李启少, 王正德, 李建运, 等. 棕红悬钩子叶绿体的基因组结构与序列特征分析[J]. 西南林业大学学报(自然科学), 2024, 44(4): 93–105. DOI: 10.11929/j.swfu.202306053
引用本文: 李启少, 王正德, 李建运, 等. 棕红悬钩子叶绿体的基因组结构与序列特征分析[J]. 西南林业大学学报(自然科学), 2024, 44(4): 93–105. DOI: 10.11929/j.swfu.202306053
Li Qishao, Wang Zhengde, Li Jianyun, Wang Fei, Li Zihan, Zhu Wen, Tang Jiaying, Xin Yaxuan, Li Bin, Xin Peiyao. Analysis on the Structure and Sequence of the Chloroplast Genome of Rubus rufus[J]. Journal of Southwest Forestry University, 2024, 44(4): 93-105. DOI: 10.11929/j.swfu.202306053
Citation: Li Qishao, Wang Zhengde, Li Jianyun, Wang Fei, Li Zihan, Zhu Wen, Tang Jiaying, Xin Yaxuan, Li Bin, Xin Peiyao. Analysis on the Structure and Sequence of the Chloroplast Genome of Rubus rufus[J]. Journal of Southwest Forestry University, 2024, 44(4): 93-105. DOI: 10.11929/j.swfu.202306053

棕红悬钩子叶绿体的基因组结构与序列特征分析

Analysis on the Structure and Sequence of the Chloroplast Genome of Rubus rufus

  • 摘要: 对棕红悬钩子叶绿体基因组测序后进行中性绘图、ENC−plot、PR2−plot 和SSR位点分析,比对并构建17个悬钩子属植物和2个大叶路边青属植物系统发育树。以棕红悬钩子叶绿体基因组为参考,分析17种植物间的核苷酸多态性值,筛选高变区位点,比较棕红悬钩子与另外9个物种的IR边界区的收缩和扩张情况。结果表明:棕红悬钩子叶绿体基因组全长156266 bp,其中大单拷贝区85849 bp,小单拷贝区18855 bp 、双向重复区25781 bp;共注释出129个基因,包括86个蛋白质编码基因、35个tRNA基因和8个rRNA基因;选择压力是影响密码子使用偏好性的首要因素,16个最优密码子均以A/U结尾;棕红悬钩子SSR偏好使用A、T碱基。棕红悬钩子与锈毛莓、蛇泡筋亲缘关系较近,17种悬钩子属植物叶绿体基因组序列之间相似度较高,基因编码区比非编码区更为保守,变异主要发生在非编码区的相邻基因间隔区内,悬钩子属植物IR/SC边界较为保守。研究结果可为后期悬钩子属植物的分类鉴定及系统发育分析提供参考。

     

    Abstract: Neutral−plot, ENC−plot, PR2−plot and SSR epitope analysis were performed on the chloroplast genome of Rubus rufus after sequencing. The sequences of 17 Rubus plants, Geum macrophyllum voucher and G. rupestre chloroplast were aligned and the phylogenetic tree was constructed. Based on the chloroplast genome of R. rufus, the nucleotide polymorphism values among 17 plants were analyzed, and the high variable location points were screened. Finally, the shrinkage and expansion of the IR boundary region of R. rufus and 9 other species were compared by using relevant software. The findings indicated that the chloroplast genome is 156,266 bp in length, including 85,849 bp of large single copy region(LSC), 18,855 bp of small single copy region(SSC) and 25,781 bp of bidirectional repeats(IRs). A total of 129 genes were annotated, including 86 protein-coding genes, 35 tRNA genes and 8 rRNA genes. Selection pressure is the primary factor affecting codon usage preference, and all the 16 optimal codons end with A/U. The SSR of R. rufus preferred to use A and T bases. R. rufus was closely related to R. reflexus and R. cochinchinensis. The chloroplast genome sequences of 17 species of Rubus have high similarity, and the gene coding region is more conservative than the non-coding region. The variation mainly occurs in the adjacent intergenic region of the non-coding region, and the IR / SC boundary of Rubus is more conservative. The results can provide support for the classification and phylogenetic analysis of Rubus plants in the later stage.

     

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