Towards Understanding the Genome of Diploid Cotton, Gossypium herbaceum Using Deep Sequencing

About 1–2 million years ago, hybridization of two Gossypium diploid (2n=26) species, one with a genome similar to the A-genomes of extant African/Asian species Gossypium herbaceum and G. arboreum, and the other one with a genome similar to the D-genome of the extant wild Peruvian diploid G. raimondii (D₅D₅) resulted in a tetraploid cotton that eventually gave rise to modern G. hirsutum; 2n = 4x = 52; 2(AD)₁) and other extant AD-genome tetraploids. Domesticated forms of G. hirsutum have since become the primary fiber textile crop worldwide due to its desirable fiber qualities and yield. Here we sequenced the A₁-genome of G. herbaceum to ca. 30-fold depth with short reads of varied length obtained from two high-throughput sequencing platforms. The assembled scaffolds represent ~83.0% of the genome and 45% of the assembly overlapped with the reference genome, G. raimondii. The A-genome reference chromosomes (A1-A13) were built with at least 87% coverage. The GC content varied between 33 - 37% and the repeats ranged between 38% - 47%. We generated comprehensive RNA-Seq data and used it to identify over 40,000 protein-coding genes using G. raimondii and Arabidopsis annotations, of which 70% were uniquely anchored to chromosomes. The Gene Ontology (GO) annotation identified transcripts associated with biological process, molecular function, and cellular components. This study identified 51 transcription factors and 51 protein domains with key roles in gene regulation and cellular processes. The annotated best matches identified were transcript homologs from rosid clade. This draft genome sequence provides insight into the evolution of cotton and will aid in understanding the complex genomes of G. hirsutum, G. barbadense and the other AD polyploids.