A high-quality assembled genome and its comparative analysis decode the adaptive molecular mechanism of the number one Chinese cotton variety CRI-12

Abstract

Background: Gossypium hirsutum L. is the most widely cultivated cotton species, and a high-quality reference genome would be a huge boost for researching the molecular mechanism of agronomic traits in cotton.

Findings: Here, Pacific Biosciences and Hi-C sequencing technologies were used to assemble a new upland cotton genome of the No. 1 Chinese cotton variety CRI-12. We generated a high-quality assembled CRI-12 genome of 2.31 Gb with a contig N50 of 19.65 Mb, which was superior to previously reported genomes. Comparisons between CRI-12 and other reported genomes revealed 7,966 structural variations and 7,378 presence/absence variations. The distribution of the haplotypes among A-genome (Gossypium arboreum), D-genome (Gossypium raimondii), and AD-genome (G. hirsutum and Gossypium barbadense) suggested that many haplotypes were lost and recombined in the process of polyploidization. More than half of the haplotypes that correlated with different tolerances were located on chromosome D13, suggesting that this chromosome may be important for wide adaptation. Finally, it was demonstrated that DNA methylation may provide advantages in environmental adaptation through whole-genome bisulfite sequencing analysis.

Conclusions: This research provides a new reference genome for molecular biology research on Gossypium hirsutum L. and helps decode the broad environmental adaptation mechanisms in the No. 1 Chinese cotton variety CRI-12.

Keywords: CRI-12; DNA methylation; annotation; genome assembly; haplotypes.

Figure 1:

Phenotype of CRI-12 and synteny relation of different cotton genomes. A, Phenotype of CRI-12. B, Hi-C map of CRI-12. From left to right, each square represents a chromosome from chromosome 1 to 26. C, Synteny analysis of different cotton species. D, Whole-genome duplications in Malvales through 4DTv analysis. The percentages of the orthologous gene pairs between CRI-12 and other species and 4DTv values were calculated. Fourfold degenerate synonymous site (4DTV) is used as an evolutionary parameter to evaluate whether a genome-wide replication event has occurred. The site of a codon at which all nucleotides encode the same amino acid is a quadruple degenerate site.

Figure 2:

Genomic landscape of CRI-12 genome. From the outside to the inside, each circle represents LTR retrotransposon density, LINE retrotransposon density, SINE retrotransposon density, DNA transposons, gene density, GC content, and miRNA density in 1-Mb sliding windows.

Figure 3:

Genome annotation of CRI-12. A, Statistical results of gene functional annotation. B, Number of common and unique gene families. C, Expansion and contraction in gene families. D, Expression analysis of partial positive selection genes under Verticilliumwilt, salt, and drought stress.

Figure 4:

Statistics of pathway enrichment of SV- and PAV-correlated genes. A, GO enrichment of SV variation–related genes. Gene Ontology (GO) contains 3 components, cellular component (CC; green), molecular function (MF; pink), and biological process (BP; orange). B, GO enrichment of PAV variation–related genes. Purple bars represent MF, orange bars represent CC, and green bars represent BP. Only several main enrichments are listed. C, Statistics of pathway enrichment of SV variation–related genes. D, Statistics of pathway enrichment of PAV variation–related genes.

Figure 5:

Haplotypes in polyploidization of diploid cottons. Red bars indicate haplotypes; the more red bars, the higher the haplotype density. A01–A13 represent 13 chromosomes in A genome (Gossypium arboreum), while D01–D13 represent 13 chromosomes in D genome (Gossypium raimondii). At and Dt represent A subgenome and D subgenome in Gossypium hirsutum L., and Chr01–Chr13 represent 13 chromosomes in each subgenome. Tetraploid cottons G. hirsutum L. and G. barbadense L. originated from the hybridization of A-genome-like ancestors and D-genome-like ancestors ∼1–1.5 million years ago (MYA).

Figure 6:

Methylation haplotypes in CRI-12 provide adaptive advantages to abiotic stresses. CRI-12 was developed from a cross between Xingtai6871 (♂) and Uganda4 (♀) in a disease nursery and serious illness field. Methylation haplotypes in 2 parents could be inherited by CRI-12. A total of 66 methylation haplotypes were discovered in CRI-12, 8 of which were located on chromosome D13. Methylation haplotypes in CRI-12 could provide adaptive advantages to different stresses.