De Novo Genome Sequence Assemblies of Gossypium raimondii and Gossypium turneri

Udall, Joshua A.; Long, Evan; Hanson, Chris; Yuan, Daojun; Ramaraj, Thiruvarangan; Conover, Justin L.; Gong, Lei; Arick, Mark A.; Grover, Corrinne E.; Peterson, Daniel G.; Wendel, Jonathan F.

doi:10.1534/g3.119.400392

Cited by 86 publications

(70 citation statements)

References 26 publications

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“…Very recently, Udall et al reported the de novo assembly of the genome of G. raimondii and its close relative Gossypium turneri using PacBio long reads, Hi-C, and Bionano optical mapping technologies, which helped to correct some minor assembly errors in previous version of the G. raimondii genome assembly [21]. Using the same strategy, another group published a draft genome of a disease-resistant species Gossypium australe with a contig N50 of 1.83 Mb [22].…”

Section: Advances In Cotton Genomicsmentioning

confidence: 99%

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

Yang

Qanmber

Wang

et al. 2020

Trends in Plant Science

119

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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.

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Section: Advances In Cotton Genomicsmentioning

confidence: 99%

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

Yang

Qanmber

Wang

et al. 2020

Trends in Plant Science

119

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“…Whole-genome alignments were generated between G. longicalyx and either G. arboreum, G. raimondii, G. turneri (Udall et al 2019), G. hirsutum (A-chromosomes), and G. barbadense (A-chromosomes) using Mummer (Marçais et al 2018) and visualized using dotPlotly (https://github.com/tpoorten/dotPlotly) in R (version 3.6.0) (R Development Core Team and Others 2011). Divergence between G. longicalyx and G. arboreum or G. raimondii was calculated using orthogroups that contain a single G. longicalyx gene with a single G. arboreum and/or single G. raimondii gene.…”

Section: Comparison Between G Arboreum and G Longicalyx For Fiber Ementioning

confidence: 99%

TheGossypium longicalyxGenome as a Resource for Cotton Breeding and Evolution

Grover

Pan

Yuan

et al. 2020

G3 Genes|Genomes|Genetics

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Cotton is an important crop that has made significant gains in production over the last century.Emerging pests such as the reniform nematode have threatened cotton production. The rare African diploid species Gossypium longicalyx is a wild species that has been used as an important source of reniform nematode immunity. While mapping and breeding efforts have made some strides in transferring this immunity to the cultivated polyploid species, the complexities of interploidal transfer combined with substantial linkage drag have inhibited progress in this area. Moreover, this species shares its most recent common ancestor with the cultivated A-genome diploid cottons, thereby providing insight into the evolution of long, spinnable fiber. Here we report a newly generated de novo genome assembly of G. longicalyx.This high-quality genome leveraged a combination of PacBio long-read technology, Hi-C chromatin conformation capture, and BioNano optical mapping to achieve a chromosome level assembly. The utility of the G. longicalyx genome for understanding reniform immunity and fiber evolution is discussed.

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“…In view of cotton's importance in human life, intensive efforts have been focused on uncovering the genome mysteries of cotton species. Three diploid cottons and two tetraploid cottons were sequenced, including G. arboreum (Li et al, 2014;Du et al, 2018;Huang et al, 2020), G. herbaceum (Huang et al, 2020), G. raimondii (Wang et al, 2012;Paterson et al, 2012;Udall et al, 2019), G. hirsutum (Li et al, 2015;Zhang et al, 2015;Hu et al, 2019;Wang M. et al, 2019;Chen et al, 2020;Huang et al, 2020) and G. barbadense (Yuan et al, 2015;Liu et al, 2015;Hu et al, 2019;Wang M. et al, 2019;Chen et al, 2020). Detailed genome information is shown in Tables 1 and 2.…”

Section: Cotton Genome Sequencing Effortsmentioning

confidence: 99%

“…G. arboretum (Li et al, 2014) G. arboretum (Du et al, 2018) G. arboretum (Huang et al, 2020) G. herbaceum (Huang et al, 2020) G. raimondii (Wang et al, 2012) G. raimondii (Paterson et al, 2012) G. raimondii (Udall et al, 2019) Total contigs 40,381 8,223 2,432 1,781 41,307 19,735 187 Contig N50 (kb) 72 1,100 1, G. hirsutum (TM-1,V1.1) (Zhang et al, 2015) G. hirsutum (TM-1) (Wang M. et al, 2019) G. hirsutum (TM-1,V2.1) (Hu et al, 2019) G. hirsutum (TM-1,updated V1) (Huang et al, 2020) G. hirsutum (TM-1) (Chen et al, 2020) G. barbadense (Xinhai21) (Liu et al, 2015) G. barbadense…”

Section: Speciesmentioning

confidence: 99%

“…(3-79) (Yuan et al, 2015) G. barbadense (3-79) (Wang M. et al, 2019) G. barbadense (Hai7124,V1.1) (Hu et al, 2019) G. barbadense (3-79,V1.1) (Chen et al, 2020) Scaffold G. raimondii genome was sequenced, and based on the cotton genetic and physical maps, 761.4 Mb data was assembled and oriented to 98.3% of the expected genome size (Paterson et al, 2012). Seven years later, deciphered using PacBio long-read technology, HiC, and Bionano optical mapping, the third genome sequence of G. raimondii was published (Udall et al, 2019). In this assembled genome, the number of contigs decreased and the length of contig N50 was much elongated (6.3 Mb).…”

Section: Speciesmentioning

confidence: 99%

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

2020

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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.

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De Novo Genome Sequence Assemblies of Gossypium raimondii and Gossypium turneri

Cited by 86 publications

References 26 publications

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

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

TheGossypium longicalyxGenome as a Resource for Cotton Breeding and Evolution

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

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