Abstract
BackgroundThe most widely cultivated cotton (Gossypium hirsutum L., AD-genome) is derived from tetraploidization between A- and D-genome species. G. arboreum L. (A-genome) and G. raimondii Ulbr. (D-genome) are two of closely-related extant progenitors. Gene expression studies in allotetraploid cotton are complicated by the homoeologous loci of A- and D-genome origins. To develop genomic resources for gene expression and cotton breeding, we sequenced and assembled expressed sequence tags (ESTs) derived from G. arboreum and G. raimondii.ResultsRoche/454 FLX sequencing technology was employed to sequence normalized cDNA libraries prepared from leaves, roots, bolls, ovules, and fibers in G. arboreum and G. raimondii, respectively. Sequencing reads from two independent libraries in each species were combined to assemble high-quality EST contigs. The combined sequencing reads included 1,699,776 from A-genome and 1,464,815 from D-genome, which were clustered into 89,588 contigs in the A-genome and 65,542 contigs in the D-genome. These contigs represented ~80% of EST collections in Cotton Gene Index 11 (CGI11, March 2011). Compared to the D-genome transcript database, 27,537 and 10,452 contigs were unique transcripts in A and D genomes, respectively. Further analysis using self-blastn reduced the unigene contig number by 52% in A-genome and 57% in D-genome, suggesting that 50% or more of contigs are paralogs or isoforms within each species. The majority of EST contigs (73–81%) were conserved between A- and D-genomes, whereas 27% and 19% contigs were specific to A- and D-genomes, respectively. Using these ESTs, we generated a total of 75,754 genome-specific single nucleotide polymorphism (SNP) (gSNPs or GNPs) or homoeologous-specific SNPs (hSNPs) of 10,885 contigs or genes between A and D genomes, indicating a possibility of separating allelic expression for those genes in allotetraploid cotton.ConclusionsExpressed genes are highly redundant within each diploid progenitor and between A and D progenitor species, suggesting that diploid progenitors in cotton are likely ancient tetraploids. This large set of A- and D-genome ESTs and GNPs will be valuable resources for genome annotation, gene expression, and crop improvement in allotetraploid cotton.Electronic supplementary materialThe online version of this article (doi:10.1186/1756-0500-7-493) contains supplementary material, which is available to authorized users.
Highlights
The most widely cultivated cotton (Gossypium hirsutum L., AD-genome) is derived from tetraploidization between A- and D-genome species
Using the Expressed sequence tag (EST), we investigated expressed genes and gene duplication within each species and between these two species and developed a comprehensive list of genome-specific single nucleotide polymorphism (SNP) (GNPs) that are useful for discriminating locus or allele-specific expression patterns in allotetraploid cotton
Sequencing and assembly of A- and D-genome ESTs Sequence libraries were made from mRNA prepared from multiple tissues including young leaves, roots, stems, ovules, and fibers in G. arboreum and young leaves, stem and whole flowers in G. raimondii
Summary
The most widely cultivated cotton (Gossypium hirsutum L., AD-genome) is derived from tetraploidization between A- and D-genome species. The modern cultivated cotton is dominated by two allotetraploid species, the Upland cotton (Gossypium hirsutum L.) and the Sea Island cotton (G. barbadense L.) [1]. These allotetraploid species were formed by hybridization and polyploidization 1–2 million years ago (Mya), followed by domestication and selection of fiber traits [2]. More genes encoding cell-fate regulatory factors and cell-cycle control components are expressed in the A-genome than in the D-genome [10,11], and some fiber QTLs are more associated with the A-genome than the D-genome [12,13] Both genomes may contribute to superior fiber agronomic traits associated with polyploidization and domestication in allotetraploid cotton [7,14]
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