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Novel structural annotation and functional expression analysis of GTP_EFTU conserved genes in pepper based on the PacBio sequencing data
Horticultural Plant Journal ( IF 5.7 ) Pub Date : 2021-06-24 , DOI: 10.1016/j.hpj.2020.09.007
Bingqian Tang , Lingling Xie , Xuefeng Li , Huiping Yang , Yi Liu , Xiang Cheng , Chenliang Liang , Juan Chen , Shudong Zhou , Duanhua Wang , Jingyuan Zheng , Xiongze Dai , Xuexiao Zou , Feng Liu

Genes containing GTP_EFTU domain mainly express elongation factors (EF), Small GTPases, and GTP-binding proteins, which are closely related to protein synthesis, extension and ATP synthesis. In this study, we identified 39 genes containing GTP_EFTU domains from peppers. The evolutionary trees constructed from capsicum, Arabidopsis, rice, and tomato are mainly divided into 7 subfamilies. Using PacBio (Pacific Biosciences) sequencing and assembly data, we extracted these 39 gene sequences, from which 25 genes had alternative splicing. Particularly, the Capana08g000545 had 16 alternative splicing processes. Accordingly, we performed promoter sequence analysis, subcellular location prediction, the expression analysis of different tissues and periods, and also the GO (Gene ontology) analysis of co-expressed genes. Lastly we did the qRT-PCR analysis in 5 stages of pepper fruit development. These analyses revealed important structural and functional information for the identified 39 genes that contain GTP_EFTU domains, providing important references for further follow-up experiments to verify the genes function on plants or their unique roles in peppers.



中文翻译:

基于PacBio测序数据的辣椒中GTP_EFTU保守基因的新型结构注释和功能表达分析

含有GTP_EFTU结构域的基因主要表达延伸因子(EF)、Small GTPases和GTP结合蛋白,与蛋白质合成、延伸和ATP合成密切相关。在这项研究中,我们从辣椒中鉴定了 39 个含有 GTP_EFTU 结构域的基因。由辣椒、拟南芥、水稻和番茄构建的进化树主要分为7个亚科。使用PacBio(Pacific Biosciences)测序和组装数据,我们提取了这39个基因序列,其中25个基因发生了可变剪接。特别是Capana08g000545有16个可选的拼接工艺。相应地,我们进行了启动子序列分析、亚细胞定位预测、不同组织和时期的表达分析,以及共表达基因的GO(基因本体)分析。最后,我们对辣椒果实发育的 5 个阶段进行了 qRT-PCR 分析。这些分析揭示了已鉴定的 39 个包含 GTP_EFTU 结构域的基因的重要结构和功能信息,为进一步的后续实验以验证基因对植物的功能或其在辣椒中的独特作用提供了重要参考。

更新日期:2021-08-26
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