Identification and Expression Analysis of TCP Genes in Saccharum spontaneum L

Lin, Jishan; Zhu, Mengting; Cai, Mingxing; Zhang, Wenping; Fatima, Mahpara; Jia, Haifeng; Li, Feifei; Ming, Ray

doi:10.1007/s12042-019-09238-y

Cited by 10 publications

(4 citation statements)

References 37 publications

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“…Gene, genome, and segmental duplications are reported to be associate with genetic novelty [48][49][50]. The sugarcane genome was identified to undergo two WGD events after divergence from its closest relative and detailed analysis of the genome showed duplications in other gene families [51][52][53][54][55][56]. The duplications of SsDofs in sugarcane originated from approximately 0.21 Mya to 15.60 Mya, which indicated the duplications of SsDofs in sugarcane took place prior and after the divergence of sugarcane and sorghum.…”

Section: Discussionmentioning

confidence: 97%

Allele specific expression of Dof genes responding to hormones and abiotic stresses in sugarcane

Cai¹,

Lin²,

Li³

et al. 2020

PLoS ONE

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Dof transcription factors plant-specific and associates with growth and development in plants. We conducted comprehensive and systematic analyses of Dof transcription factors in sugarcane, and identified 29 SsDof transcription factors in sugarcane genome. Those SsDof genes were divided into five groups, with similar gene structures and conserved motifs within the same groups. Segmental duplications are predominant in the evolution of Dof in sugarcane. Cis-element analysis suggested that the functions of SsDofs were involved in growth and development, hormones and abiotic stresses responses in sugarcane. Expression patterns indicated that SsDof7, SsDof23 and SsDof24 had a comparatively high expression in all detected tissues, indicating these genes are crucial in sugarcane growth and development. Moreover, we examined the transcription levels of SsDofs under four plant hormone treatments, SsDof7-3 and SsDof7-4 were down-regulated after ABA treatment, while SsDof7-1 and SsDof7-2 were induced after the same treatment, indicating different alleles may play different roles in response to plant hormones. We also analyzed SsDofs' expression profiling under four abiotic stresses, SsDof5 and SsDof28 significantly responded to these four stresses, indicating they are associate with abiotic stresses responses. Collectively, our results yielded allele specific expression of Dof genes responding to hormones and abiotic stresses in sugarcane, and their cis-elements could be crucial for sugarcane improvement. et al. (2020) Allele specific expression of Dof genes responding to hormones and abiotic stresses in sugarcane. PLoS ONE 15(1): e0227716. https://

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Section: Discussionmentioning

confidence: 97%

Allele specific expression of Dof genes responding to hormones and abiotic stresses in sugarcane

Cai¹,

Lin²,

Li³

et al. 2020

PLoS ONE

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“…The research on TCP genes has focused mainly on model species and major cereal crops. Encouragingly, more and more TCP family members from different species have been studied [27,51]. Regarding TCP genes, biological and molecular mechanism studies have focused mainly on plant development, but little is known about salt stress.…”

Section: Discussionmentioning

confidence: 99%

BpTCP3 Transcription Factor Improves Salt Tolerance of Betula platyphylla by Reducing Reactive Oxygen Species Damage

Ren

Jiang

et al. 2021

Forests

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The plant-specific transcription factors TEOSINTE BRANCHED1/CYCLO IDEA/PROLIFERATING CELL FACTOR1 (TCP) act as developmental regulators that have many roles in the growth and development processes throughout the entire life span of plants. TCP transcription factors are responsive to endogenous and environmental signals, such as salt stress. However, studies on the role of the TCP genes in salt stress response have rarely focused on woody plants, especially forest trees. In this study, the BpTCP3 gene, a CYC/TB1 subfamily member, isolated from Betula platyphylla Sukaczev, was significantly influenced by salt stress. The β-glucuronidase (GUS) staining analysis of transgenic B. platyphylla harboring the BpTCP3 promoter fused to the reporter gene GUS (pBpTCP3::GUS) further confirmed that the BpTCP3 gene acts a positive regulatory position in salt stress. Under salt stress, we found that the BpTCP3 overexpressed lines had increased relative/absolute high growth but decreased salt damage index, hydrogen peroxide (H2O2), and malondialdehyde (MDA) levels versus wild-type (WT) plants. Conversely, the BpTCP3 suppressed lines exhibited sensitivity to salt stress. These results indicate that the BpTCP3 transcription factor improves the salt tolerance of B. platyphylla by reducing reactive oxygen species damage, which provides useful clues for the functions of the CYC/TB1 subfamily gene in the salt stress response of B. platyphylla.

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“…Only in 2018 did an approach coupling next-generation and long-read sequencing with high-throughput chromatin conformation capture enable a chromosome-and allele-level genome of a Ssp clone to be assembled (Zhang et al, 2018). This study paved the way for several comprehensive analyses of gene families in this species (Hu et al, 2018;Hua-Ying et al, 2019;Lin et al, 2019;Shi et al, 2019;Wang et al, 2019a, b, c;Zhang et al, 2019b;Feng et al, 2020;Huang et al, 2020;Li et al, 2020b;Su et al, 2020a, Zhang andYin, 2020). In the present work, however, we analyzed the kinome of not only sugarcane but also sorghum, a close diploid relative.…”

Section: Discussionmentioning

confidence: 99%

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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Identification and Expression Analysis of TCP Genes in Saccharum spontaneum L

Cited by 10 publications

References 37 publications

Allele specific expression of Dof genes responding to hormones and abiotic stresses in sugarcane

Allele specific expression of Dof genes responding to hormones and abiotic stresses in sugarcane

BpTCP3 Transcription Factor Improves Salt Tolerance of Betula platyphylla by Reducing Reactive Oxygen Species Damage

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

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