Dalbergia odorifera is an economically and culturally important species in the Fabaceae because of the high-quality lumber and traditional Chinese medicines made from this plant, however, overexploitation has increased the scarcity of D. odorifera. Given the rarity and the multiple uses of this species, it is important to expand the genomic resources for utilizing in applications such as tracking illegal logging, determining effective population size of wild stands, delineating pedigrees in marker assisted breeding programs, and resolving gene networks in functional genomics studies. Even the nuclear and chloroplast genomes have been published for D. odorifera, the complete mitochondrial genome has not been assembled or assessed for sequence transfer to other genomic compartments until now. Such work is essential in understanding structural and functional genome evolution in a lineage (Fabaceae) with frequent intergenomic sequence transfers. We integrated Illumina short-reads and PacBio CLR long-reads to assemble and annotate the complete mitochondrial genome of D. odorifera. The mitochondrial genome was organized as a single circular structure of 435 Kb in length containing 33 protein coding genes, 4 rRNA and 17 tRNA genes. Nearly 4.0% (17,386 bp) of the genome was annotated as repetitive DNA. From the sequence transfer analysis, it was found that 114 Kb of DNA originating from the mitochondrial genome has been transferred to the nuclear genome, with most of the transfer events having taken place relatively recently. The high frequency of sequence transfers from the mitochondria to the nuclear genome was similar to that of sequence transfer from the chloroplast to the nuclear genome. For the first-time, the complete mitochondrial genome of D. odorifera was assembled in this study, which will provide a baseline resource in understanding genomic evolution in the highly specious Fabaceae. In particular, the assessment of intergenomic sequence transfer suggests that transfers have been common and recent indicating a possible role in environmental adaptation as has been found in other lineages. The high turnover rate of genomic colinearly and large differences in mitochondrial genome size found in the comparative analyses herein providing evidence for the rapid evolution of mitochondrial genome structure compared to chloroplasts in Faboideae. While phylogenetic analyses using functional genes indicate that mitochondrial genes are very slowly evolving compared to chloroplast genes.

中文翻译：

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香紫檀（Dalbergia odorifera, Fabaceae）的完整线粒体基因组与基因组结构和基因组间序列转移的比较分析

黄檀是豆科植物中的重要经济和文化物种，因为该植物的优质木材和中药材，但过度开发增加了 D. odorifera 的稀缺性。鉴于该物种的稀有性和多种用途，重要的是扩大基因组资源以用于跟踪非法采伐、确定野生林分的有效种群规模、在标记辅助育种计划中描绘谱系以及解析基因网络等应用。功能基因组学研究。即使已经公布了 D. odorifera 的核和叶绿体基因组，但直到现在还没有组装或评估完整的线粒体基因组以将序列转移到其他基因组区室。这些工作对于理解具有频繁基因组间序列转移的谱系（豆科）的结构和功能基因组进化至关重要。我们整合了 Illumina 短读长和 PacBio CLR 长读长来组装和注释 D. odorifera 的完整线粒体基因组。线粒体基因组被组织为长度为 435 Kb 的单个环状结构，其中包含 33 个蛋白质编码基因、4 个 rRNA 和 17 个 tRNA 基因。近 4.0% (17,386 bp) 的基因组被注释为重复 DNA。从序列转移分析中发现，来自线粒体基因组的 114 Kb DNA 已转移到核基因组，大多数转移事件发生在最近。从线粒体到核基因组的序列转移频率与从叶绿体到核基因组的序列转移频率相似。在这项研究中首次组装了 D. odorifera 的完整线粒体基因组，这将为理解高度似是而非的豆科植物的基因组进化提供基线资源。特别是，基因组间序列转移的评估表明，转移很常见，而且最近表明在环境适应中可能发挥作用，正如在其他谱系中发现的那样。在本文的比较分析中发现的基因组共线的高周转率和线粒体基因组大小的巨大差异为与 Faboideae 中的叶绿体相比线粒体基因组结构的快速进化提供了证据。