Comparative transcriptome analysis of Pima and Acala cotton during boll development using 454 pyrosequencing technology

Information on gene expression during cotton fiber development for high fiber quality genotypes including Pima (Gossypium barbadense L.) and Acala cotton (G. hirsutum L.) is lacking, impeding the discovery of novel genes and DNA markers for fiber quality traits. In the present study, massively parallel sequencing technology was used to generate a total of 394,301 expressed sequence tag (EST) sequence reads, totaling over 42 million bp, from immature ovaries at 10 days post-anthesis of Pima Phy 76 and Acala 1517-99. For Pima Phy 76, 1,900 EST contigs were tentatively assembled from 21.8% (50,876) ESTs which resulted in 1,541 tentative consensus sequences (TCs). 1,005 and 1,064 EST contigs were homologous to TCs from the A2 and D5 genomes, respectively, while 738 of the EST contigs were shared by both genomes. For Acala 1517-99, 2,151 EST contigs were tentatively assembled from 24.5% (39,368) ESTs and resulted in 1,787 TCs. 1,220 and 1,206 EST contigs were homologous to known transcripts from A2 and D5 genomes and only 452 of the EST contigs were shared by both genomes. 691 EST contigs are also homologous (E-value ≤ 1 × 10−10) between Pima Phy 76 and Acala 1517-99, of which 38 contigs pairs were highly homologous (E-value ≤ 1 × 10−60) with sequence variations, predominantly single nucleotide polymorphisms (SNPs). A Blast search of a sample of contigs to Upland cotton ESTs in GenBank indicated that more than 75% EST contigs may contain SNPs. This report represents the first research in cotton using 454 pyrosequencing technology to enrich ESTs for high fiber quality cotton.