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.

Background: Mitochondria are organelles within eukaryotic cells that are central to the metabolic processes of cellular respiration and ATP production. However, the evolution of mitochondrial genomes (mitogenomes) in plants is virtually unknown compared to animal mitogenomes or plant plastids, due to complex structural variation and long stretches of repetitive DNA making accurate genome assembly more challenging. Comparing the structural and sequence differences of organellar genomes within and between sorghum species is an essential step in understanding evolutionary processes such as organellar sequence transfer to the nuclear genome as well as improving agronomic traits in sorghum related to cellular metabolism.Results: Here, we assembled seven sorghum mitochondrial and plastid genomes and resolved reticulated mitogenome structures with multilinked relationships that could be grouped into three structural conformations that differ in the content of repeats and genes by contig. The grouping of these mitogenome structural types reflects the two domestication events for sorghum in east and west Africa.Conclusions: We report seven mitogenomes of sorghum from different cultivars and wild sources. The assembly method used here will be helpful in resolving complex genomic structures in other plant species. Our findings give new insights into the structure of sorghum mitogenomes that provides an important foundation for future research into the improvement of sorghum traits related to cellular respiration, cytonuclear incompatibly, and disease resistance.

Mitochondrial genomes (mitogenomes) in plants exhibit substantial structural diversity, offering insights into evolutionary processes such as intracellular gene transfer (IGT), gene loss and genomic rearrangements. In this study, we present a detailed comparative analysis of the mitogenomes of four Dendrobium species (D. lasianthera, D. tangerinum, D. huoshanense and D. chrysotoxum), which are from the highly diverse Orchidaceae family. Using high-quality read data, including Illumina, PacBio and HiFi reads, we assembled and annotated their complete mitogenomes. Our findings reveal notable variability in mitogenome size (ranging from 485,249 to 773,276 bp), gene content (including differences in the number of protein-coding genes and tRNAs) and structural organization (such as conserved syntenic blocks and rearranged regions), reflecting the dynamic evolution of mitogenomes among these Dendrobium species. Notably, we observed high levels of simple sequence repeats (SSRs), with variations in repeat content across species, reflecting the dynamic nature of these genomes. Synteny analysis revealed extensive conserved genomic regions between the mitogenomes of D. lasianthera and D. tangerinum, indicating strong structural similarity. In contrast, other species pairs such as D. lasianthera and D. huoshanense, or D. tangerinum and D. chrysotoxum, exhibited weaker syntenic relationships, reflecting a greater degree of structural variation in their mitogenomes. Furthermore, our analysis identified IGT between mitogenome and plastome, providing clear evidence that IGT has contributed to the mitogenome evolution of these species. Phylogenetic analysis based on mitogenome coding sequences (CDSs) revealed a well-supported topology within Dendrobium, identifying D. lasianthera and D. tangerinum as closely related sister species. Although our sampling is limited to four Dendrobium species, the mitogenome CDS data still provide informative phylogenetic signals and offer complementary insights when interpreted alongside plastid-based phylogenies. This study provides new insights into the structural and genomic diversity of mitogenomes in Dendrobium and contributes to the broader understanding of mitogenome evolution in plants.

The chloroplast is one of two organelles containing a separate genome that codes for essential and distinct cellular functions such as photosynthesis. Given the importance of chloroplasts in plant metabolism, the genomic architecture and gene content have been strongly conserved through long periods of time and as such are useful molecular tools for evolutionary inferences. At present, complete chloroplast genomes from over 4000 species have been deposited into publicly accessible databases. Despite the large number of complete chloroplast genomes, comprehensive analyses regarding genome architecture and gene content have not been conducted for many lineages with complete species sampling. In this study, we employed the genus Populus to assess how more comprehensively sampled chloroplast genome analyses can be used in understanding chloroplast evolution in a broadly studied lineage of angiosperms. We conducted comparative analyses across Populus in order to elucidate variation in key genome features such as genome size, gene number, gene content, repeat type and number, SSR (Simple Sequence Repeat) abundance, and boundary positioning between the four main units of the genome. We found that some genome annotations were variable across the genus owing in part from errors in assembly or data checking and from this provided corrected annotations. We also employed complete chloroplast genomes for phylogenetic analyses including the dating of divergence times throughout the genus. Lastly, we utilized re-sequencing data to describe the variations of pan-chloroplast genomes at the population level for P. euphratica. The analyses used in this paper provide a blueprint for the types of analyses that can be conducted with publicly available chloroplast genomes as well as methods for building upon existing datasets to improve evolutionary inference.

The Mendelian pea (Pisum sativa), a member of the Fabaceae family, is widely cultivated worldwide as an important food resource. While extensive genetic studies have been conducted on pea, a comprehensive pan-plastome assembly has not yet been achieved. The present study combined 103 newly assembled pea plastomes with 42 previously published plastomes to construct the first pea pan-plastome. The lengths of plastomes varied from 120,826 to 122,547 bp, with an average GC content of 34.8%. Protein-coding genes in the pan-plastome exhibited a strong bias towards A/T in the third codon position, with a notably high frequency of the amino acid arginine (RSCU value = 4.8) among plastome-encoded proteins. Additionally, the codon usage of petB, psbA, rpl16, rps14, and rps18 showed extreme influence from natural selection. Moreover, the genes ycf1, rpoC2, and matK were identified as hypervariable regions, suggesting their potential utility as DNA barcoding loci to distinguish maternal lineages for breeding and other agronomic purpose. The phylogenetic results indicated that cultivated peas had undergone at least two independent domestications, originating from the PA and PS groups. Compared to former research based on nuclear data, the PSeI-a group and PSeI-b group were newly found branched between the PA group and PF group.