Genome-wide analysis of AP2/ERF Transcription Factors in sugarcane Saccharum spontaneum L. Reveals Functional Divergence During Drought, Salt Stress and Plant Hormones Treatment

Li, Piting; Chai, Zhe; Lin, Pingping; Huang, Chaohua; Huang, Guoqiang; Xu, Ling; Deng, Zixin; Zhang, Yu; Zhao, Xuhong

doi:10.21203/rs.3.rs-19836/v1

Cited by 2 publications

(1 citation statement)

References 58 publications

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“…We found that in the two kinomes the large majority of segmentally duplicated PKs were under negative selection (Ka/Ks<1), while a smaller percentage were under positive selection (Ka/Ks>1), and very few were under neutral selection (Ka/Ks=1). This pattern is similar to those observed in the soybean, grapevine and pineapple kinomes (Liu et al, 2015;Zhu et al, 2018a, b) and to those reported in smaller gene families in Ssp (Wang et al, 2019c;Li et al, 2020a) and sorghum (Malviya et al, 2016;Anand et al, 2017;Mittal et al, 2017).…”

Section: Discussionsupporting

confidence: 90%

The sugarcane and sorghum kinomes: insights into evolutionary expansion and diversification

Aono

Pimenta

Garcia

et al. 2020

Preprint

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The protein kinase (PK) superfamily is one of the largest superfamilies in plants and is the core regulator of cellular signaling. Even considering this substantial importance, the kinomes of sugarcane and sorghum have not been profiled. Here we identified and profiled the complete kinomes of the polyploid Saccharum spontaneum (Ssp) and Sorghum bicolor (Sbi), a close diploid relative. The Sbi kinome was composed of 1,210 PKs; for Ssp, we identified 2,919 PKs when disregarding duplications and allelic copies, which were related to 1,345 representative gene models. The Ssp and Sbi PKs were grouped into 20 groups and 120 subfamilies and exhibited high compositional similarities and evolutionary divergences. By utilizing the collinearity between these species, this study offers insights about Sbi and Ssp speciation, PK differentiation and selection. We assessed the PK subfamily expression profiles via RNA-Seq, identifying significant similarities between Sbi and Ssp. Moreover, through coexpression networks, we inferred a core structure of kinase interactions with specific key elements. This study is the first to categorize the allele specificity of a kinome and provides a wide reservoir of molecular and genetic information, enhancing the understanding of the evolutionary history of Sbi and Ssp PKs.HighlightThis study describes the catalog of kinase gene family in Saccharum spontaneum and Sorghum bicolor, providing a reservoir of molecular features and expression patterns based on RNA-Seq and co-expression networks.

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Section: Discussionsupporting

confidence: 90%

The sugarcane and sorghum kinomes: insights into evolutionary expansion and diversification

Aono

Pimenta

Garcia

et al. 2020

Preprint

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Sucrose metabolism analysis in a high sucrose sugarcane mutant clone at a mature stage in contrast to low sucrose parental clone through the transcriptomic approach

Khan

Qin

Guo

et al. 2023

Chem. Biol. Technol. Agric.

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Background The significance of sugarcane as a major crop is due to the production of sucrose and a significant source of ethanol. Sucrose phosphate synthase (SPS), Sucrose synthase (SuSy), and cell wall invertase (CWIN) genes regulate sucrose metabolism and accumulation in high sucrose sugarcane; such genes are significant for manipulating sucrose content. The current study explored the genes associated with sucrose metabolism and accumulation in a high sucrose sugarcane mutant clone GXB9 compared to its low sucrose parental clone B9. Results A total of 100, 262 differentially expressed genes were obtained, and 69, 637 (69.46%) got annotation in public databases COG, GO, KEGG, KOG, Pfam, eggNOG, NR, and Swiss-Prot. The SPS5 gene was significantly up-regulated in the maturing internodes of GXB9 and downregulated in B9. The SuSy and CWIN genes were up-regulated in the immature internodes; however, no expression was found in the maturing internodes of GXB9. The genes involved in trehalose synthesis were downregulated in GXB9 while up-regulated in B9. The cellulose synthase (CeS) genes were significantly up-regulated in the immature internodes than in maturing internodes of GXB9. Conclusions The key finding of this research suggests that the SPS5 gene has a predominant role in enhancing the sucrose accumulation ability of GXB9. No expression of SuSy and CWIN genes in maturing internodes and downregulation of trehalose genes in GXB9 may also have contributed to the higher sucrose accumulation in the stalk of high sucrose mutant. The current finding is a source for sugarcane breeding, particularly improving sucrose content. Graphical Abstract

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Genome-wide analysis of AP2/ERF Transcription Factors in sugarcane Saccharum spontaneum L. Reveals Functional Divergence During Drought, Salt Stress and Plant Hormones Treatment

Cited by 2 publications

References 58 publications

The sugarcane and sorghum kinomes: insights into evolutionary expansion and diversification

The sugarcane and sorghum kinomes: insights into evolutionary expansion and diversification

Sucrose metabolism analysis in a high sucrose sugarcane mutant clone at a mature stage in contrast to low sucrose parental clone through the transcriptomic approach

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