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Characterization and comparative analysis of the plastome sequence from Justicia ventricosa (Lamiales: Acanthaceae)
Mitochondrial DNA Part B ( IF 0.610 ) Pub Date : 2021-09-14 , DOI: 10.1080/23802359.2021.1922099
Junchen Zhou 1, 2 , Qing Du 1, 3 , Mei Jiang 1 , Shengyu Liu 4 , Liqiang Wang 5 , Haimei Chen 1 , Bin Wang 2 , Chang Liu 1
Affiliation  

Abstract

Justicia ventricosa is a characteristic ethnic herb commonly used to treat Orthopedic pains. Here, to confirm its phylogenetic position and to develop molecular markers that can distinguish different Justicia species, we obtained and analyzed the plastome of Justicia ventricosa. The plastome was sequenced using the Illumina HiSeq sequencing platform, assembled with NOVOPlasty, and annotated with CPGAVAS2. The genome has a circular structure of 149,700 bp, containing a large single-copy region of 82,324 bp, a small single-copy region of 17,260 bp, and two reverse repeat regions of 25,058 bp each. It encodes 112 unique genes, including 76 protein-coding genes, eight ribosomal RNA genes, and 28 transfer RNA genes. Twenty cis-splicing genes were found. In total, we predicted 19 microsatellite repeats and 13 tandem repeat sequences. For distributed repeats, four were palindrome repeats and five were direct repeats. To find the highly variable intergenic spacer (IGS) regions, we calculated the K2P distances for IGS regions from four Justicia species. The K2P values ranged from 6.11 to 57.82. The largest K2P distances were found for ccsA-ndhD, petB-petD, psbK-psbI, and ycf4-cemA. Phylogenetic analysis results showed that J. ventricosa was most closely related to J. leptostachya. To determine how Justicia species adapt to the environment, we performed selection pressure analysis. Nine genes were found to have undergone positive selection. Lastly, we performed a genome-wise DNA barcode prediction, seven pairs of primers were found. The results provide valuable information that can be used for molecular marker development and bioprospecting in Justicia species.



中文翻译:

来自 Justicia ventricosa (Lamiales: Acanthaceae) 的塑性体序列的表征和比较分析

摘要

Justicia ventricosa是一种典型的民族草药,常用于治疗骨科疼痛。在这里,为了确认其系统发育位置并开发可以区分不同Justicia物种的分子标记,我们获得并分析了Justicia ventricosa的塑性体使用 Illumina HiSeq 测序平台对质体进行测序,使用 NOVOPlasty 组装,并使用 CPGAVAS2 进行注释。该基因组具有149,700 bp的环状结构,包含一个82,324 bp的大单拷贝区域、一个17,260 bp的小单拷贝区域和两个25,058 bp的反向重复区域。它编码 ​​112 个独特的基因,包括 76 个蛋白质编码基因、8 个核糖体 RNA 基因和 28 个转移 RNA 基因。发现了二十个顺式剪接基因。我们总共预测了 19 个微卫星重复序列和 13 个串联重复序列。对于分布式重复,四个是回文重复,五个是直接重复。为了找到高度可变的基因间间隔 (IGS) 区域,我们计算了来自四个Justicia 的IGS 区域的 K2P 距离物种。K2P 值范围从 6.11 到 57.82。ccs A -ndh D、pet B -pet D、psb K -psb I和ycf 4 -cem A的K2P距离最大。系统发育分析结果表明J. ventricosaJ. leptostachya的亲缘关系最密切。确定Justicia如何物种适应环境,我们进行了选择压力分析。发现九个基因经历了正选择。最后,我们进行了基因组 DNA 条形码预测,发现了七对引物。结果提供了宝贵的信息,可用于Justicia物种的分子标记开发和生物勘探。

更新日期:2021-09-15
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