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The chloroplast genome sequence of mungbean (Vigna radiata) determined by high-throughput pyrosequencing: structural organization and phylogenetic relationships.

Tangphatsornruang S, Sangsrakru D, Chanprasert J, Uthaipaisanwong P, Yoocha T, Jomchai N, Tragoonrung S - DNA Res. (2009)

Bottom Line: Of these, 75 are predicted protein-coding genes, 4 ribosomal RNA genes and 29 tRNA genes.We detected sequence length polymorphism in the cp homopolymeric regions at the intra- and inter-specific levels in the Vigna species.Phylogenetic analysis demonstrated a close relationship between Vigna and Phaseolus in the phaseolinae subtribe and provided a strong support for a monophyletic group of the eurosid I.

View Article: PubMed Central - PubMed

Affiliation: Genome Institute, National Center for Genetic Engineering and Biotechnology, Pathumthani, Thailand. sithichoke.tan@biotec.or.th

ABSTRACT
Mungbean is an economically important crop which is grown principally for its protein-rich dry seeds. However, genomic research of mungbean has lagged behind other species in the Fabaceae family. Here, we reported the complete chloroplast (cp) genome sequence of mungbean obtained by the 454 pyrosequencing technology. The mungbean cp genome is 151 271 bp in length which includes a pair of inverted repeats (IRs) of 26 474 bp separated by a small single-copy region of 17 427 bp and a large single-copy region of 80 896 bp. The genome contains 108 unique genes and 19 of these genes are duplicated in the IR. Of these, 75 are predicted protein-coding genes, 4 ribosomal RNA genes and 29 tRNA genes. Relative to other plant cp genomes, we observed two distinct rearrangements: a 50-kb inversion between accD/rps16 and rbcL/trnK-UUU, and a 78-kb rearrangement between trnH/rpl14 and rps19/rps8. We detected sequence length polymorphism in the cp homopolymeric regions at the intra- and inter-specific levels in the Vigna species. Phylogenetic analysis demonstrated a close relationship between Vigna and Phaseolus in the phaseolinae subtribe and provided a strong support for a monophyletic group of the eurosid I.

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The MP phylogenetic tree is based on 25 protein-coding genes from 34 plant taxa. The MP tree has a length of 29 081 with a consistency index of 0.4939 and a retention index of 0.6399. Numbers above node are bootstrap support values. Ordinal and higher level group names are also indicated. The ML tree has the same topology but is not shown.
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DSP025F4: The MP phylogenetic tree is based on 25 protein-coding genes from 34 plant taxa. The MP tree has a length of 29 081 with a consistency index of 0.4939 and a retention index of 0.6399. Numbers above node are bootstrap support values. Ordinal and higher level group names are also indicated. The ML tree has the same topology but is not shown.

Mentions: Our phylogenetic data set included 25 protein-coding genes for 34 plant taxa (Supplementary Table S3), including 32 angiosperms and two outgroup gymnosperms (Pinus and Ginkgo). These 25 genes are commonly present in all the 34 cp genomes, therefore should reduce missing data from the sequence alignment. The sequence alignment that was used for phylogenetic analyses comprised 20 454 characters. MP analysis resulted in a single resolved tree with a length of 29 081, a consistency index of 0.4939 and a retention index of 0.6399 (Fig. 4). Bootstrap analyses indicated that there were 27 out of 31 nodes with values ≥95%, and 25 of these had a bootstrap value of 100%. ML analysis resulted in a single tree with −ln L = −166 999.997. ML bootstrap values were also high, with values of ≥95% for 29 of the 32 nodes, and 27 nodes with 100% bootstrap support. Both MP and ML trees had the same topologies which formed two major clades, monocots and eudicots. The trees revealed a monophyly of the monocots and eudicots where Ranunculales was placed as sister to the remaining eudicots. Within the eudicots, there were two major clades: rosids and asterids. Within the rosid clade, there were two major groups, the eurosids I and eurosids II which were sister to the Myrtales group. The placement of Cucumis has been problematic in previous reports.45,59 In some studies, Cucumis was placed with the Myrtales,45 or in the eurosids I.58,71,72 In our study, both MP and ML trees provided a strong support for the monophyly of the eurosids I clade because Cucumis is sister to the legume taxa. Among seven legumes with complete cp DNA sequences, Cicer, Medicago and Trifolium were grouped together as IR lacking millettioids clade (IRLC) and placed as sister to Lotus. IRLC members have been shown to form a monophyletic group supported by phylogenetic trees based on matK24 and nuclear rDNA sequences.73 Vigna was sister to Phaseolus in the Phaseolinae subtribe and was sister to Glycine in the tribe Phaseoleae. A monophyletic group of the Phaseolinae subtribe was also supported by previously reported trees, based on the matK gene24 and a distinct 78-kb rearrangement of the cp genome.25


The chloroplast genome sequence of mungbean (Vigna radiata) determined by high-throughput pyrosequencing: structural organization and phylogenetic relationships.

