Master graph: an essential integrated assembly model for the plant mitogenome based on a graph-based framework

Abstract

Unlike the typical single circular structure of most animal mitochondrial genomes (mitogenome), the drastic structural variation of plant mitogenomes is a result of a mixture of molecules of various sizes and structures. Obtaining the full panoramic plant mitogenome is still considered a roadblock in evolutionary biology. In this study, we developed a graph-based sequence assembly toolkit (GSAT) to construct the pan-structural landscape of plant mitogenome with high-quality mitochondrial master graphs (MMGs) for model species including rice (Oryza sativa) and thale cress (Arabidopsis thaliana). The rice and thale cress MMGs have total lengths of 346 562 and 358 041 bp, including 9 and 6 contigs and 12 and 8 links, respectively, and could be further divided into 6 and 3 minimum master circles and 4 and 2 minimum secondary circles separately. The nuclear mitochondrial DNA segments (NUMTs) in thale cress strongly affected the frequency evaluation of the homologous structures in the mitogenome, while the effects of NUMTs in rice were relatively weak. The mitochondrial plastid DNA segments (MTPTs) in both species had no effects on the assessment of the MMGs. All potential recombinant structures were evaluated, and the findings revealed that all, except for nuclear-homologous structures, MMG structures are present at a much higher frequency than non-MMG structures are. Investigations of potential circular and linear molecules further supported multiple dominant structures in the mitogenomes and could be completely summarized in the MMG. Our study provided an efficient and accurate model for assembling and applying graph-based plant mitogenomes to assess their pan-structural variations.

Mitochondrial Genome Sequence of Salvia officinalis (Lamiales: Lamiaceae) Suggests Diverse Genome Structures in Cogeneric Species and Finds the Stop Gain of Genes through RNA Editing Events

“…In cultured Chenopodium album (L.) cells, linear, circular, sigma-like, branched, and rosette-like structures were observed by electron microscopy [ 29 ]. The plant mitogenomes assembled from high-throughput DNA sequencing data are also found to have complex structures [ 30 ]. For example, the cucumber mitogenome was assembled into a single circular master chromosome and a collection of sub-master circular chromosomes [ 31 ].…”

“…In this case, they are best represented with a graph. Recently, a graph-based sequence assembly toolkit (GSAT) was developed to assemble and obtain high-quality mitochondrial master graphs (MMGs) to represent the full spectrum of structural conformations of plant mitogenomes [ 30 ], demonstrating another level of mitogenomic structural diversity.…”

Mitochondrial genome variation and intergenomic sequence transfers in Hevea species

“…The short reads were filtered using Trimmomatic v0.38 ( Bolger et al., 2014 ), and their de novo assembly was performed using SPAdes v3.5.0 with different K-mer parameters ( Bankevich et al., 2012 ). GSAT software ( He et al., 2022 ) was used to calculate the mitochondrial genome graph-based framework, the genomic structure maps of H. camargoana and H. spruceana mitochondria shows complex relationships between genomic sequences ( Supplementary Figure S2 ). The obtained PacBio reads were de novo assembled using canu v2.2 and PAMT ( Koren et al., 2017 ; Bi et al., 2024 ) in hifi mode, with a genome size set to 2M, and default parameters for the rest, and the draft assemblies were polished by Pilon ( Walker et al., 2014 ).…”

“…At the same time, mitochondrial protein-coding genes are conserved, hence a potential for addressing unresolved phylogenetic questions ( Tian et al., 2006 ; Hao et al., 2022 ). With the continuous development of sequencing technology and assembly methods ( He et al., 2022 ), more and more plant mitochondrial genomes have been sequenced. In previous studies, we sequenced the complete nuclear genome of rubber tree ( Liu et al., 2020 ).…”

Complete mitochondrial genome of Angelica dahurica and its implications on evolutionary analysis of complex mitochondrial genome architecture in Apiaceae

“…Furthermore, these rearrangements play a crucial role in the regulation of gene expression and mitochondrial function, underscoring the importance of understanding mitochondrial genome architecture in plant biology and breeding strategies ( Yang et al., 2022 ). More graph-based assembly tools have been published, including GSAT and PMAT ( He et al., 2023 ; Wang et al., 2024 ).…”