Browsing by Author "Tang, Haibao"
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Item A comparative genomics examination of desiccation tolerance and sensitivity in two sister grass species(2022) Chávez Montes, Ricardo A. (TTU); Haber, Anna; Pardo, Jeremy; Powell, Robyn F.; Divisetty, Upendra K.; Silva, Anderson T.; Hernández-Hernández, Tania; Silveira, Vanildo; Tang, Haibao; Lyons, Eric; Herrera Estrella, Luis Rafael (TTU); VanBuren, Robert; Oliver, Melvin J.Desiccation tolerance is an ancient and complex trait that spans all major lineages of life on earth. Although important in the evolution of land plants, the mechanisms that underlay this complex trait are poorly understood, especially for vegetative desiccation tolerance (VDT). The lack of suitable closely related plant models that offer a direct contrast between desiccation tolerance and sensitivity has hampered progress. We have assembled high-quality genomes for two closely related grasses, the desiccation-tolerant Sporobolus stapfianus and the desiccation-sensitive Sporobolus pyramidalis. Both species are complex polyploids; S. stapfianus is primarily tetraploid, and S. pyramidalis is primarily hexaploid. S. pyramidalis undergoes a major transcriptome remodeling event during initial exposure to dehydration, while S. stapfianus has a muted early response, with peak remodeling during the transition between 1.5 and 1.0 grams of water (gH2O) g21 dry weight (dw). Functionally, the dehydration transcriptome of S. stapfianus is unrelated to that for S. pyramidalis. A comparative analysis of the transcriptomes of the hydrated controls for each species indicated that S. stapfianus is transcriptionally primed for desiccation. Cross-species comparative analyses indicated that VDT likely evolved from reprogramming of desiccation tolerance mechanisms that evolved in seeds and that the tolerance mechanism of S. stapfianus represents a recent evolution for VDT within the Chloridoideae. Orthogroup analyses of the significantly differentially abundant transcripts reconfirmed our present understanding of the response to dehydration, including the lack of an induction of senescence in resurrection angiosperms. The data also suggest that failure to maintain protein structure during dehydration is likely critical in rendering a plant desiccation sensitive.Item Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres(2012) Paterson, Andrew H.; Wendel, Jonathan F.; Gundlach, Heidrun; Guo, Hui; Jenkins, Jerry; Jin, Dianchuan; Llewellyn, Danny; Showmaker, Kurtis C.; Shu, Shengqiang; Udall, Joshua; Yoo, Mi Jeong; Byers, Robert; Chen, Wei; Doron-Faigenboim, Adi; Duke, Mary V.; Gong, Lei; Grimwood, Jane; Grover, Corrinne; 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, Lucia V.; Hovav, Ran; Jones, Donald C.; Lemke, Cornelia; Mansoor, Shahid; Rahman, Mehboob Ur; Rainville, Lisa N.; Rambani, Aditi; Reddy, Umesh K.; Rong, Jun Kang; Saranga, Yehoshua; Scheffler, Brian E.; Scheffler, Jodi A.; Stelly, David M.; Triplett, Barbara A.; Van Deynze, Allen; Vaslin, Maite F.S.; Waghmare, Vijay N.; Walford, Sally A.; Wright, Robert J. (TTU); Zaki, Essam A.; Zhang, Tianzhen; Dennis, Elizabeth S.; Mayer, Klaus F.X.; Peterson, Daniel G.; Rokhsar, Daniel S.; Wang, Xiyin; Schmutz, JeremyPolyploidy often confers emergent properties, such as the higher fibre productivity and quality of tetraploid cottons than diploid cottons bred for the same environments. Here we show that an abrupt five-to sixfold ploidy increase approximately 60million years (Myr) ago, and allopolyploidy reuniting divergent Gossypium genomes approximately 1-2 Myr ago, conferred about 30-36-fold duplication of ancestral angiosperm (flowering plant) genes in elite cottons (Gossypium hirsutum and Gossypium barbadense), genetic complexity equalled only by Brassica among sequenced angiosperms. Nascent fibre evolution, before allopolyploidy, is elucidated by comparison of spinnable-fibred Gossypium herbaceum A and non-spinnable Gossypium longicalyx F genomes to one another and the outgroup D genome of non-spinnable Gossypium raimondii. The sequence of a G. hirsutum A t D t (in which t' indicates tetraploid) cultivar reveals many non-reciprocal DNA exchanges between subgenomes that may have contributed to phenotypic innovation and/or other emergent properties such as ecological adaptation by polyploids. Most DNA-level novelty in G. hirsutum recombines alleles from the D-genome progenitor native to its New World habitat and the Old World A-genome progenitor in which spinnable fibre evolved. Coordinated expression changes in proximal groups of functionally distinct genes, including a nuclear mitochondrial DNA block, may account for clusters of cotton-fibre quantitative trait loci affecting diverse traits. Opportunities abound for dissecting emergent properties of other polyploids, particularly angiosperms, by comparison to diploid progenitors and outgroups. © 2012 Macmillan Publishers Limited. All rights reserved.