Tangphatsornruang S, Sangsrakru D, Chanprasert J, Uthaipaisanwong P, Yoocha T, Jomchai N, Tragoonrung S - DNA Res. (2009)

The MP phylogenetic tree is based on 25 protein-coding genes from 34 plant taxa. The MP tree has a length of 29 081 with a consistency index of 0.4939 and a retention index of 0.6399. Numbers above node are bootstrap support values. Ordinal and higher level group names are also indicated. The ML tree has the same topology but is not shown.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC2818187&req=5

DSP025F4: The MP phylogenetic tree is based on 25 protein-coding genes from 34 plant taxa. The MP tree has a length of 29 081 with a consistency index of 0.4939 and a retention index of 0.6399. Numbers above node are bootstrap support values. Ordinal and higher level group names are also indicated. The ML tree has the same topology but is not shown.
Mentions: Our phylogenetic data set included 25 protein-coding genes for 34 plant taxa (Supplementary Table S3), including 32 angiosperms and two outgroup gymnosperms (Pinus and Ginkgo). These 25 genes are commonly present in all the 34 cp genomes, therefore should reduce missing data from the sequence alignment. The sequence alignment that was used for phylogenetic analyses comprised 20 454 characters. MP analysis resulted in a single resolved tree with a length of 29 081, a consistency index of 0.4939 and a retention index of 0.6399 (Fig. 4). Bootstrap analyses indicated that there were 27 out of 31 nodes with values ≥95%, and 25 of these had a bootstrap value of 100%. ML analysis resulted in a single tree with −ln L = −166 999.997. ML bootstrap values were also high, with values of ≥95% for 29 of the 32 nodes, and 27 nodes with 100% bootstrap support. Both MP and ML trees had the same topologies which formed two major clades, monocots and eudicots. The trees revealed a monophyly of the monocots and eudicots where Ranunculales was placed as sister to the remaining eudicots. Within the eudicots, there were two major clades: rosids and asterids. Within the rosid clade, there were two major groups, the eurosids I and eurosids II which were sister to the Myrtales group. The placement of Cucumis has been problematic in previous reports.45,59 In some studies, Cucumis was placed with the Myrtales,45 or in the eurosids I.58,71,72 In our study, both MP and ML trees provided a strong support for the monophyly of the eurosids I clade because Cucumis is sister to the legume taxa. Among seven legumes with complete cp DNA sequences, Cicer, Medicago and Trifolium were grouped together as IR lacking millettioids clade (IRLC) and placed as sister to Lotus. IRLC members have been shown to form a monophyletic group supported by phylogenetic trees based on matK24 and nuclear rDNA sequences.73 Vigna was sister to Phaseolus in the Phaseolinae subtribe and was sister to Glycine in the tribe Phaseoleae. A monophyletic group of the Phaseolinae subtribe was also supported by previously reported trees, based on the matK gene24 and a distinct 78-kb rearrangement of the cp genome.25

Bottom Line: Of these, 75 are predicted protein-coding genes, 4 ribosomal RNA genes and 29 tRNA genes.We detected sequence length polymorphism in the cp homopolymeric regions at the intra- and inter-specific levels in the Vigna species.Phylogenetic analysis demonstrated a close relationship between Vigna and Phaseolus in the phaseolinae subtribe and provided a strong support for a monophyletic group of the eurosid I.

View Article: PubMed Central - PubMed

Affiliation: Genome Institute, National Center for Genetic Engineering and Biotechnology, Pathumthani, Thailand. sithichoke.tan@biotec.or.th

ABSTRACT
Mungbean is an economically important crop which is grown principally for its protein-rich dry seeds. However, genomic research of mungbean has lagged behind other species in the Fabaceae family. Here, we reported the complete chloroplast (cp) genome sequence of mungbean obtained by the 454 pyrosequencing technology. The mungbean cp genome is 151 271 bp in length which includes a pair of inverted repeats (IRs) of 26 474 bp separated by a small single-copy region of 17 427 bp and a large single-copy region of 80 896 bp. The genome contains 108 unique genes and 19 of these genes are duplicated in the IR. Of these, 75 are predicted protein-coding genes, 4 ribosomal RNA genes and 29 tRNA genes. Relative to other plant cp genomes, we observed two distinct rearrangements: a 50-kb inversion between accD/rps16 and rbcL/trnK-UUU, and a 78-kb rearrangement between trnH/rpl14 and rps19/rps8. We detected sequence length polymorphism in the cp homopolymeric regions at the intra- and inter-specific levels in the Vigna species. Phylogenetic analysis demonstrated a close relationship between Vigna and Phaseolus in the phaseolinae subtribe and provided a strong support for a monophyletic group of the eurosid I.

Show MeSH
Related in: MedlinePlus