The draft genome of a diploid cotton Gossypium raimondii

Abstract

Cotton is one of the most economically important crop plants worldwide. Its fiber, commonly known as cotton lint, is the principal natural source for the textile industry. Approximately 33 million ha (5% of the world's arable land) is used for cotton planting 1 , with an annual global market value of textile mills of approximately $630.6 billion in 2011 (MarketPublishers; see URLs). Apart from its economic value, cotton is also an excellent model system for studying polyploidization, cell elongation and cell wall biosynthesis 2-5 .The Gossypium genus contains 5 tetraploid (AD 1 to AD 5 , 2n = 4×) and over 45 diploid (2n = 2×) species (where n is the number of chromosomes in the gamete of an individual), which are believed to have originated from a common ancestor approximately 5-10 million years ago 6 . Eight diploid subgenomes, designated as A to G and K, have been found across North America, Africa, Asia and Australia. The haploid genome size of diploid cottons (2n = 2× = 26) varies from about 880 Mb (G. raimondii Ulbrich) in the D genome to 2,500 Mb in the K genome 7,8 . Diploid cotton species share a common chromosome number (n = 13), and high levels of synteny or colinearity are observed among them 9-12 . The tetraploid cotton species (2n = 4× = 52), such as G. hirsutum L. and Gossypium barbadense L., are thought to have formed by an allopolyploidization event that occurred approximately 1-2 million years ago, which involved a D-genome species as the pollen-providing parent and an A-genome species as the maternal parent 13,14 . To gain insights into the cultivated polyploid genomes-how they have evolved and how their subgenomes interact-it is first necessary to have a basic knowledge of the structure of the component genomes. Therefore, we have created a draft sequence of the putative D-genome parent, G. raimondii, using DNA samples prepared from Cotton Microsatellite Database (CMD) 10 (refs. 15,16), a genetic standard originated from a single seed (accession D 5 -3) in 2004 and brought to near homozygosity by six successive generations of self-fertilization. We believe that sequencing of the G. raimondii genome will not only provide a major source of candidate genes important for the genetic improvement of cotton quality and productivity, but it may also serve as a reference for the assembly of the tetraploid G. hirsutum genome. RESULTS Sequencing and assemblyA whole-genome shotgun strategy was used to sequence and assemble the G. raimondii genome. A total of 78.7 Gb of next-generation Illumina paired-end 50-bp, 100-bp and 150-bp reads was generated by sequencing genome shotgun libraries of different fragment lengths (170 bp, 250 bp, 500 bp, 800 bp, 2 kb, 5 kb, 10 kb, 20 kb and 40 kb) that covered 103.6-fold of the 775.2-Mb assembled G. raimondii genome (Supplementary Table 1). The resulting assembly appeared to cover a very large proportion of the euchromatin of the G. raimondii genome. The unassembled genomic regions are likely to contain heterochromatic satellites, large repetitive sequences or ribosoma...

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

“…The assembled A subgenome (1,477 Mb) is nearly twice the size of the D subgenome (831 Mb), which is consistent with the genome size difference between G. arboreum 2 and G. raimondii 3,4 . At least 64.8% of the assembled genome are transposable elements (TEs), which was substantially higher than that in canola (>34.8%) 9 , but lower than in wheat (>76.6%) 6 .…”

“…6a and 7). However, this colinearity was not obvious with either the A-progenitor genome (G. arboreum) 2 or another version of the D-progenitor genome (G. raimondii) 3 because of numerous mis-assemblies. For example, many scaffolds from several different pseudochromosomes were present in one pseudomolecule ( Supplementary Figs.…”

The draft genome of tropical fruit durian (Durio zibethinus)

“…A WGD has also previously been shown for the cotton lineage, after its speciation with cacao 25,26 . We investigated whether the WGDs associated with cotton and durian reflect the same event or represent two distinct evolutionary events, by resolving the ordering and dates of the WGDs alongside the durian-cotton divergence event.…”

A genome-wide analysis of SWEET gene family in cotton and their expressions under different stresses

“…With the release of genomes sequences of two diploid cotton (A2, D5) and two allotetraploid cotton (AD1, AD2) (Phillips et al 2017;Li et al 2014;Paterson et al 2012;Wang et al 2012;Li et al 2015;Zhang et al 2015;Yuan et al 2015;Liu et al 2015) facilitates the survey of SWEETs in cotton. In this study, we identified the SWEETs in four cotton species by genome-wide analysis.…”