Limits...
Sequencing and analysis of the gene-rich space of cowpea.

Timko MP, Rushton PJ, Laudeman TW, Bokowiec MT, Chipumuro E, Cheung F, Town CD, Chen X - BMC Genomics (2008)

Bottom Line: With a nuclear genome size estimated at ~620 Mb, the cowpea genome is an ideal target for reduced representation sequencing.The availability of extensive publicly available genomic data for cowpea, a non-model legume with significant importance in the developing world, represents a significant step forward in legume research.The micro and macrosyntenic relationships detected between cowpea and other cultivated and model legumes should simplify the identification of informative markers for marker-assisted trait selection and map-based gene isolation necessary for cowpea improvement.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, University of Virginia, Charlottesville, Virginia 22903, USA. mpt9g@virginia.edu

ABSTRACT

Background: Cowpea, Vigna unguiculata (L.) Walp., is one of the most important food and forage legumes in the semi-arid tropics because of its drought tolerance and ability to grow on poor quality soils. Approximately 80% of cowpea production takes place in the dry savannahs of tropical West and Central Africa, mostly by poor subsistence farmers. Despite its economic and social importance in the developing world, cowpea remains to a large extent an underexploited crop. Among the major goals of cowpea breeding and improvement programs is the stacking of desirable agronomic traits, such as disease and pest resistance and response to abiotic stresses. Implementation of marker-assisted selection and breeding programs is severely limited by a paucity of trait-linked markers and a general lack of information on gene structure and organization. With a nuclear genome size estimated at ~620 Mb, the cowpea genome is an ideal target for reduced representation sequencing.

Results: We report here the sequencing and analysis of the gene-rich, hypomethylated portion of the cowpea genome selectively cloned by methylation filtration (MF) technology. Over 250,000 gene-space sequence reads (GSRs) with an average length of 610 bp were generated, yielding ~160 Mb of sequence information. The GSRs were assembled, annotated by BLAST homology searches of four public protein annotation databases and four plant proteomes (A. thaliana, M. truncatula, O. sativa, and P. trichocarpa), and analyzed using various domain and gene modeling tools. A total of 41,260 GSR assemblies and singletons were annotated, of which 19,786 have unique GenBank accession numbers. Within the GSR dataset, 29% of the sequences were annotated using the Arabidopsis Gene Ontology (GO) with the largest categories of assigned function being catalytic activity and metabolic processes, groups that include the majority of cellular enzymes and components of amino acid, carbohydrate and lipid metabolism. A total of 5,888 GSRs had homology to genes encoding transcription factors (TFs) and transcription associated factors (TAFs) representing about 5% of the total annotated sequences in the dataset. Sixty-two (62) of the 64 well-characterized plant transcription factor (TF) gene families are represented in the cowpea GSRs, and these families are of similar size and phylogenetic organization to those characterized in other plants. The cowpea GSRs also provides a rich source of genes involved in photoperiodic control, symbiosis, and defense-related responses. Comparisons to available databases revealed that about 74% of cowpea ESTs and 70% of all legume ESTs were represented in the GSR dataset. As approximately 12% of all GSRs contain an identifiable simple-sequence repeat, the dataset is a powerful resource for the design of microsatellite markers.

Conclusion: The availability of extensive publicly available genomic data for cowpea, a non-model legume with significant importance in the developing world, represents a significant step forward in legume research. Not only does the gene space sequence enable the detailed analysis of gene structure, gene family organization and phylogenetic relationships within cowpea, but it also facilitates the characterization of syntenic relationships with other cultivated and model legumes, and will contribute to determining patterns of chromosomal evolution in the Leguminosae. The micro and macrosyntenic relationships detected between cowpea and other cultivated and model legumes should simplify the identification of informative markers for marker-assisted trait selection and map-based gene isolation necessary for cowpea improvement.

Show MeSH

Related in: MedlinePlus

The ERF gene family of cowpea transcription factors. GSRs encoding the conserved DNA binding domain of ERFs were identified, the 111 cowpea ERF genes were arbitrarily assigned names, and the conserved domains were aligned using ClustalW. An unrooted phylogenetic tree was produced using the PHYLIP program based on the neighbor-joining method and presented using PhyloDraw. The cowpea ERF family is separated into two major clades. A line divides the CBF/DREB subfamily from the ERF subfamily. Subgroups, indicated by roman numerals, were identified as described in [58]. For additional information see Additional file 5 and Additional file 6.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2279124&req=5

Figure 3: The ERF gene family of cowpea transcription factors. GSRs encoding the conserved DNA binding domain of ERFs were identified, the 111 cowpea ERF genes were arbitrarily assigned names, and the conserved domains were aligned using ClustalW. An unrooted phylogenetic tree was produced using the PHYLIP program based on the neighbor-joining method and presented using PhyloDraw. The cowpea ERF family is separated into two major clades. A line divides the CBF/DREB subfamily from the ERF subfamily. Subgroups, indicated by roman numerals, were identified as described in [58]. For additional information see Additional file 5 and Additional file 6.

Mentions: The phylogenetic structure of the cowpea ERF gene family (Figure 3) is similar to that of Arabidopsis. Two major clades are recognized, the ERF and CBF/DREB subfamilies, consisting of the ten major subgroups. Subgroup IX contains the largest number of genes and is divided into two branches. The placement of Group V genes in cowpea differs significantly from what is observed in Arabidopsis [44], with the cowpea Group V ERFs forming separate branches in both the CBF/DREB and ERF clades. This may be a more common feature of the ERF family, since the Group V genes of tobacco also form separate branches in both the CBF/DREB and ERF clades [54], and in rice, some Group V genes cluster with Group XI [58].


