dit is moontlik as gevolg van eensydige data-insameling, aangesien al die spesies wat in die analise gebruik word (behalwe Z. cordifolium L.f. en Z. morgsana L.) aan die seksie Capensia Engl. behoort. Die trnL-gebied data ondersteun die oordra van die monotipiese seksie Morgsana Huysst. van die subgenus Agrophyllum na die subgenus Zygophyllum. Die molekulêre data bied ode inligting oor die biogeografie van Zygophyllum. Die suider-Afrikaanse Agrophyllum taksa is verwant aan Oos-Afrika en Midde-Oosterse Zygophyllum spesies, terwyl lede van die Suid-Afrikaanse subgenus Zygophyllum nouverwant is aan Zygophyllum spesies in Australië.

Thesis (Ph. D.)--Ohio State University, 2003.
Title from first page of PDF file. Document formatted into pages; contains xiv, 119 p.; also includes graphics (some col.). Includes abstract and vita. Advisor: Andrea D. Wolfe, Dept. of Evolution, Ecology, and Organismal Biology. Includes bibliographical references (p. 109-119).

Dentre as orquídeas terrícolas brasileiras, dois grupos são particularmente importantes do ponto de vista taxonômico, sistemático e biogeográfico: as orquídeas das subtribo Chloraeinae e Spiranthinae. Na sua atual delimitação, Chloraeinae compreende aproximadamente 70 espécies em três gêneros: Chloraea, Bipinnula e Gavilea. Por outro lado, Spiranthinae compreende cerca de 470 espécies exclusivamente neotropicais, distribuídas em 42 gêneros. As análises filogenéticas mais recentes suportam a existência de quatro grupos: os clados Stenorhynchos, Pelexia, Eurystyles+Lankesterella e Spiranthes. Assim, os objetivos deste estudo são: 1) realizar um estudo taxonômico e nomenclatural das orquídeas brasileiras do clado Pelexia; 2) documentar a morfologia floral e vegetativa, com ênfase nos caracteres diagnósticos; 3) realizar um estudo taxonômico e nomenclatural das espécies brasileiras de Chloraeinae; 4) construir uma filogenia molecular mais completa e representativa do clado Pelexia; 5) estabelecer se os gêneros do clado Pelexia são monofiléticos; 6) construir uma filogenia molecular mais completa e representativa de Chloraeinae, com a inclusão de táxons brasileiros; 7) estabelecer um conjunto de caracteres diagnósticos para os gêneros envolvidos neste estudo e, se necessário, propor uma nova delimitação genérica; e 8) propor cenários para a provável evolução de caracteres de importância ecológica. Os resultados de um estudo detalhado, bem como de análises morfológicas e moleculares são: 1) propostas de 48 tipificações, novas sinonímias e notas taxonômicas para as espécies de Goodyerinae e Spiranthinae descritas por José Velloso e Barbosa Rodrigues; 2) novos registros de Pteroglossa e Lyroglossa para o Rio Grande do Sul; 3) uma correção nomenclatural de Spiranthes bicolor e 4) uma sinopse taxonômica das Chloraeinae brasileiras; 5) uma análise filogenética molecular para testar a monofilia dos gêneros atualmente circunscritos no clado Pelexia; 6) uma atualização das relações filogenéticas de Chloraeinae, incluindo espécies Pampeanas de Bipinnula e a espécie tipo do gênero, B. biplumata; 7) um panorama sobre a biologia reprodutiva de duas espécies de Pachygenium e dados adicionais sobre Brachystele e Cyclopogon s.l.; e 8) um estudo detalhado da morfologia floral, biologia da polinização e sistema reprodutivo de Chloraea membranacea (Chloraeinae).
Among the Brazilian terrestrial orchids, two groups are particularly important from a taxonomic, systematic and biogeographical aspects: orchids of subtribe Chloraeinae and Spiranthinae. In its current delimitation, Chloraeinae comprises approximately 70 species distributed in three genera: Chloraea, Bipinnula and Gavilea. On the other hand, Spiranthinae comprises about 470 exclusively neotropical species distributed in ca. 42 genera. The most recent phylogenetic analyses support the existence of four clades: Stenorrhynchos, Pelexia, Eurystyles+Lankesterella and Spiranthes clade, respectively. Thus, the aims of this study are: 1) to make a taxonomic and nomenclatural study of Brazilian orchids of Pelexia clade; 2) to document the floral and vegetative morphology, with emphasis on diagnostic features; 3) to make a taxonomic and nomenclatural study of the Brazilian species of Chloraeinae; 4) to assemble a more complete and representative molecular phylogeny of the Pelexia clade; 5) to establish if the genera of the Pelexia clade are monophyletic; 6) to construct a more complete and representative molecular phylogeny of the Chloraeinae, with the inclusion of Brazilian taxa; 7) to establish sets of diagnostic characters for the genera involved in this study and, if necessary, propose a new generic delimitation; and 8) to propose scenarios for the evolution of characters of ecological importance. The main results are: 1) 48 typifications, new synonymies and taxonomic notes for Spiranthinae and Goodyerinae species described by José Velloso and Rodrigues Barbosa; 2) new records of Pteroglossa and Lyroglossa to Rio Grande do Sul; 3) a nomenclatural correction of Spiranthes bicolor and 4) a taxonomic synopsis of Brazilian Chloraeinae; 5) molecular phylogenetic analyses to test the monophyly of the currently circumscribed genera in the Pelexia clade; 6) an update of the phylogenetic relationships of the Chloraeinae, including Pampean species of Bipinnula, and the type species of the genus, B. biplumata; 7) an overview on the reproductive biology of two Pachygenium species and additional data on Brachystele and Cyclopogon s.l.; and 8) a detailed study of the floral morphology, pollination biology and reproductive system of Chloraea membranacea (Chloraeinae).

