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

Abstract

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.

The Complete Mitochondrial Genome of Ophioglossum vulgatum L. Is with Highly Repetitive Sequences: Intergenomic Fragment Transfer and Phylogenetic Analysis

“…The complete cp genome sequences have been extensively used to reconstruct plant phylogeny [ 3 , 21 ]. In contrast, mt genome sequences appear to have been relatively scarce in this respect [ 21 ].…”

“…The mitochondrion plays an important role in metabolic processes. It provides energy for eukaryotes and is the site of ATP synthesis [ 3 ]. The mitochondrial (mt) genomes of plants are large and complex, with a length of 200–2000 kbp and a variable structure [ 4 ].…”

“…Generally, transfers of mt sequences into cp genome occur much less frequently [ 15 , 16 ]. Typical events of intergenomic fragment transfers detected in higher plants include transfers of mt coxII gene into nucleus via RNA mediation [ 11 ] and cp photosynthesis-related genes or fragments into nuclear or mt genomes (Orobanchaceae) [ 14 , 17 ], cp sequences into nucleus (mitochondria as a bridge, Actinidia ) [ 18 ], and mt sequences into nucleus ( Dalbergia odorifera ) [ 3 ]. These findings suggest that intergenomic fragment transfers may reflect a common evolutionary phenomenon [ 14 ], underlining their importance for understanding plant mt genome evolution.…”

Comparative analysis of mitochondrial genomes of Broussonetia spp. (Moraceae) reveals heterogeneity in structure, synteny, intercellular gene transfer, and RNA editing

“…Plant mitogenomes have evolved from with dramatic and rapid structural changes, thus many unique features can be found compared with conserved plant plastomes and compact animal mitogenomes. These features include huge genome size variations, active multipartite arrangements, low gene density, abundant post-transcribed RNA editing, gene sequence transfer or loss, and foreign sequence capture ( Hong et al., 2021 ; Wu et al., 2022 ). Although plant mitogenomes are conventionally reported as circular structures, much like the circular chromosomes found in animal mitochondria and bacteria, many studies have shown that the simple circular model of genome structure that applies to most animal species is inadequate when trying to understand plant mitochondria that can have multiple circular replicons, branched, linear, or mixed forms of genomic structure, i.e., Silene noctiflora has a mitogenome that is arranged into numerous circular chromosomes, that is, one ring cannot rule them all ( Sloan, 2013 ; Wu et al., 2015 ) based on mapping to a circular reference.…”

Use of Sequencing Methods for Species Identification Exemplified by Phylogenetic Relationships Within Genus Hedysarum L.

“…angulari, Phaseolus vulgaris L., Cicer arietinum, Arachis hypogaea, Astragalus membranaceus var. mongholicus, Hedysarum polybotrys [8][9][10][11].…”