文献类型：期刊文献

英文题名：A complete mitochondrial genome for fragrant Chinese rosewood (Dalbergia odorifera, Fabaceae) with comparative analyses of genome structure and intergenomic sequence transfers

作者：Hong, Zhou[1] Liao, Xuezhu[2] Ye, Yuanjun[3] Zhang, Ningnan[1] Yang, Zengjiang[1] Zhu, Weidong[2] Gao, Wei[2,4] Sharbrough, Joel[5] Tembrock, Luke R.[6] Xu, Daping[1] Wu, Zhiqiang[2]

第一作者：洪舟

通信作者：Xu, DP[1];Wu, ZQ[2];Tembrock, LR[3]

机构：[1]Chinese Acad Forestry, State Key Lab Tree Genet & Breeding, Res Inst Trop Forestry, Guangzhou 510520, Peoples R China;[2]Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Minist Agr,Shenzhen Branch, Genome Anal Lab,Guangdong Lab Lingnan Modern Agr, Shenzhen 518120, Peoples R China;[3]Guangdong Acad Agr Sci, Guangdong Prov Key Lab Ornamental Plant Germplasm, Environm Hort Res Inst, Guangzhou 510640, Peoples R China;[4]Huazhong Agr Univ, Coll Plant Sci & Technol, Wuhan 430070, Hubei, Peoples R China;[5]New Mexico Inst Min & Technol, Biol Dept, Socorro, NM 87801 USA;[6]Colorado State Univ, Dept Agr Biol, Ft Collins, CO 80523 USA

年份：2021

卷号：22

期号：1

外文期刊名：BMC GENOMICS

收录：;Scopus(收录号：2-s2.0-85115194910);WOS:【SCI-EXPANDED(收录号:WOS:000697528700001)】；

基金：This study was co-supported by the Research Funds for the Central Nonprofit Research Institution of Chinese Academy of Forestry (CAFYBB2017ZA001-7, CAFYBB2020SZ005) and National Natural Science Foundation of China (31500537). And this work was co-funded by the National Natural Science Foundation of China (31970244), Science, Technology and Innovation Commission of Shenzhen Municipality (STIC: RCYX20200714114538196).

语种：英文

外文关键词：Plant mitochondrial genome; Chloroplast genome; Horizontal gene transfer; Repetitive DNA; Phylogeny; Threatened species

摘要：Background 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. Results 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. Conclusion 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.