Subtribe Alopecurinae (Poeae, Poaceae) sensu lato‘s seven genera share interesting morphological similarities (dense spicate panicles and one-flowered spikelets) that were widely thought to have a common origin. However, recent molecular evidence for three of the genera has suggested that the subtribe may be polyphyletic. To test this, five DNA regions were sequenced and analyzed using phylogenetic methods. Results confirm that Alopecurinae s.l. as presently treated is polyphyletic and should be dissolved. Additionally, the genus Cornucopiae may be just another Alopecurus. Limnas and Pseudophleum are not closely allied to Alopecurus or each other, and are even further from Phleum. Phleum is a distinct lineage that is not closely allied to any other included Alopecurinae genus. Evidence for revising infrageneric classifications of Alopecurus and Phleum is presented, as is evidence for separating A. magellanicus into two or more subspecies.

碩士
中央警察大學
鑑識科學研究所
90
The intron of trnL(UAA) and intergenic spacer (IGS) of trnL(UAA) - trnF(GAA) in the chloroplast genome were used as phylogenetic makers in many researches. The sequence variances represent the relationship of evolution among each plant. This research collected 335 samples from common plants including 221 species of 72 families in north Taiwan. The trnL intron and trnL-trnF IGS of each sample was sequenced to assess phylogenetic analysis for forensic applications. The 55 of 65 species for trnL intron and the 62 of 66 species for trnL-trnF IGS conformed to the species which have been known in the phylogenetic analysis. The remaining 4 species could not refer to the known groups by combining analyses of trnL intron and trnL-trnF IGS. Also 2 of 25 genuses could not entirely refer to the identified genuses in the phylogenetic analyses. The genetic distance and bootstrap values in phylogenetic analysis could refer to the species and genus of unknown sample. This study indicated that the trnL intron and trnL-trnF IGS could be used as efficient phylogenetic markers for forensic sciences.

碩士
中國文化大學
生物科技研究所
99
Cinnamomum osmophloeum Kaneh. (CO) belongs to the Lauraceae family. It is considerable market demand, because not only can be used as traditional Chinese edicine but also as a spice. Traditionally, morphological or histological identification of plants using characteristics of the effect is limited. In particular, the characteristics can be distinguished in the seedlings stage are less, so that difficult to distinguish. And type of identification may lead to mixing or misuse of medicinal plants. Therefore, we used DNA molecular marker technology to identify Cinnamomum osmophloeum Kaneh. This study attempts to identify the gene resources of Cinnamomum osmophloeum Kaneh. by analyzing the nucleotide sequences of the partial non-coding internal transcribed spacer 2 (pITS2) of the ribosomal DNA and the trnL-trnF chloroplast genome. Seventy-three geographical strains of CO, preserved in the Lien Hua-Chin Research Center of the Forestry Research Institute and the Hua-Lin Forestry Center of Chinese Culture University, were collected and analyzed by PCR amplification and DNA sequencing to study the genetic diversity and nucleotide sequence polymorphisms of the tested specimens. Our results allowed us to accurately identify the lineage of CO and to conclude that the strains belonging to the Lien Hua-Chin Research Center had much higher genetic diversity than those preserved in the Hua-Lin Forestry Center. Multiple sequence alignments demonstrated that the variability of the nucleotide sequence polymorphisms for the pITS2 region was higher than those of the trnL intron and trnL-trnF IGS regions among the 73 tested specimens of CO. Cluster analyses, using the neighbor-joining and maximum parsimony methods, for the 73 tested geographical strains of CO and species of Cinnamomum registered in the GenBank and EMBL databases were performed to demonstrate the genus and species distribution of the samples. Here, we describe the use of pITS2 polymorphisms as a genetic classifier and report the establishment of a DNA sequence database for CO gene resource identification. The sequence database described in this study can be used to identify CO specimens at the inter- or intra-species level using pITS2 DNA sequences, which illustrates its value in gene resource identification.

