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Insilco identification and characterization of superoxide dismutase gene family in Brassica rapa
Saudi Journal of Biological Sciences Pub Date : 2021-08-08 , DOI: 10.1016/j.sjbs.2021.08.009
Asif M Iqbal Qureshi 1 , Mehraj Uddin Sofi 2 , N A Dar 1 , M H Khan 1 , S S Mahdi 3 , Zahoor A Dar 4 , Shabir Bangroo 5 , Hamed A El-Serehy 6 , Daniel Ingo Hefft 7 , Simona Mariana Popescu 8
Affiliation  

Superoxide Dismutase SODs are defense associated proteins that detoxify ROS and primarily serve as scavengers. They have been described in numerous plant species, but their in-depth characterization in Brassica rapa has not been reported. Therefore, the present investigation on genome wide study of SOD gene family was conducted to identify BrSOD genes, their domain-based organization, gene structure analysis, phylogenetic analysis, intron-exon structure of genes and expression analysis. The sequence characterization of Super oxide dismutase gene family in Brassica rapa, their syntenic associateship of conserved motifs and phylogenetic correlationship, prediction of cis-elements and determing the expression analysis in distinct tissues namely plant callus, root, stem, leaf, flower, and silique under abiotic conditions have been analysed using different software’s. The study on SOD gene family identified 17 BrSOD genes which were grouped into eight BrCu-ZnSODs and nine BrFe-MnSODs domain-based organization. Furthermore, the conserved character of BrSODs were confirmed by intron-exon organisation, motif arrangements and domain architectural investigations. Expression analysis using RNA Sequence data of different developmental stages proclaimed that genes were manifested in all six tissues with an exception of BrCu-ZnSOD3, which was not manifested in roots; however, whose transcript was detected in all other tested tissues. The study has genome wide insight into the occurrence and functional specifications of BrSOD gene family in Brassica rapa that can be potentially utilized in breeding program for resilience to climate change and abiotic stresses tolerance Brassica variety.



中文翻译:

油菜超氧化物歧化酶基因家族的Insilco鉴定与表征

超氧化物歧化酶SOD是防御相关蛋白,可解毒 ROS 并主要用作清除剂。它们已在许多植物物种中得到描述,但尚未在芸苔中对其进行深入表征。因此,目前对SOD基因家族的全基因组研究进行了调查,以鉴定 Br SOD基因、基于域的组织、基因结构分析、系统发育分析、基因的内含子-外显子结构和表达分析。油菜超氧化物歧化酶基因家族的序列特征、保守基序的同线关联和系统发育相关性、顺式预测已经使用不同的软件分析了非生物条件下不同组织即植物愈伤组织、根、茎、叶、花和长角果中的元素和确定表达分析。SOD基因家族的研究鉴定了 17 个 Br SOD基因,这些基因分为 8 个 Br Cu-ZnSODs和 9 个 Br Fe- MnSODs结构域结构。此外,内含子-外显子组织、基序排列和域结构研究证实了Br SODs的保守特性。使用不同发育阶段的 RNA 序列数据进行的表达分析表明,除 Br Cu-ZnSOD3 外,所有六种组织中都有基因表达没有体现在根上;然而,在所有其他测试组织中都检测到了其转录本。该研究对芸苔中 Br SOD基因家族的发生和功能特性具有全基因组洞察力,可潜在地用于育种计划以适应气候变化和非生物胁迫耐受性芸苔品种。

更新日期:2021-09-19
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