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1.
Gene ; 530(2): 229-35, 2013 Nov 10.
Artigo em Inglês | MEDLINE | ID: mdl-23973725

RESUMO

The sequence of the chloroplast genome, which is inherited maternally, contains useful information for many scientific fields such as plant systematics, biogeography and biotechnology because its characteristics are highly conserved among species. There is an increase in chloroplast genomes of angiosperms that have been sequenced in recent years. In this study, the nucleotide sequence of the chloroplast genome (cpDNA) of Veratrum patulum Loes. (Melanthiaceae, Liliales) was analyzed completely. The circular double-stranded DNA of 153,699 bp consists of two inverted repeat (IR) regions of 26,360 bp each, a large single copy of 83,372 bp, and a small single copy of 17,607 bp. This plastome contains 81 protein-coding genes, 30 distinct tRNA and four genes of rRNA. In addition, there are six hypothetical coding regions (ycf1, ycf2, ycf3, ycf4, ycf15 and ycf68) and two open reading frames (ORF42 and ORF56), which are also found in the chloroplast genomes of the other species. The gene orders and gene contents of the V. patulum plastid genome are similar to that of Smilax china, Lilium longiflorum and Alstroemeria aurea, members of the Smilacaceae, Liliaceae and Alstroemeriaceae (Liliales), respectively. However, the loss rps16 exon 2 in V. patulum results in the difference in the large single copy regions in comparison with other species. The base substitution rate is quite similar among genes of these species. Additionally, the base substitution rate of inverted repeat region was smaller than that of single copy regions in all observed species of Liliales. The IR regions were expanded to trnH_GUG in V. patulum, a part of rps19 in L. longiflorum and A. aurea, and whole sequence of rps19 in S. china. Furthermore, the IGS lengths of rbcL-accD-psaI region were variable among Liliales species, suggesting that this region might be a hotspot of indel events and the informative site for phylogenetic studies in Liliales. In general, the whole chloroplast genome of V. patulum, a potential medicinal plant, will contribute to research on the genetic applications of this genus.


Assuntos
Cloroplastos/genética , Genoma de Cloroplastos , Genômica , Filogenia , RNA de Plantas/genética , Veratrum/genética , Cloroplastos/classificação , Mapeamento Cromossômico , DNA Circular , Sequências Repetidas Invertidas , Liliaceae/classificação , Liliaceae/genética , RNA de Plantas/classificação , RNA Ribossômico/classificação , RNA Ribossômico/genética , RNA de Transferência/classificação , RNA de Transferência/genética , Smilacaceae/classificação , Smilacaceae/genética , Veratrum/classificação
2.
Mol Phylogenet Evol ; 68(2): 300-11, 2013 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-23578597

RESUMO

The Smilax hispida group (Smilacaceae) exhibits a discontinuous distribution in eastern Asia, eastern and western United States, and Mexico. A broad scale phylogeographic analysis was conducted for this group to evaluate the hypotheses of accelerated allopatric divergence in eastern Asia and a northern origin of the temperate elements in Mexico. Phylogeny was inferred using seven plastid and nuclear DNA sequences. Species delineation was assessed using genealogical sorting indices (GSI). Lineage divergence time, haplotype diversification rates, and ancestral distributions were estimated using Bayesian methods. Phylogeographic patterns in eastern Asia and North America were compared by analyzing 539 individuals from 64 populations to assess allopatric diversification. Results strongly supported delineation of six allopatric species, the origin of this group from a Mexican ancestor around 11.42mya, and Mexican origins of the temperate species in Mexico. Significant geographic structure of haplotypes was found in eastern Asia, and greater haplotype diversification rate was observed for the North American lineage. Our data support allopatric speciation in eastern Asia but do not find evidence of an elevated diversification rate. Greater species diversity of the study system in eastern Asia may be due to a longer evolutionary history. Our results do not support northern origins of the Mexican temperate species.


Assuntos
Evolução Molecular , Genes de Plantas , Filogenia , Smilacaceae/genética , DNA de Cloroplastos/genética , Extremo Oriente , Especiação Genética , Variação Genética , Genomas de Plastídeos , Haplótipos , México , Modelos Genéticos , Tipagem de Sequências Multilocus , Filogeografia , Smilacaceae/classificação
3.
Ann Bot ; 103(3): 459-75, 2009 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-19033282

RESUMO

BACKGROUND AND AIMS: There is an extensive literature on the diversity of karyotypes found in genera within Liliaceae, but there has been no attempt to analyse these data within a robust phylogenetic framework. In part this has been due to a lack of consensus on which genera comprise Liliaceae and the relationships between them. Recently, however, this changed with the proposal for a relatively broad circumscription of Liliaceae comprising 15 genera and an improved understanding of the evolutionary relationships between them. Thus there is now the opportunity to examine patterns and trends in chromosome evolution across the family as a whole. METHODS: Based on an extensive literature survey, karyo-morphometric features for 217 species belonging to all genera in Liliaceae sensu the APG (Angiosperm Phylogeny Group) were obtained. Included in the data set were basic chromosome number, ploidy, chromosome total haploid length (THL) and 13 different measures of karyotype asymmetry. In addition, genome size estimates for all species studied were inferred from THLs using a power regression model constructed from the data set. Trends in karyotype evolution were analysed by superimposing the karyological data onto a phylogenetic framework for Liliaceae. KEY RESULTS AND CONCLUSIONS: Combining the large amount of data enabled mean karyotypes to be produced, highlighting marked differences in karyotype structure between the 15 genera. Further differences were noted when various parameters for analysing karyotype asymmetry were assessed. By examining the effects of increasing genome size on karyotype asymmetry, it was shown that in many but not all (e.g. Fritillaria and all of Tulipeae) species, the additional DNA was added preferentially to the long arms of the shorter chromosomes rather than being distributed across the whole karyotype. This unequal pattern of DNA addition is novel, contrasting with the equal and proportional patterns of DNA increase previously reported. Overall, the large-scale analyses of karyotype features within a well-supported phylogenetic framework enabled the most likely patterns of chromosome evolution in Liliaceae to be reconstructed, highlighting diverse modes of karyotype evolution, even within this comparatively small monocot family.


Assuntos
Cromossomos de Plantas/genética , Evolução Molecular , Variação Genética , Liliaceae/genética , Centrômero/genética , Análise por Conglomerados , Genoma de Planta/genética , Haploidia , Cariotipagem , Filogenia , Poliploidia , Análise de Regressão , Smilacaceae/genética
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