Variability in the genetic information DNA tracking individuals carry is easy to detect using molecular markers. In the thesis we examined related Dracaena species. For the study of genetic diversity in the genus Dracaena are used mainly noncoding regions of cpDNA, spacer trnH -- psbA, regions trnL -- trnF and trnS -- trnG -- trnG, which are more variable than coding regions. Also used in this work were coding regions of matK and rbcL. In the genus Dracaena belongs xerophytic species that are characterized by typical shaped treetop. 14 representatives of species were used in thesis growing in tropical regions of the African continent and adjacent islands and the southeastern part of the Arabian peninsula. They are monocotyledonous trees with atypical abilities of secondary thickness of trunk, which I find interesting. The massive trunk is very strong and there is potencial to used it for wood. Trees are very significant for their red plant sap which flowing from demaged trunk. The sap is very precious resource which is used in many areas of industry, for example pharmacy, traditional medicine, dye making etc. Determination of genetic affinity was based on an amplification of cpDNA template of individual Dracaena samples with primers for the studied regions. Data was obtained and evaluated by Multiple alignment program ClustalX and BioEdit after their sequencing. Evalueted data was used to create dendograms affinity. According the resulting phylogenetic tree we find out similarities and identified relationship of the monitored species of the genus Dracaena. The main purpose of research was to get answers to understand phylogenetic relationship between group of Dracaena forestry used trees. The thesis was made in cooperation of Department of Forest Botany, Dendrology and Geobiocoenology, Faculty of Forestry and Wood Technology of Mendel University in Brno.

