Genomic analysis of SBP gene family in Saccharum spontaneum reveals their association with vegetative and reproductive development.
Genomic analysis of SBP gene family in Saccharum spontaneum reveals their association with vegetative and reproductive development.
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Saccharum spontaneum 中 SBP 基因家族的基因组分析揭示了它们与营养和生殖发育的关联
DOI：
10.1186/s12864-021-08090-3
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发表时间：
2021-10-27
期刊：
影响因子：
4.4
通讯作者：
Niu X
中科院分区：
文献类型：
--
作者：
Liu Y;Aslam M;Yao LA;Zhang M;Wang L;Chen H;Huang Y;Qin Y;Niu X
背景
SQUAMOSA 启动子结合蛋白 (SBP) 基因编码参与各种生长和发育过程的植物特异性转录因子家族，包括花和果实发育、叶起始、相变和胚胎发育。 SBP 基因家族已在许多物种中得到鉴定和表征，但尚未对甘蔗中的 SBP 基因家族进行系统分析。
结果
在本研究中，通过全基因组分析鉴定出30个SBP基因的总共50个序列，并根据其染色体分布指定为SsSBP1至SsSBP30。根据系统发育树、基因结构和基序特征，SsSBP基因分为八组（I至VIII）。通过同线性分析，SsSBP基因中存在27对同源基因，甘蔗和高粱之间存在37对直系同源基因。不同组织（包括营养器官和生殖器官）中的表达分析显示SsSBP基因的差异表达模式，表明它们在各种发育过程中的功能多样性。此外，22 个 SsSBP 基因被预测为 miR156 的潜在靶标。 miR156的差异表达模式表现出不同组织中miR156与SsSBP基因的转录水平呈负相关。
结论
甘蔗基因组拥有30个SsSBP基因，它们在其亚科中具有相似的基因结构和基序特征。基于转录和qRT-PCR分析，发现大多数SsSBP基因调节叶片初始和雌性生殖发育。本研究全面、系统地分析了甘蔗中SsSBP基因，为进一步研究SsSBP基因在不同发育过程中的功能特性奠定了基础。
Background
SQUAMOSA promoter binding proteins (SBPs) genes encode a family of plant-specific transcription factors involved in various growth and development processes, including flower and fruit development, leaf initiation, phase transition, and embryonic development. The SBP gene family has been identified and characterized in many species, but no systematic analysis of the SBP gene family has been carried out in sugarcane.
Results
In the present study, a total of 50 sequences for 30 SBP genes were identified by the genome-wide analysis and designated SsSBP1 to SsSBP30 based on their chromosomal distribution. According to the phylogenetic tree, gene structure and motif features, the SsSBP genes were classified into eight groups (I to VIII). By synteny analysis, 27 homologous gene pairs existed in SsSBP genes, and 37 orthologous gene pairs between sugarcane and sorghum were found. Expression analysis in different tissues, including vegetative and reproductive organs, showed differential expression patterns of SsSBP genes, indicating their functional diversity in the various developmental processes. Additionally, 22 SsSBP genes were predicted as the potential targets of miR156. The differential expression pattern of miR156 exhibited a negative correlation of transcription levels between miR156 and the SsSBP gene in different tissues.
Conclusions
The sugarcane genome possesses 30 SsSBP genes, and they shared similar gene structures and motif features in their subfamily. Based on the transcriptional and qRT-PCR analysis, most SsSBP genes were found to regulate the leaf initial and female reproductive development. The present study comprehensively and systematically analyzed SBP genes in sugarcane and provided a foundation for further studies on the functional characteristics of SsSBP genes during different development processes.
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影响因子：
3.7
作者：
Du H;Feng BR;Yang SS;Huang YB;Tang YX
通讯作者：
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影响因子：
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模因套件：用于发现和搜索的工具。
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作者：
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通讯作者：
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影响因子：
4.4
作者：
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Henry RJ