Limits...
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.


Related in: MedlinePlus

A region in soybean chromosome 8 showing the position of CHS gene clusters. The region encompassing 8.3~8.5 Mb of soybean chromosome 8 of Williams 82 Gmax275 (a) and Enrei cultivar (b) is characterized by CHS gene clusters. Most of the CHS genes correspond in both cultivars as indicated by the position and UniProt annotation of identified genes. However many CHS genes could not be localized in Enrei cultivar due to fragmented sequence.
© Copyright Policy - open-access
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4493290&req=5

fig3: A region in soybean chromosome 8 showing the position of CHS gene clusters. The region encompassing 8.3~8.5 Mb of soybean chromosome 8 of Williams 82 Gmax275 (a) and Enrei cultivar (b) is characterized by CHS gene clusters. Most of the CHS genes correspond in both cultivars as indicated by the position and UniProt annotation of identified genes. However many CHS genes could not be localized in Enrei cultivar due to fragmented sequence.

Mentions: In soybeans, several chalcone synthesis genes, namely, CHS3 (P19168), CHS1 (P24826), CHS7 (P30081), CHS4 (Q6X0N0), and CHS8 (AY237728), are associated with seed coat pigmentation [29]. The physical position of these CHS genes was determined using BAC assembly [30, 31] for loci associated with RNA silencing and WGS assembly [7]. The corresponding genes in the Gmax275 genome assembly are as follows: CHS1 (Glyma.08G109400), CHS2 (Glyma.05G153200), CHS3 (Glyma.08G110300 and Glyma.08G110900), CHS4 (Glyma.08G110500 and Glyma.08G110700), CHS5 (Glyma.08G109200, Glyma.08G109300, and Glyma.08G110400), CHS6 (Glyma.09G075200), CHS7 (Glyma.01G228700), CHS8 (Glyma.11G011500), and CHS9 (Glyma.08G109500). Most of the genes in the pathway were commonly represented in both cultivars (Figure 2). However, one 4CL gene in chromosome 7, 5 CHS genes in chromosome 8, 3 CHI genes in 14, 15, and 19, respectively, 1 FLS gene in chromosome 14, and 6 DFR genes on chromosomes 2, 14, 15, and 17 were not found in the Enrei genome. Most of the CHS genes correspond in both cultivars as indicated by the position and UniProt annotation of identified genes except for those genes that could not be localized in the Enrei cultivar due to fragmented sequence (Figure 3). As most of these genes are involved in pigmentation of seed and hilum color in soybean, the absence of these genes in the Enrei genome in relation to anthocyanin and flavonoid biosynthesis pathway may be associated with gene silencing due to siRNA activity [32, 33].


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)

A region in soybean chromosome 8 showing the position of CHS gene clusters. The region encompassing 8.3~8.5 Mb of soybean chromosome 8 of Williams 82 Gmax275 (a) and Enrei cultivar (b) is characterized by CHS gene clusters. Most of the CHS genes correspond in both cultivars as indicated by the position and UniProt annotation of identified genes. However many CHS genes could not be localized in Enrei cultivar due to fragmented sequence.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig3: A region in soybean chromosome 8 showing the position of CHS gene clusters. The region encompassing 8.3~8.5 Mb of soybean chromosome 8 of Williams 82 Gmax275 (a) and Enrei cultivar (b) is characterized by CHS gene clusters. Most of the CHS genes correspond in both cultivars as indicated by the position and UniProt annotation of identified genes. However many CHS genes could not be localized in Enrei cultivar due to fragmented sequence.
Mentions: In soybeans, several chalcone synthesis genes, namely, CHS3 (P19168), CHS1 (P24826), CHS7 (P30081), CHS4 (Q6X0N0), and CHS8 (AY237728), are associated with seed coat pigmentation [29]. The physical position of these CHS genes was determined using BAC assembly [30, 31] for loci associated with RNA silencing and WGS assembly [7]. The corresponding genes in the Gmax275 genome assembly are as follows: CHS1 (Glyma.08G109400), CHS2 (Glyma.05G153200), CHS3 (Glyma.08G110300 and Glyma.08G110900), CHS4 (Glyma.08G110500 and Glyma.08G110700), CHS5 (Glyma.08G109200, Glyma.08G109300, and Glyma.08G110400), CHS6 (Glyma.09G075200), CHS7 (Glyma.01G228700), CHS8 (Glyma.11G011500), and CHS9 (Glyma.08G109500). Most of the genes in the pathway were commonly represented in both cultivars (Figure 2). However, one 4CL gene in chromosome 7, 5 CHS genes in chromosome 8, 3 CHI genes in 14, 15, and 19, respectively, 1 FLS gene in chromosome 14, and 6 DFR genes on chromosomes 2, 14, 15, and 17 were not found in the Enrei genome. Most of the CHS genes correspond in both cultivars as indicated by the position and UniProt annotation of identified genes except for those genes that could not be localized in the Enrei cultivar due to fragmented sequence (Figure 3). As most of these genes are involved in pigmentation of seed and hilum color in soybean, the absence of these genes in the Enrei genome in relation to anthocyanin and flavonoid biosynthesis pathway may be associated with gene silencing due to siRNA activity [32, 33].

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.


Related in: MedlinePlus