Bauhinia s.l. est le plus vaste genre de la tribu des Cercideae (Ceasalpinioideae, Leguminoseae), avec plus de 300 espèces. Il présente une distribution pantropicale et une grande variabilité morphologique. Ces deux caractéristiques ont limité les études taxonomiques sur le genre complet, résultant en plusieurs études taxonomiques de certains groupes seulement. En 1987, Wunderlin et al. proposent une vaste révision taxonomique de la tribu des Cercideae, basée sur des données morphologiques, et divisent le genre Bauhinia en quatre sous-genres. En 2005, Lewis et Forest publient une nouvelle classification préliminaire basée sur des données moléculaires, mais sur un échantillonnage taxonomique restreint. Leurs conclusions remettent en question le monophylétisme du genre Bauhinia et suggèrent plutôt la reconnaissance de huit genres au sein du grade Bauhinia s.l. Afin de vérifier les hypothèses de Lewis et Forest, et obtenir une vision plus claire de l’histroire de Bauhinia s.l., nous avons séquencé deux régions chloroplastiques (trnL-trnF et matK-trnK) et deux régions nucléaires (Leafy et Legcyc) pour un vaste échantillonnage représentatif des Cercideae. Une première phylogénie de la tribu a tout d’abord été réalisée à partir des séquences de trnL-trnF seulement et a confirmé le non-monoplylétisme de Bauhinia s.l., avec l’inclusion du genre Brenierea, traditionnellement reconnu comme genre frère de Bauhinia s.l. Afin de ne pas limiter notre vision de l’histoire évolutive des Cercideae à un seul type de données moléculaires et à une seule région, une nouvelle série d’analyse a été effectuée, incluant toutes les séquences chloroplastiques et nucléaires. Une phylogénie individuelle a été reconstruite pour chacune des régions du génome, et un arbre d’espèce ainsi qu’un arbre de supermatrice ont été reconstruits. Bien que certaines contradictions apparaissent entre les phylogénies, les grandes lignes de l’histoire des Cercideae ont été résolues. Bauhinia s.l. est divisée en deux lignées : les groupes Phanera et Bauhinia. Le groupe Bauhinia est constitué des genres Bauhinia s.s., Piliostigma et Brenierea. Le groupe Phanera est constitué des genres Gigasiphon, Tylosema, Lysiphyllum, Barklya, Phanera et Schnella. Les genres Cercis, Adenolobus et Griffonia sont les groupes-frères du clade Bauhinia s.l. Au minimum un événement de duplication de Legcyc a été mis en évidence pour la totalité de la tribu des Cercideae, excepté Cercis, mais plusieurs évènements sont suggérés à la fois par Legcyc et Leafy. Finalement, la datation et la reconstruction des aires ancestrales de la tribu ont été effectuées. La tribu est datée de 49,7 Ma et est originaire des régions tempérées de l’hémisphère nord, probablement autour de la mer de Thétys. La tribu s’est ensuite dispersée vers les régions tropicales sèches de l’Afrique, où la séparation des groupes Bauhinia et Phanera a eu lieu. Ces deux groupes se sont ensuite dispersés en parallèle vers l’Asie du sud-est au début du Miocène. À la même période, une dispersion depuis l’Afrique de Bauhinia s.s. a permis la diversification des espèces américaines de ce genre, alors que le genre Schnella (seul genre américain du groupe Phanera) est passé par l’Australie afin de rejoindre le continent américain. Cette dispersion vers l’Australie sera également à l’origine des genres Lysiphyllum et Barklya
Bauhinia s.l. is the largest genus of the tribe Cercideae (Ceasalpinioideae, Leguminoseae), with over 300 species. It has a pantropical distribution and high morphological variability. These two features have resulted in few studies that focus on the entire genus, resulting in several regional studies or studies of certain subgroups only. In 1987, Wunderlin et al. presented a broad taxonomic revision of the tribe Cercideae, based on morphological data, and divided the genus Bauhinia into four subgenera. In 2005, Lewis and Forest published a new preliminary classification based on molecular data, but for a limited taxonomic sampling. Their findings question the monophyly of the genus Bauhinia and suggest instead the recognition of eight genera in the Bauhinia s.l. grade. To test the hypotheses of Lewis and Forest, and to obtain a clearer view of the history of Bauhinia s.l., we sequenced two chloroplast regions (trnL-trnF and matK-trnK) and two nuclear regions (Leafy and Legcyc) for a large representative sampling of the Cercideae. A primary phylogeny of the tribe was first generated based on trnL-trnF sequences only and confirmed the non-monophyly of Bauhinia s.l., with the inclusion of the genus Brenierea, traditionally recognized as sister group of Bauhinia s.l. In order to obtain a deaper view of the evolutionary history of the Cercideae, a new series of analysis was performed, including all nuclear and chloroplast sequences. Individual phylogenies were reconstructed for each region of the genome, and both a species and a supermatrix trees were reconstructed. Although certain conflicting relationships appear between phylogenies, the outline of the history of the Cercideae has been resolved. Bauhinia s.l. is divided into two lineages: Phanera and Bauhinia groups. The Bauhinia group includes Bauhinia s.s., Piliostigma and Brenierea. The Phanera group is composed of Gigasiphon, Tylosema, Lysiphyllum, Barklya, Phanera and Schnella. Cercis, Griffonia and Adenolobus are sister groups of Bauhinia s.l. At least one duplication event of Legcyc has been highlighted for the entire tribe Cercideae, excluding Cercis. Several other duplication events are also suggested by both Legcyc and Leafy . Finally, a divergence time analysis and a reconstruction of ancestral areas were conducted. The root of the tribe is evaluated to be 49.7 Mya old, and to originate from temperate regions in the northern hemisphere, mostly around the Tethys Sea. The tribe then dispersed into drier biomes in Africa, where the separation of the Bauhinia and the Phanera groups occurred. These two lineages then dispersed following parallel routes to Southeast Asia in the early Miocene. At the same time, a dispersal of the African Bauhinia s.s. to South America permitted the diversification of the American species of this genus, and Schnella (the only American genus within the Phanera group) dispersed to the American continent from Australia. This dispersal to Australia is also at the origin of Lysiphyllum and Barklya.