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The Glycine max cv. Enrei Genome for Improvement of Japanese Soybean Cultivars.

Shimomura M, Kanamori H, Komatsu S, Namiki N, Mukai Y, Kurita K, Kamatsuki K, Ikawa H, Yano R, Ishimoto M, Kaga A, Katayose Y - Int J Genomics (2015)

Bottom Line: Phylogenetic analysis provided glimpses into the ancestral relationships of both cultivars and their divergence from the complex that include the wild relatives of soybean.The gene models were analyzed in relation to traits associated with anthocyanin and flavonoid biosynthesis and an overall profile of the proteome.The sequence data are made available in DAIZUbase in order to provide a comprehensive informatics resource for comparative genomics of a wide range of soybean cultivars in Japan and a reference tool for improvement of soybean cultivars worldwide.

View Article: PubMed Central - PubMed

Affiliation: Mitsubishi Space Software Co., Ltd., Takezono, Tsukuba, Ibaraki 305-0032, Japan.

ABSTRACT
We elucidated the genome sequence of Glycine max cv. Enrei to provide a reference for characterization of Japanese domestic soybean cultivars. The whole genome sequence obtained using a next-generation sequencer was used for reference mapping into the current genome assembly of G. max cv. Williams 82 obtained by the Soybean Genome Sequencing Consortium in the USA. After sequencing and assembling the whole genome shotgun reads, we obtained a data set with about 928 Mbs total bases and 60,838 gene models. Phylogenetic analysis provided glimpses into the ancestral relationships of both cultivars and their divergence from the complex that include the wild relatives of soybean. The gene models were analyzed in relation to traits associated with anthocyanin and flavonoid biosynthesis and an overall profile of the proteome. The sequence data are made available in DAIZUbase in order to provide a comprehensive informatics resource for comparative genomics of a wide range of soybean cultivars in Japan and a reference tool for improvement of soybean cultivars worldwide.

No MeSH data available.


Phylogenetic tree of G. max cv. Williams 82 (Gmw), G. max cv. Enrei (Gme), A. thaliana (Ath), A. lyrata (Aly), and M. truncatula (Mtr). The pink bar represents the 95% probability density. Mya represents a unit in million years.
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fig1: Phylogenetic tree of G. max cv. Williams 82 (Gmw), G. max cv. Enrei (Gme), A. thaliana (Ath), A. lyrata (Aly), and M. truncatula (Mtr). The pink bar represents the 95% probability density. Mya represents a unit in million years.

Mentions: We applied OrthoMCL [19] to the clustered and aligned gene models of A. thaliana [16], A. lyrata [17], G. max cv. Williams 82 [7], G. max cv. Enrei, M. truncatula [18], and O. sativa (annotation data on Os-Nipponbare-Reference-IRGSP-1.0.). A set of filtered single copy genes was selected to calculate the phylogenetic relationships and divergence time among these species (Supplementary Table S1). Based on the phylogenetic divergence of A. thaliana which occurred about 13 Mya [27], the divergence between G. max cv. Williams 82 and cv. Enrei was estimated at 0.34 Mya (95PD: 0.78–0.10 Mya), much later than the calculated divergence time between A. thaliana and A. lyrata (95PD: 19.30–8.52 Mya; Figure 1). The divergence between the Glycine clade and M. truncatula was estimated to have occurred around 56.76 Mya (95PD: 84.54–36.99 Mya). On the other hand, the divergence between the G. max/M. truncatula clade and the Arabidopsis clade must have occurred much earlier around 83.67 Mya (95PD: 122.51–55.57 Mya). Previous studies have shown a divergence time of 54 Mya between M. truncatula and the Glycine clade [28]. A whole genome duplication (WGD) which occurred around 58 Mya had been a major factor in shaping the M. truncatula genome [18].


The Glycine max cv. Enrei Genome for Improvement of Japanese Soybean Cultivars.

Shimomura M, Kanamori H, Komatsu S, Namiki N, Mukai Y, Kurita K, Kamatsuki K, Ikawa H, Yano R, Ishimoto M, Kaga A, Katayose Y - Int J Genomics (2015)

Phylogenetic tree of G. max cv. Williams 82 (Gmw), G. max cv. Enrei (Gme), A. thaliana (Ath), A. lyrata (Aly), and M. truncatula (Mtr). The pink bar represents the 95% probability density. Mya represents a unit in million years.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4493290&req=5

fig1: Phylogenetic tree of G. max cv. Williams 82 (Gmw), G. max cv. Enrei (Gme), A. thaliana (Ath), A. lyrata (Aly), and M. truncatula (Mtr). The pink bar represents the 95% probability density. Mya represents a unit in million years.
Mentions: We applied OrthoMCL [19] to the clustered and aligned gene models of A. thaliana [16], A. lyrata [17], G. max cv. Williams 82 [7], G. max cv. Enrei, M. truncatula [18], and O. sativa (annotation data on Os-Nipponbare-Reference-IRGSP-1.0.). A set of filtered single copy genes was selected to calculate the phylogenetic relationships and divergence time among these species (Supplementary Table S1). Based on the phylogenetic divergence of A. thaliana which occurred about 13 Mya [27], the divergence between G. max cv. Williams 82 and cv. Enrei was estimated at 0.34 Mya (95PD: 0.78–0.10 Mya), much later than the calculated divergence time between A. thaliana and A. lyrata (95PD: 19.30–8.52 Mya; Figure 1). The divergence between the Glycine clade and M. truncatula was estimated to have occurred around 56.76 Mya (95PD: 84.54–36.99 Mya). On the other hand, the divergence between the G. max/M. truncatula clade and the Arabidopsis clade must have occurred much earlier around 83.67 Mya (95PD: 122.51–55.57 Mya). Previous studies have shown a divergence time of 54 Mya between M. truncatula and the Glycine clade [28]. A whole genome duplication (WGD) which occurred around 58 Mya had been a major factor in shaping the M. truncatula genome [18].

Bottom Line: Phylogenetic analysis provided glimpses into the ancestral relationships of both cultivars and their divergence from the complex that include the wild relatives of soybean.The gene models were analyzed in relation to traits associated with anthocyanin and flavonoid biosynthesis and an overall profile of the proteome.The sequence data are made available in DAIZUbase in order to provide a comprehensive informatics resource for comparative genomics of a wide range of soybean cultivars in Japan and a reference tool for improvement of soybean cultivars worldwide.

View Article: PubMed Central - PubMed

Affiliation: Mitsubishi Space Software Co., Ltd., Takezono, Tsukuba, Ibaraki 305-0032, Japan.

ABSTRACT
We elucidated the genome sequence of Glycine max cv. Enrei to provide a reference for characterization of Japanese domestic soybean cultivars. The whole genome sequence obtained using a next-generation sequencer was used for reference mapping into the current genome assembly of G. max cv. Williams 82 obtained by the Soybean Genome Sequencing Consortium in the USA. After sequencing and assembling the whole genome shotgun reads, we obtained a data set with about 928 Mbs total bases and 60,838 gene models. Phylogenetic analysis provided glimpses into the ancestral relationships of both cultivars and their divergence from the complex that include the wild relatives of soybean. The gene models were analyzed in relation to traits associated with anthocyanin and flavonoid biosynthesis and an overall profile of the proteome. The sequence data are made available in DAIZUbase in order to provide a comprehensive informatics resource for comparative genomics of a wide range of soybean cultivars in Japan and a reference tool for improvement of soybean cultivars worldwide.

No MeSH data available.