DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton

Page, Justin T.; Liechty, Zach S.; Alexander, Rich H.; Clemons, Kimberly; Hulse‐Kemp, Amanda M.; Ashrafi, Hamid; Deynze, Allen Van; Stelly, David M.; Udall, Joshua A.

doi:10.1371/journal.pgen.1006012

Cited by 34 publications

(39 citation statements)

References 47 publications

(95 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…1a ; Additional file 8 : Dataset 1). The subsequently produced neighbor-joining (NJ) tree resulted in two largely divergent clades: the G. hirsutum clade ( n = 85) and the G. barbadense clade ( n = 52), consistent with a previous study, although with a limited number of accessions [ 23 ]. Both studies suggested a strong divergence between G. hirsutum and G. barbadense .…”

Section: Resultssupporting

confidence: 86%

Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons

et al. 2017

View full text Add to dashboard Cite

BackgroundCotton has been cultivated and used to make fabrics for at least 7000 years. Two allotetraploid species of great commercial importance, Gossypium hirsutum and Gossypium barbadense, were domesticated after polyploidization and are cultivated worldwide. Although the overall genetic diversity between these two cultivated species has been studied with limited accessions, their population structure and genetic variations remain largely unknown.ResultsWe resequence the genomes of 147 cotton accessions, including diverse wild relatives, landraces, and modern cultivars, and construct a comprehensive variation map to provide genomic insights into the divergence and dual domestication of these two important cultivated tetraploid cotton species. Phylogenetic analysis shows two divergent groups for G. hirsutum and G. barbadense, suggesting a dual domestication processes in tetraploid cottons. In spite of the strong genetic divergence, a small number of interspecific reciprocal introgression events are found between these species and the introgression pattern is significantly biased towards the gene flow from G. hirsutum into G. barbadense. We identify selective sweeps, some of which are associated with relatively highly expressed genes for fiber development and seed germination.ConclusionsWe report a comprehensive analysis of the evolution and domestication history of allotetraploid cottons based on the whole genomic variation between G. hirsutum and G. barbadense and between wild accessions and modern cultivars. These results provide genomic bases for improving cotton production and for further evolution analysis of polyploid crops.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-017-1167-5) contains supplementary material, which is available to authorized users.

show abstract

Section: Resultssupporting

confidence: 86%

Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons

et al. 2017

View full text Add to dashboard Cite

show abstract

“…During rediploidization, pseudogenized genes lost function, or underwent sub-functionalization to partition ancestral gene function, or neo-functionalization to obtain a new function [ 57 , 58 , 60 , 63 ]. Two paralogs generally showed a dominant, biased or silencing expression pattern [ 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 , 75 , 76 ]. In this study, we revealed a significantly biased expression of Eccxcr4a and Ec_cxcr4b in adult tissue, gonads and embryos at different stages.…”

Section: Discussionmentioning

confidence: 99%

Divergent Expression Patterns and Function of Two cxcr4 Paralogs in Hermaphroditic Epinephelus coioides

Zhou

Gao

et al. 2018

IJMS

View full text Add to dashboard Cite

Chemokine receptor Cxcr4 evolved two paralogs in the teleost lineage. However, cxcr4a and cxcr4b have been characterized only in a few species. In this study, we identified two cxcr4 paralogs from the orange-spotted grouper, Epinephelus coioides. The phylogenetic relationship and gene structure and synteny suggest that the duplicated cxcr4a/b should result from the teleost-specific genome duplication (Ts3R). The teleost cxcr4 gene clusters in two paralogous chromosomes exhibit a complementary gene loss/retention pattern. Ec_cxcr4a and Ec_cxcr4b show differential and biased expression patterns in grouper adult tissue, gonads, and embryos at different stages. During embryogenesis, Ec_cxcr4a/b are abundantly transcribed from the neurula stage and mainly expressed in the neural plate and sensory organs, indicating their roles in neurogenesis. Ec_Cxcr4a and Ec_Cxcr4b possess different chemotactic migratory abilities from the human SDF-1α, Ec_Cxcl12a, and Ec_Cxcl12b. Moreover, we uncovered the N-terminus and TM5 domain as the key elements for specific ligand–receptor recognition of Ec_Cxcr4a-Ec_Cxcl12b and Ec_Cxcr4b-Ec_Cxcl12a. Based on the biased and divergent expression patterns of Eccxcr4a/b, and specific ligand–receptor recognition of Ec_Cxcl12a/b–Ec_Cxcr4b/a, the current study provides a paradigm of sub-functionalization of two teleost paralogs after Ts3R.

show abstract

“…GWAS have been used to analyze millions of genetic variants among the genomes of several individuals to unravel genotype-phenotype associations, genetics of fiber quality and yield, and environmental adaptation-related traits [8,18,25,37,39]. GhFL1, GhFL2, and GhXIK were found to be involved in fiber cell elongation, and a chaperone DnaJ-domain superfamily gene (Gh_A07G1769) was shown to be related to fiber strength.…”

Section: Gwas In Cottonmentioning

confidence: 99%

Gossypium Genomics: Trends, Scope, and Utilization for Cotton Improvement

Yang

Qanmber

Wang

et al. 2020

Trends in Plant Science

110

View full text Add to dashboard Cite

Cotton (Gossypium spp.) is the most important natural fiber crop worldwide. The diversity of Gossypium species also provides an ideal model for investigating evolution and domestication of polyploids. However, the huge and complex cotton genome hinders genomic research. Technical advances in high-throughput sequencing and bioinformatics analysis have now largely overcome these obstacles, bringing about a new era of cotton genomics. Here, we review recent progress in Gossypium genomics based on whole genome sequencing, resequencing, and comparative genomics, which have provided insights about the genomic basis of fiber biogenesis and the landscape of cotton functional genomics. We address current challenges and present multidisciplinary genomics-enabled breeding strategies covering the breadth of high fiber yield, quality, and environmental resilience for future cotton breeding programs. Gossypium Genomics at a Glance As the world's most important fiber crop and a major source of seed oil and protein, cotton is cultivated in more than 75 countries around the globe [1]. Cotton fibers are seed trichomes, up to 65 mm long, composed of almost pure cellulose, and provide a unique single-celled model system for studying cell elongation and cell wall biogenesis [2]. The Gossypium genus is extraordinarily diverse, with eight diploid genome groups (A-G, and K) and one allopolyploid group (AD) [3,4]. Hybridization and polyploidization of two parental diploids, an A genome-like species with a D genome-like species, has resulted in at least seven allotetraploid species. Two allotetraploid species, Gossypium hirsutum and Gossypium barbadense, evolved independently; these two account for over 90% of annual commercial fiber production. Gossypium is ideal for investigating the origin, evolution, and domestication of polyploids [5-7]. Highlights Cotton is an important natural fiber crop cultivated worldwide that also provides an ideal model for investigating evolution and domestication of polyploids Combinations of the latest technologies, such as optical mapping, high-throughput chromosome conformation capture (Hi-C), and Pacific Biosciences (PacBio) long-reads, have been used to generate multiple high-quality reference genomes of diploid and allotetraploid cotton. Comparative population genomics illuminated the genetic history of cotton domestication and identified the genomic variation determining fiber yield, quality, and stress resistance.

show abstract

DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton

Cited by 34 publications

References 47 publications

Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons

Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons

Divergent Expression Patterns and Function of Two cxcr4 Paralogs in Hermaphroditic Epinephelus coioides

Gossypium Genomics: Trends, Scope, and Utilization for Cotton Improvement

Contact Info

Product

Resources

About