Sequencing and analysis of the gene-rich space of cowpea.

Timko MP, Rushton PJ, Laudeman TW, Bokowiec MT, Chipumuro E, Cheung F, Town CD, Chen X - BMC Genomics (2008)

The ERF gene family of cowpea transcription factors. GSRs encoding the conserved DNA binding domain of ERFs were identified, the 111 cowpea ERF genes were arbitrarily assigned names, and the conserved domains were aligned using ClustalW. An unrooted phylogenetic tree was produced using the PHYLIP program based on the neighbor-joining method and presented using PhyloDraw. The cowpea ERF family is separated into two major clades. A line divides the CBF/DREB subfamily from the ERF subfamily. Subgroups, indicated by roman numerals, were identified as described in [58]. For additional information see Additional file 5 and Additional file 6.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2279124&req=5

Figure 3: The ERF gene family of cowpea transcription factors. GSRs encoding the conserved DNA binding domain of ERFs were identified, the 111 cowpea ERF genes were arbitrarily assigned names, and the conserved domains were aligned using ClustalW. An unrooted phylogenetic tree was produced using the PHYLIP program based on the neighbor-joining method and presented using PhyloDraw. The cowpea ERF family is separated into two major clades. A line divides the CBF/DREB subfamily from the ERF subfamily. Subgroups, indicated by roman numerals, were identified as described in [58]. For additional information see Additional file 5 and Additional file 6.
Mentions: The phylogenetic structure of the cowpea ERF gene family (Figure 3) is similar to that of Arabidopsis. Two major clades are recognized, the ERF and CBF/DREB subfamilies, consisting of the ten major subgroups. Subgroup IX contains the largest number of genes and is divided into two branches. The placement of Group V genes in cowpea differs significantly from what is observed in Arabidopsis [44], with the cowpea Group V ERFs forming separate branches in both the CBF/DREB and ERF clades. This may be a more common feature of the ERF family, since the Group V genes of tobacco also form separate branches in both the CBF/DREB and ERF clades [54], and in rice, some Group V genes cluster with Group XI [58].

Bottom Line: With a nuclear genome size estimated at ~620 Mb, the cowpea genome is an ideal target for reduced representation sequencing.The availability of extensive publicly available genomic data for cowpea, a non-model legume with significant importance in the developing world, represents a significant step forward in legume research.The micro and macrosyntenic relationships detected between cowpea and other cultivated and model legumes should simplify the identification of informative markers for marker-assisted trait selection and map-based gene isolation necessary for cowpea improvement.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, University of Virginia, Charlottesville, Virginia 22903, USA. mpt9g@virginia.edu

ABSTRACT

Background: Cowpea, Vigna unguiculata (L.) Walp., is one of the most important food and forage legumes in the semi-arid tropics because of its drought tolerance and ability to grow on poor quality soils. Approximately 80% of cowpea production takes place in the dry savannahs of tropical West and Central Africa, mostly by poor subsistence farmers. Despite its economic and social importance in the developing world, cowpea remains to a large extent an underexploited crop. Among the major goals of cowpea breeding and improvement programs is the stacking of desirable agronomic traits, such as disease and pest resistance and response to abiotic stresses. Implementation of marker-assisted selection and breeding programs is severely limited by a paucity of trait-linked markers and a general lack of information on gene structure and organization. With a nuclear genome size estimated at ~620 Mb, the cowpea genome is an ideal target for reduced representation sequencing.

Results: We report here the sequencing and analysis of the gene-rich, hypomethylated portion of the cowpea genome selectively cloned by methylation filtration (MF) technology. Over 250,000 gene-space sequence reads (GSRs) with an average length of 610 bp were generated, yielding ~160 Mb of sequence information. The GSRs were assembled, annotated by BLAST homology searches of four public protein annotation databases and four plant proteomes (A. thaliana, M. truncatula, O. sativa, and P. trichocarpa), and analyzed using various domain and gene modeling tools. A total of 41,260 GSR assemblies and singletons were annotated, of which 19,786 have unique GenBank accession numbers. Within the GSR dataset, 29% of the sequences were annotated using the Arabidopsis Gene Ontology (GO) with the largest categories of assigned function being catalytic activity and metabolic processes, groups that include the majority of cellular enzymes and components of amino acid, carbohydrate and lipid metabolism. A total of 5,888 GSRs had homology to genes encoding transcription factors (TFs) and transcription associated factors (TAFs) representing about 5% of the total annotated sequences in the dataset. Sixty-two (62) of the 64 well-characterized plant transcription factor (TF) gene families are represented in the cowpea GSRs, and these families are of similar size and phylogenetic organization to those characterized in other plants. The cowpea GSRs also provides a rich source of genes involved in photoperiodic control, symbiosis, and defense-related responses. Comparisons to available databases revealed that about 74% of cowpea ESTs and 70% of all legume ESTs were represented in the GSR dataset. As approximately 12% of all GSRs contain an identifiable simple-sequence repeat, the dataset is a powerful resource for the design of microsatellite markers.

Conclusion: The availability of extensive publicly available genomic data for cowpea, a non-model legume with significant importance in the developing world, represents a significant step forward in legume research. Not only does the gene space sequence enable the detailed analysis of gene structure, gene family organization and phylogenetic relationships within cowpea, but it also facilitates the characterization of syntenic relationships with other cultivated and model legumes, and will contribute to determining patterns of chromosomal evolution in the Leguminosae. The micro and macrosyntenic relationships detected between cowpea and other cultivated and model legumes should simplify the identification of informative markers for marker-assisted trait selection and map-based gene isolation necessary for cowpea improvement.

Show MeSH
Related in: MedlinePlus