Comparative genomic analysis of vertebrate mitochondrial reveals a differential of rearrangements rate between taxonomic class

Abstract

Vertebrate mitochondrial genomes have been extensively studied for genetic and evolutionary purposes, these are normally believed to be extremely conserved, however, different cases of gene rearrangements have been reported. To verify the level of rearrangement and the mitogenome evolution, we performed a comparative genomic analysis of the 2831 vertebrate mitochondrial genomes representing 12 classes available in the NCBI database. Using a combination of bioinformatics methods, we determined there is a high number of errors in the annotation of mitochondrial genes, especially in tRNAs. We determined there is a large variation in the proportion of rearrangements per gene and per taxonomic class, with higher values observed in Actinopteri, Amphibia and Reptilia. We highlight that these are results for currently available vertebrate sequences, so an increase in sequence representativeness in some groups may alter the rearrangement rates, so in a few years it would be interesting to see if these rates are maintained or altered with the new mitogenome sequences. In addition, within each vertebrate class, different patterns in rearrangement proportion with distinct hotspots in the mitochondrial genome were found. We also determined that there are eleven convergence events in gene rearrangement, nine of which are new reports to the scientific community.

Complete Mitogenomes of Ticks Ixodes acutitarsus and Ixodes ovatus Parasitizing Giant Panda: Deep Insights into the Comparative Mitogenomic and Phylogenetic Relationship of Ixodidae Species

“…Gene arrangement comparison is an important tool for resolving deep-level phylogenetic relationships [ 97 , 98 ]. Genome rearrangement analysis is a routine analysis in comparative mitochondrial genomics [ 33 , 72 , 73 , 99 , 100 , 101 ]. Regarding the Ixodidae mitogenomes, Black and Roehrdanz first reported two gene arrangement types [ 102 ], and Shao et al further summed up three types [ 59 ], which were confirmed by another study [ 76 ].…”

Mitochondrial genome evolution in the Diprionidae: Major gene rearrangement in the basal Hymenoptera

“…Genomic architecture is probably the most fruitful Genome-level character, with new findings including two co-existing and divergent mt-molecules in single individuals in vertebrate [2] and invertebrates [3], changes in the transcriptional orientations of genes [2], architectural variation of individual genes [4], etc.. Recent meta-analysis [5,6] reinforced more variable rearrangements than anticipated, and identified convergence events. However, as taxonomy experience shows, evolution patterns differ along ranks [7,8].…”

Heteroplasmy and tandem repeats reveal adaptation to elevation in the New World Jays (Aves: Corvidae)

“…Older methods can produce inaccuracies due to the amplification of nuclear mitochondrial DNA segments (NUMTs), the variation of sequences at primer bonding sites and changes in gene structure (Mueller & Boore, 2005; Cameron, 2014; Parakatselaki et al, 2022). On the other hand, mitogenomes still present challenges that only LRS can overcome, such as accurately capturing gene arrangements, long TRs and long duplications (Konrad et al, 2017; Torres et al, 2019; Zardoya, 2020; Montaña-Lozano et al, 2022).…”