Methods for assembling complex mitochondrial genomes in land plants

Abstract

The large size and complex structural rearrangements inherent in mitochondrial genomes of land plants pose challenges for their sequencing. Originally, the assembly of these genomes required the cloning of mitochondrial DNA fragments, followed by Sanger sequencing. Subsequently, the advent of next-generation sequencing significantly expedited the process. This review highlights instances of plant mitochondrial genome assembly employing various technologies, including 454 sequencing, Illumina short sequencing reads, and Pacific Biosciences or Oxford Nanopore Technology long sequencing reads. The combination of short and long reads in hybrid assembly has proven to be the most efficient approach for achieving reliable assemblies of land plant mitochondrial genomes.

Chloroplast genome sequencing in winged bean (Psophocarpus tetragonolobus L.) and comparative analysis with other legumes

“…A large proportion of repeats were also found in the genes namely ycf2, ndhA, ndhF, rps12, rpl22, pafI and psaA, indicating potential functional implications. The prevalence of repeats in intergenic regions highlights their role in genomic rearrangements and evolutionary dynamics 120,121 . Leveraging these conserved patterns as genetic markers can enhance phylogenetic and population studies in legumes, providing insights into chloroplast genome evolution and plant adaptation [120][121][122] .…”

TIPPo: A User-Friendly Tool for De Novo Assembly of Organellar Genomes with HiFi Data

“…Compared to nuclear genomes, much less attention has been paid to the high-quality assembly of organellar genomes. Short read data are useful, with some caveats, for the assembly of the relatively small and conserved mitochondrial genomes of animals and chloroplast genomes of plants (Dierckxsens et al 2017;Jin et al 2020), but their utility is limited for the larger and more complex mitochondrial genomes of plants (Štorchová and Krüger 2024). Long and highly accurate read data have substantially enhanced our ability to assemble nuclear genomes (Wenger et al 2019;Sereika et al 2022).…”