CottonGen (www.cottongen.org) is the worldwide community database for cotton, housing data and tools that facilitate research discovery and cultivar improvement. It provides access to publicly available genomics, genetics and breeding data for cotton that is curated and integrated with a suite of analysis and visualization tools. These include genome, map and pathway viewers such as JBrowse, MapViewer and CottonCyc, as well as many search interfaces that allow researchers to readily search and retrieve data. CottonGen recently released a Cotton Trait Ontology, CottonGen Reference Transcriptomes (RefTrans) and new MapViewer. The Breeding Information Management System (BIMS) is now available in CottonGen providing both a public and private site that individual breeders can use to manage and analyze their breeding program data while also leveraging the publicly available GGB data in their decision-making. In this presentation the role of CottonGen for research is explored and future plans elaborated. CottonGen is directly supported by Cotton Incorporated, USDA-ARS, the cotton industry, NIFA USDA NRSP10, US Land Grant Universities and indirectly by NSF and USDA SCRI awards.

Cotton (Gossypium spp.) is one of the most important economic crops in the world. It not only produces natural fiber for textile industry, but also provides a large quantity of cottonseeds enriched with high-quality protein and oil. However, the presence of gossypol limits the utilization of the cottonseeds. Two pairs of cotton near isogenic lines (NILs) with different types of pigment glands, CRI12 and CRI12W and Coker 312 and Coker 312W, exhibit different gossypol contents in plants. The glandless traits of CRI12W and Coker 312W are mainly controlled by dominant and recessive genes. However, less is known about genomic differences in NILs. In the current study, next-generation sequencing was used to discover the relationship between phenotypes and DNA polymorphisms in these NILs. The whole genomes of CRI12, CRI12W, Coker 312 and Coker 312W were resequenced. The sequencing depths were 34.01, 37.60, 36.27 and 35.88, respectively. Genomic variations of the NILs were identified in comparison with the reference genome of TM-1. A total of 2371614, 2045733, 2013021 and 1974262 SNPs, 181706, 180714, 177324 and 167971 Indels, 4208, 4026, 3963 and 3771 SVs, and 46741, 35976, 36388 and 34765 CNVs for CRI12, CRI12W, Coker 312 and Coker 312W were uncovered, respectively. Gene Ontology (GO) analysis of the genes with differential SNPs and Indels in two NILs revealed that variations were enriched in different ontology terms. KEGG pathway analysis figured out genes with differential SNPs and Indels were mainly enriched in biosynthesis of secondary metabolites pathway and sesquiterpenoid and triterpenoid biosynthesis pathway. Quantitative RT-PCR (qRT-PCR) analysis revealed that key genes with variations participating in the pathway of gossypol biosynthesis and pigment glands formation had a different expression pattern in two NILs. Through next-generation sequencing, a large number of genomic variations were revealed. These DNA polymorphisms provided deeper insight into cotton lines with different types of pigment glands. Further comprehensive analysis revealed that genomic variations were tightly associated with phenotypic difference.

Transposable elements (TEs) are the most abundant DNA components in most characterized genomes of high eukaryotes. Based on their structural features and transposition mechanisms, TEs are generally classified into two classes: retrotransposons and DNA transposons. In plants, retrotransposons are further classified into two distinct orders, long terminal repeat (LTR)-retrotransposons (Ty1/Copia and Ty3/Gypsy) and non-LTR retrotransposons (LINE and SINE), whereas DNA transposons are traditionally separated into two main orders, terminal inverted repeat (TIR) (Tc1-Mariner, hAT, Mutator, PIF/Harbinger and CACTA) and Helitron (Helitron). Although TEs are often considered as ‘junk DNA’ due to their continuous reproduction and potential disruption of the regular host genes, more evidence has unambiguously shown that they play important roles in altering gene structures, regulation of gene expression, affecting genome evolution and creating new genes. Thus, complete identification and characterization of TEs have become a priority in genome sequencing projects, and this will largely contribute to accurate annotation of protein-coding genes and other genomic components, and play significant roles in investigating potential interaction between TEs and functional genes. Recently, several diploid and tetroploid Gossypium species' genomes have been sequenced, and the availability of their draft genome sequences has provided an unprecedented opportunity for identification, structural and functional characterization and evolutionary analysis of TEs in this economically important crop. Gossypium raimondii (DD; 2n = 6), one of the putative D-genome parents of tetraploid cotton species (such as G. hirsutum L. and G. barbadense L.) has a smaller genome size (∼737.8 Mb). So, we carried out the characterization of almost all families of TEs in the G. raimondii genome using comprehensive methods and constructed a comprehensive, specific, and user-friendly web-based database, Gossypium raimondii transposable elements database (GrTEdb). A total of 14 332 TEs were structurally annotated and clearly categorized in the G. raimondii genome, and these elements have been classified into seven distinct superfamilies based on the order of protein-coding domains, structures and/or sequence similarity, including 2929 Copia-like elements, 10 368 Gypsy-like elements, 299 L1, 12 Mutators, 435 PIF-Harbingers, 275 CACTAs and 14 Helitrons. Meanwhile, web-based sequence browsing, searching, downloading and blast tools were implemented to help users easily and effectively annotate the TEs or TE fragments in genomic sequences from G. raimondii and other closely related Gossypium species. Thus, GrTEdb provides the first web-based friendly user interface database of TEs in Gossypium species, and will also facilitate genome evolution analysis within or across Gossypium species, evaluating the impact of TEs on their host genomes, and investigating the potential interaction between TEs and protein-coding genes.

Kokia and Gossypioides are sister genera to Gossypium. Kokia is limited to the Hawaiian Islands while Gossypioides is found only in Madagascar and East Africa. Recently, we sequenced the genome of Kokia drynarioides and annotated the K. drynarioides and existing Gossypioidies kirkii draft genomes. Comparison of these two genomes with each other and that of Gossypium raimondii allowed us to generate estimates of divergence based on 13,000 gene orthologs. Our analysis indicates that the Kokia/Gossypioides lineage diverged from Gossypium roughly 10 MYA, while Kokia and Gossypioides diverged about 5 MYA after a 17,500 km transoceanic dispersal event delivered a Kokia ancestor to Hawaii. Study of the gene contents of the three species indicates that both Kokia and Gossypioides have experienced significant net gene losses (30% or about 10,000 genes) since their divergence from Gossypium raimondii. As the vast majority of gene deletions are common to both G. kirkii and K. drynarioides, it is likely that most gene deletion events occurred prior to the Gossypioides/Kokia split. With regard to repeat sequences, Kokia and Gossypioides have statistically indistinguishable repeat sequence contents and distributions despite representing different genera. In contrast, G. raimondii has a greatly reduced repeat content compared to G. herbaceum and G. arboreum. Not surprisingly, the major repeat sequence differences between Gossypioides kirkii, K. drynarioides, G. ramondii, and the A-genome cottons is a reflection of the relative abundance of LTR/Gypsy retrotransposons. The genome sequences of Kokia and Gossypioides are of interest not only as outgroups to Gossypium, but because their high levels of gene deletion make them interesting subjects for studying gene reduction in non-parasitic plants.