（L. Henry）Holub 线粒体基因组的组装和特征分析。

Assembly and Characterization of the Mitochondrial Genome of (L. Henry) Holub.

机构信息

Qinghai Key Laboratory of Phytochemistry on Qinghai-Tibet Plateau, Qinghai Minzu University, 810007 Xining, Qinghai, China.

College of Pharmacy, Qinghai Minzu University, 810007 Xining, Qinghai, China.

出版信息

Front Biosci (Landmark Ed). 2023 Sep 28;28(10):233. doi: 10.31083/j.fbl2810233.

DOI:10.31083/j.fbl2810233

PMID:37919084

Abstract

BACKGROUND

(L. Henry) Holub is a perennial semi-shrub with both ornamental and medicinal value. The mitochondrial genomes of plants contain valuable genetic traits that can be utilized for the exploitation of genetic resources. The parsing of mitochondrial genome can provide insight into the role of mitochondria in plant growth and development, metabolism regulation, evolution, and response to environmental stress.

METHODS

In this study, we sequenced the mitochondrial genome of using the Illumina NovaSeq 6000 platform and Nanopore platform. We conducted a comprehensive analysis of the mitochondrial genome of , which involved examining various aspects such as gene composition, repetitive sequences, RNA editing sites, phylogeny, and organelle genome homology. To achieve this, we employed several bioinformatics methods including sequence alignment analysis, repetitive sequence analysis, phylogeny analysis, and more.

RESULTS

The mitochondrial genome of has 64 genes, including 34 protein-coding genes (PCGs), three rRNAs, and 27 tRNAs. There were 77 short tandem repeat sequences detected in the mitochondrial genome, five tandem repeat sequences identified by Tandem Repeats Finder (TRF), and 50 scattered repeat sequences observed, including 22 forward repeat sequences and 28 palindrome repeat sequences. A total of 367 RNA coding sites were predicted in PCGs, with the highest number (33) found within . values estimated for mitochondrial genes of and three closely related species representing Caryophyllales were less than 1 for most of the genes. The maximum likelihood evolutionary tree showed that and × are most closely related.

CONCLUSIONS

In this study, we obtained basic information on the mitochondrial genome of and this study investigated repeat sequences and homologous segments, predicted RNA editing sites, and utilized the ratio to estimate the selection pressure on mitochondrial genes of . We also discussed the systematic evolutionary position of based on mitochondrial genome sequences. Our study revealed variations in the sequence and structure of mitochondrial genomes in Caryophyllales. These findings are of great significance for identifying and improving valuable plant traits and serve as a reference for future molecular studies of

摘要

背景

（L. Henry）Holub 是一种常年半灌木，具有观赏和药用价值。植物的线粒体基因组包含有价值的遗传特征，可用于开发遗传资源。线粒体基因组的解析可以深入了解线粒体在植物生长发育、代谢调控、进化和对环境胁迫的响应中的作用。

方法

本研究使用 Illumina NovaSeq 6000 平台和 Nanopore 平台对的线粒体基因组进行了测序。我们对的线粒体基因组进行了全面分析，包括检查基因组成、重复序列、RNA 编辑位点、系统发育和细胞器基因组同源性等各个方面。为此，我们采用了序列比对分析、重复序列分析、系统发育分析等多种生物信息学方法。

结果

的线粒体基因组有 64 个基因，包括 34 个蛋白质编码基因（PCGs）、3 个 rRNA 和 27 个 tRNA。在线粒体基因组中检测到 77 个短串联重复序列，使用 Tandem Repeats Finder（TRF）鉴定了 5 个串联重复序列，观察到 50 个分散重复序列，包括 22 个正向重复序列和 28 个回文重复序列。在 PCGs 中预测到 367 个 RNA 编码位点，其中的数量最多（33 个）。大多数基因的值均小于 1，和三个近缘种 Caryophyllales 的线粒体基因。最大似然进化树显示和 × 最为密切相关。

结论

本研究获得了的线粒体基因组的基本信息，并对重复序列和同源片段进行了研究，预测了 RNA 编辑位点，并利用比值估计了的线粒体基因的选择压力。我们还根据线粒体基因组序列讨论了的系统进化地位。本研究揭示了 Caryophyllales 中线粒体基因组序列和结构的变异。这些发现对于鉴定和改进有价值的植物性状具有重要意义，并为未来的分子研究提供了参考。