Dataset Information

Molecular Evolution and Expansion of the KUP Family in the Allopolyploid Cotton Species Gossypium hirsutum and Gossypium barbadense.

ABSTRACT: The comprehensive analysis of gene family evolution will elucidate the origin and evolution of gene families. The K+ uptake (KUP) gene family plays important roles in K+ uptake and transport, plant growth and development, and abiotic stress responses. However, the current understanding of the KUP family in cotton is limited. In this study, 51 and 53 KUPs were identified in Gossypium barbadense and Gossypium hirsutum, respectively. These KUPs were divided into five KUP subfamilies, with subfamily 2 containing three groups. Different subfamilies had different member numbers, conserved motifs, gene structures, regulatory elements, and gene expansion and loss rates. A paleohexaploidization event caused the expansion of GhKUP and GbKUP in cotton, and duplication events in G. hirsutum and G. barbadense have happened in a common ancestor of Gossypium. Meanwhile, the KUP members of the two allopolyploid subgenomes of G. hirsutum and G. barbadense exhibited unequal gene proportions, gene structural diversity, uneven chromosomal distributions, asymmetric expansion rates, and biased gene loss rates. In addition, the KUP families of G. hirsutum and G. barbadense displayed evolutionary conservation and divergence. Taken together, these results illustrated the molecular evolution and expansion of the KUP family in allopolyploid cotton species.

SUBMITTER: Fan K

PROVIDER: S-EPMC7554350 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Publications

Molecular Evolution and Expansion of the KUP Family in the Allopolyploid Cotton Species Gossypium hirsutum and Gossypium barbadense.

Fan Kai K Mao Zhijun Z Zheng Jiaxin J Chen Yunrui Y Li Zhaowei Z Lin Weiwei W Zhang Yongqiang Y Huang Jinwen J Lin Wenxiong W

Frontiers in plant science 20200930

The comprehensive analysis of gene family evolution will elucidate the origin and evolution of gene families. The K+ uptake (KUP) gene family plays important roles in K+ uptake and transport, plant growth and development, and abiotic stress responses. However, the current understanding of the KUP family in cotton is limited. In this study, 51 and 53 KUPs were identified in Gossypium barbadense and Gossypium hirsutum, respectively. These KUPs were divided into five KUP subfamilies, ...[more]

PMID: 33101325

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Project description:BackgroundHow to develop new cotton varieties possessing high yield traits of Upland cotton and superior fiber quality traits of Sea Island cotton remains a key task for cotton breeders and researchers. While multiple attempts bring in little significant progresses, the development of Chromosome Segment Substitution Lines (CSSLs) from Gossypium barbadense in G. hirsutum background provided ideal materials for aforementioned breeding purposes in upland cotton improvement. Based on the excellent fiber performance and relatively clear chromosome substitution segments information identified by Simple Sequence Repeat (SSR) markers, two CSSLs, MBI9915 and MBI9749, together with the recurrent parent CCRI36 were chosen to conduct transcriptome sequencing during the development stages of fiber elongation and Secondary Cell Wall (SCW) synthesis (from 10DPA and 28DPA), aiming at revealing the mechanism of fiber development and the potential contribution of chromosome substitution segments from Sea Island cotton to fiber development of Upland cotton.ResultsIn total, 15 RNA-seq libraries were constructed and sequenced separately, generating 705.433 million clean reads with mean GC content of 45.13% and average Q30 of 90.26%. Through multiple comparisons between libraries, 1801 differentially expressed genes (DEGs) were identified, of which the 902 up-regulated DEGs were mainly involved in cell wall organization and response to oxidative stress and auxin, while the 898 down-regulated ones participated in translation, regulation of transcription, DNA-templated and cytoplasmic translation based on GO annotation and KEGG enrichment analysis. Subsequently, STEM software was performed to explicate the temporal expression pattern of DEGs. Two peroxidases and four flavonoid pathway-related genes were identified in the "oxidation-reduction process", which could play a role in fiber development and quality formation. Finally, the reliability of RNA-seq data was validated by quantitative real-time PCR of randomly selected 20 genes.ConclusionsThe present report focuses on the similarities and differences of transcriptome profiles between the two CSSLs and the recurrent parent CCRI36 and provides novel insights into the molecular mechanism of fiber development, and into further exploration of the feasible contribution of G. barbadense substitution segments to fiber quality formation, which will lay solid foundation for simultaneously improving fiber yield and quality of upland cotton through CSSLs.

Dataset Information

Molecular Evolution and Expansion of the KUP Family in the Allopolyploid Cotton Species Gossypium hirsutum and Gossypium barbadense.

Publications

Molecular Evolution and Expansion of the KUP Family in the Allopolyploid Cotton Species <i>Gossypium hirsutum</i> and <i>Gossypium barbadense</i>.

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