Sequencing Multiple Cotton Genomes Reveals Complex Structures and Lays Foundation for Breeding

Abstract

Cotton is a major fiber plant, which provides raw materials for clothing, protecting humans from the harsh environment of cold or hot weathers, enriching the culture and custom of human societies. Due to its importance, the diploid and tetraploid genomes of different cotton plants have been repeatedly sequenced to obtain their complete and fine genome sequences. These valuable genome data sets revealed the evolutionary past of the cotton plants, which were recursively affected by polyploidization, with a decaploidization contributing to the formation of the genus Gossypium, and a neo-tetraploidization contributing to the formation of nowadays widely cultivated cotton plants. Postpolyploidization genome instability resulted in numerous structural changes of the genomes, such as gene loss, DNA inversion and translocation, illegitimate recombination, and accumulation of repetitive sequences, and functional innovation accompanied by elevated evolutionary rates of genes. Many these changes have been asymmetric between subgnomes of the tetraploid cottons, rendering their divergent profiles of biological regulation and function. The availability of whole-genome sequences has now paved the way to identify and clone functional genes, e.g., those relating to fiber development, and to enhance breeding efforts to cultivate cottons to produce high-yield and high-quality fibers, and to resist environmental and biological stress.

Unravelling cotton RNAseq repositories to the fiber development specific modules and their alliance with the fiber-related traits

“…Additionally, to understand the molecular and biological functions of genes involved in cotton fiber growth and development, the multi-omics approach was also taken into consideration (Pang et al, 2009; Rai et al, 2013; Song et al, 2015; Zou et al, 2016; Song et al, 2017; Kumar et al, 2018; Ayubov et al, 2019; Li et al, 2019). In recent years, many researchers were reannotated the cotton genome sequence by third and fourth generation sequencing techniques to get the high contiguity genome (Pan et al, 2020). Prior to cotton genome sequence was available, several transcriptome data (Wang et al, 2010; Nigam et al, 2014; Peng et al, 2014; Cheng et al, 2016; Parekh et al, 2018) were generated that would not have been mapped properly due to the unavailability of a well furnished reference genome.…”

Cotton as a Model for Polyploidy and Fiber Development Study

“…However, the frequency of occurrence of Copia LTR retrotransposons is higher in G. raimondii (D5 genome) -the smallest genome size (885 Mb). At the same time, the occurrence frequency of the Gypsy LTR retroelements is higher in species with a large genome size [6,[32][33][34]. Additionally, it was established that the wide distribution of GORGE3 (Gossypium retrotransposable gypsy-like element) in A-and AD-genome was the reason for their upsizing [31,32,35,36].…”

“…Cotton fiber is basically elongated single cell of seed epidermis (trichome) with a clear gradation of development stages: fiber initiation, elongation, secondary biosynthesis of the cell walls and maturation [33,46,47]. It first appeared among ancestral diploid cotton with A-genome after divergence with F-genome [1,6,48].…”

“…At the same time, in tetraploid species, the expression and co-expression of genes at different stages of fiber development is different: some genes are expressed at the stage of fiber initiation, others -at the stages of fiber elongation and secondary cell walls biosynthesis [53,54]. It has been shown that genes in the Dt-subgenome are predominantly expressed at the stage of fiber initiation, very important parameter to the fiber yield [1,33].…”

“…Summarizing the aforementioned, due to Gossypium diversity including both diploid (2n = 2x = 26) and tetraploid (2n = 4x = 52) species, cotton may be an ideal model for studying the evolution of allopolyploids, as well as the influence of ploidy for the most important agronomic traits -cotton fiber quality [1,6,33,55]. In addition, the presence four cultivated species (diploid -G. arboretum and G. herbaceum and tetraploid -G. hirsutum and G. barbadense) allow to use this plant as a model for studying the effect of artificial selection in domestication process to shift of the homeologous expression level in tetraploid towards one of the subgenome [1,6,33,55]. Moreover, because of cotton fiber is a single and easily isolated cell with a clear gradated of developmental stages, it is a good model to study of fiber development mechanisms [47].…”