Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres

Paterson, Andrew H.; Wendel, Jonathan F.; Gundlach, Heidrun; Guo, Hui; Jenkins, Jerry; Jin, Dianchuan; Llewellyn, Danny; Showmaker, Kurt C.; Shu, Shengqiang; Udall, Joshua A.; Yoo, Mi‐Jeong; Byers, Richard; Chen, Wei; Doron‐Faigenboim, Adi; Duke, Mary V.; Gong, Lei; Grimwood, Jane; Grover, Corrinne E.; Grupp, Kara; Hu, Guanjing; Lee, Tae‐Ho; Li, Jingping; Lin, Lifeng; Liu, Tao; Marler, Barry S.; Page, Justin T.; Roberts, Alison W.; Romanel, Elisson; Sanders, William S.; Szadkowski, Emmanuel; Tan, Xu; Tang, Haibao; Xu, Chunming; Wang, Jinpeng; Wang, Zining; Zhang, Dong; Zhang, Lan; Ashrafi, Hamid; Bedon, Frank; Bowers, John E.; Brubaker, Curt L.; Chee, Peng W.; Das, Sayan; Gingle, Alan R.; Haigler, Candace H.; Harker, David; Hoffmann, Lúcia Vieira; Hovav, Ran; Jones, Douglas T.; Lemke, Cornelia; Mansoor, Shahid; Rahman, Md Jamilur; Rainville, Lisa N.; Rambani, Aditi; Reddy, Umesh K.; Rong, Junkang; Saranga, Yehoshua; Scheffler, Brian E.; Scheffler, Jodi A.; Stelly, David M.; Triplett, Barbara A.; Deynze, Allen Van; Vaslin, Maite F S; Waghmare, V. N.; Walford, Sally A.; Wright, Robert J.; Zaki, Essam A.; Zhang, Tianzhen; Dennis, Elizabeth S.; Mayer, Klaus; Peterson, Daniel G.; Rokhsar, Daniel S.; Wang, Xiyin; Schmutz, Jeremy

doi:10.1038/nature11798

Cited by 1,120 publications

(1,451 citation statements)

References 44 publications

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“…A WGD has also previously been shown for the cotton lineage, after its speciation with cacao 25,26 . We investigated whether the WGDs associated with cotton and durian reflect the same event or represent two distinct evolutionary events, by resolving the ordering and dates of the WGDs alongside the durian-cotton divergence event.…”

Section: Comparative Phylogenomics Shows Durian Paleopolyploidymentioning

confidence: 60%

“…First, other subfamilies within Malvaceae, after divergence from the Byttnerioideae subfamily (including cacao), are also likely to have the cotton-specific WGD. Second, this WGD event, which has been proposed to have driven the evolution of unique Gossypium traits 26 , may also have been involved in driving the evolution of unique durian traits, as well as the radiation of different Malvaceae subfamilies around the same time 47,48 .…”

Section: Discussionmentioning

confidence: 99%

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The draft genome of tropical fruit durian (Durio zibethinus)

et al. 2017

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Section: Comparative Phylogenomics Shows Durian Paleopolyploidymentioning

confidence: 60%

Section: Discussionmentioning

confidence: 99%

The draft genome of tropical fruit durian (Durio zibethinus)

et al. 2017

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“…Alternatively, unstable allotetraploids in early generations were eliminated by selection. Here we show that in allotetraploid cotton, overall gene order and colinearity are largely conserved between the A and D subgenomes and the extant D-progenitor genome (G. raimondii) 4 (Fig. 2a, Supplementary Figs.…”

Section: Comparative Genome Analysesmentioning

confidence: 77%

“…2). The genome assembly accuracy and completeness were validated by matching 98% of mRNA sequences in G. raimondii 4 Table 4) and 99.5% of full-length mRNAs of G. hirsutum, which were downloaded from the NCBI GenBank (https://www.ncbi.nlm.nih.gov/genbank/) (Supplementary Table 5). This indicates that the sequence contained most genic regions.…”

Section: Validation Of the Assemblymentioning

confidence: 99%

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

et al. 2015

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“…Expression data of cell lines were downloaded from Cancer Cell Line Encyclopedia (CCLE) 46,47 and were normalized by Robust Multiarray Averaging (RMA) method. Probesets annotation and differential gene expression were carried out as described above.…”

Section: Methodsmentioning

confidence: 99%

Smoker and non-smoker lung adenocarcinoma is characterized by distinct tumor immune microenvironments

et al. 2018

OncoImmunology

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Tobacco smoking causes DNA damages in epithelial cells and immune dysfunction in the lung, which collectively contribute to lung carcinogenesis and progression. However, potential mechanisms by which tumor-infiltrating immune cells contribute to lung cancer survival and their differential contributions in ever-smokers and never-smokers are not well studied. Here, we performed integrative analysis of 11 lung cancer gene-expression datasets, including 1,111 lung adenocarcinomas and 200 adjacent normal lung samples. Distinct pathways were altered in lung carcinogenesis in ever-smokers and never-smokers. Never-smoker patients had a better outcome than ever-smoker patients. We characterized compositional patterns of 21 types of immune cells in lung adenocarcinomas and revealed the complex association between immune cell composition and clinical outcomes. Interestingly, we found two subsets of immune cells, mast cells and CD4+ memory T cells, which had completely opposite associations with outcomes in resting and activated status. We further discovered that several chemokines and their associated receptors (e.g., CXCL11-CX3CR1 axis) were selectively altered in lung tumors in response to cigarette smoking and their abundances showed stronger correlation with fractions of these immune subsets in ever-smokers than never-smokers. The status switched from the resting to activated forms in mast cells and CD4+ memory T cells might manifest some important processes induced by cigarette smoking during tumor development and progression. Our findings suggested that aberrant activation of mast cells and CD4+ memory T cells plays crucial roles in cigarette smoking-induced immune dysfunction in the lung, which contributes to tumor development and progression.

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Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres

Cited by 1,120 publications

References 44 publications

The draft genome of tropical fruit durian (Durio zibethinus)

The draft genome of tropical fruit durian (Durio zibethinus)

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

Smoker and non-smoker lung adenocarcinoma is characterized by distinct tumor immune microenvironments

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