Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton

Hu, Yan; Chen, Jiedan; Fang, Lei; Zhang, Zhiyuan; Ma, Wei; Niu, Yongchao; Ju, Longzhen; Deng, Jieqiong; Zhao, Ting; Lian, Jinmin; Baruch, Kobi; Fang, David D.; Liu, Xia; Ruan, Yong‐Ling; Rahman, Mehboob‐ur; Han, Jinlei; Wang, Kai; Wang, Qiong; Wu, Huaitong; Mei, Gaofu; Zang, Yihao; Han, Zegang; Xu, Chenyu; Shen, Weijuan; Yang, Dan; Si, Zhanfeng; Dai, Fan; Zou, Liangfeng; Huang, Fei; Bai, Yulin; Zhang, Yugao; Brodt, Avital; Ben-Hamo, Hilla; Zhu, Xiefei; Zhou, Baoliang; Guan, Xueying; Zhu, Shuijin; Chen, Xiaoya; Zhang, Tianzhen

doi:10.1038/s41588-019-0371-5

Cited by 716 publications

(879 citation statements)

References 101 publications

(121 reference statements)

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“…As an indication of the improved contiguity (Supplementary Note), the contig length in the Gh genome increases 6.9-fold with a 7.7-fold reduction in fragmentation (6,733 versus 51,849), compared to the published sequences 22 . The improvement is substantial in the Gb genome with a 15.9-fold reduction in N50 contigs and a 23-fold increase in N50 contig length (from 77.6 to 1,800 kilobase pairs (kb)).…”

Section: Resultsmentioning

confidence: 99%

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

et al. 2020

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olyploidy or whole-genome duplication provides genomic opportunities for evolutionary innovations in many animal groups and all flowering plants 1-5 , including most important crops such as wheat, cotton and canola or oilseed rape 6-8. The common occurrence of polyploidy may suggest its advantage and potential for selection and adaptation 2,3,9 , through rapid genetic and genomic changes as observed in newly formed Brassica napus 10 , Tragopogon miscellus 11 and polyploid wheat 12 , and/or largely epigenetic modifications as in Arabidopsis and cotton polyploids 5,13. Cotton is a powerful model for revealing genomic insights into polyploidy 3 , providing a phylogenetically defined framework of polyploidization (~1.5 million years ago (Ma)) 14 , followed by natural diversification and crop domestication 15. The evolutionary history of the polyploid cotton clade is longer than that of some other allopolyploids, such as hexaploid wheat (~8,000 years) 12 , tetraploid canola (~7,500 years) 16 and tetraploid Tragopogon (~150 years) 11. Polyploidization between an A-genome African species (Gossypium arboreum (Ga)-like) and a D-genome American species (G. raimondii (Gr)-like) in the New World created a new allotetraploid or amphidiploid (AD-genome) cotton clade (Fig. 1a) 14 , which has diversified into five polyploid lineages, G. hirsutum (Gh) (AD) 1 , G. barbadense (Gb) (AD) 2 , G. tomentosum (Gt) (AD) 3 , G. mustelinum (Gm) (AD) 4 and G. darwinii (Gd) (AD) 5. G. ekmanianum and G. stephensii are recently characterized and closely related to Gh 17. Gh and Gb were separately domesticated from perennial shrubs to become annualized Upland and Pima cottons 15. To date, global cotton production provides income for ~100 million families across ~150 countries, with an annual economic impact of ~US$500 billion worldwide 6. However, cotton supply is reduced due to aridification, climate change and pest emergence. Future improvements in cotton and sustainability will involve use of the genomic resources and gene-editing tools becoming available in many crops 9,18,19. Cotton genomes have been sequenced for the D-genome (Gr) 20 and A-genome (Ga) 21 diploids and two cultivated tetraploids 22-26. These analyses have shown structural, genetic and gene expression variation related to fiber traits and stress responses in cultivated

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Section: Resultsmentioning

confidence: 99%

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

et al. 2020

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“…Continuity and completeness are important indicators of genome assembly. PacBio-based genome assembly plus error corrections based on Illumina data could greatly improve continuity and completeness [56][57][58][59] . Our genome assembly of I. indigotica by this strategy showed a highly resolved result with an N50 = 1.22 Mb and longest contig length = 8.99 Mb.…”

Section: Discussionmentioning

confidence: 99%

A chromosome-scale genome assembly of Isatis indigotica, an important medicinal plant used in traditional Chinese medicine

Kang

Yang

et al. 2020

Hortic Res

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Isatis indigotica (2n = 14) is an important medicinal plant in China. Its dried leaves and roots (called Isatidis Folium and Isatidis Radix, respectively) are broadly used in traditional Chinese medicine for curing diseases caused by bacteria and viruses such as influenza and viral pneumonia. Various classes of compounds isolated from this species have been identified as effective ingredients. Previous studies based on transcriptomes revealed only a few candidate genes for the biosynthesis of these active compounds in this medicinal plant. Here, we report a high-quality chromosome-scale genome assembly of I. indigotica with a total size of 293.88 Mb and scaffold N50 = 36.16 Mb using single-molecule real-time long reads and high-throughput chromosome conformation capture techniques. We annotated 30,323 highconfidence protein-coding genes. Based on homolog searching and functional annotations, we identified many candidate genes involved in the biosynthesis of main active components such as indoles, terpenoids, and phenylpropanoids. In addition, we found that some key enzyme-coding gene families related to the biosynthesis of these components were expanded due to tandem duplications, which likely drove the production of these major active compounds and explained why I. indigotica has excellent antibacterial and antiviral activities. Our results highlighted the importance of genome sequencing in identifying candidate genes for metabolite synthesis in medicinal plants. Data availabilityThe PacBio long reads and Illumina short reads were uploaded to the NCBI SRA database under BioProject PRJNA549758. The final chromosome-scale genome assembly was submitted to the NCBI with accession number VHIU00000000. The genome fasta and gff3 files were uploaded to Figshare.

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“…Gene models with an AED greater than 0.47 were removed from further analyses, and the remaining gene models were functionally annotated using .0] (Jones et al 2014) and BlastP [v2.9.0+] (Camacho et al 2009) searches against the Uniprot SwissProt database. Orthologs between the G. longicalyx annotations and the existing annotations for G. arboreum (Du et al 2018), G. raimondii (Paterson et al 2012), G. hirsutum (Hu et al 2019), and G. barbadense (n=26;Hu et al 2019) were predicted by OrthoFinder using default settings Kelly 2015, 2019). All genomes are hosted through CottonGen (https://www.cottongen.org; Yu et al 2014) and running parameters are available from https://github.com/Wendellab/longicalyx.…”

Section: Plant Materials and Sequencing Methodsmentioning

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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Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton

Cited by 716 publications

References 101 publications

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

A chromosome-scale genome assembly of Isatis indigotica, an important medicinal plant used in traditional Chinese medicine

TheGossypium longicalyxGenome as a Resource for Cotton Breeding and Evolution

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