Comparative Mitogenomics in Hyalella (Amphipoda: Crustacea)

Abstract

We present the sequencing and comparative analysis of 17 mitochondrial genomes of Nearctic and Neotropical amphipods of the genus Hyalella, most from the Andean Altiplano. The mitogenomes obtained comprised the usual 37 gene-set of the metazoan mitochondrial genome showing a gene rearrangement (a reverse transposition and a reversal) between the North and South American Hyalella mitogenomes. Hyalella mitochondrial genomes show the typical AT-richness and strong nucleotide bias among codon sites and strands of pancrustaceans. Protein-coding sequences are biased towards AT-rich codons, with a preference for leucine and serine amino acids. Numerous base changes (539) were found in tRNA stems, with 103 classified as fully compensatory, 253 hemi-compensatory and the remaining base mismatches and indels. Most compensatory Watson–Crick switches were AU -> GC linked in the same haplotype, whereas most hemi-compensatory changes resulted in wobble GU and a few AC pairs. These results suggest a pairing fitness increase in tRNAs after crossing low fitness valleys. Branch-site level models detected positive selection for several amino acid positions in up to eight mitochondrial genes, with atp6 and nad5 as the genes displaying more sites under selection.

Comparative mitogenomic analyses provide evolutionary insights into the retrolateral tibial apophysis clade (Araneae: Entelegynae)

“…The atp8 gene had the highest Ka/Ks value, consistent with the previously identified Ka/Ks ratios in spider species (Kumar et al, 2020;Li et al, 2021), and insects (Chakraborty et al, 2018;Li et al, 2019;Chang et al, 2020;Ye et al, 2021). It has been reported that different mitochondrial PCGs evolved at different rates (Li et al, 2012;Zapelloni et al, 2021), as has been found in RTA species. The Ka/Ks ratios of atp8 >1 indicated that atp8 was under strong pressure of positive selection and might evolve more quickly than the other 12 PCGs in the spider mitogenomes (Chen et al, 2021;Li et al, 2021).…”

“…However, the strength of the skews in the mitogenomes of the RTA clade showed the opposite pattern, indicating that the J-strands of these mitogenomes have strand asymmetry reversal and favored T and G. This seemed to be a common phenomenon in Araneae Frontiers in Genetics frontiersin.org (Wang et al, 2016). And similar modes of nucleotide skew were also found in mitogenomes of some arthropod taxa, such as those of scorpions (Masta et al, 2009), insects (Monnens et al, 2020;Yan et al, 2021) and other arthropods (Zapelloni et al, 2021). Through comparison of the nucleotide skews among all the sequenced spider mitogenomes, the divergence between the two suborders was detected (Wang et al, 2016).…”

“…The atp8 gene was a core subunit of the Complex V (ATP synthase), which played an important role in phosphorylating ADP to synthesize an adenosine triphosphate molecule ( Finch et al, 2014 ). Positive selection was found in genes involved in the OXPHOS pathway, i.e., atp6 ( Li et al, 2018 ; Yuan et al, 2020 ; Zapelloni et al, 2021 ), nad5 ( Li et al, 2018 ; Yuan et al, 2020 ; Zapelloni et al, 2021 ), and atp8 ( Li et al, 2018 ; Zapelloni et al, 2021 ), suggesting that the evolution of energy metabolism genes was critical for adaptation to new environments ( Castoe et al, 2008 ; Castoe et al, 2013 ). The atp8 gene in RTA mitogenomes may have experienced a positive selection in adaption to the environment.…”

Exploring mitogenome evolution in Branchiopoda (Crustacea) lineages reveals gene order rearrangements in Cladocera

“…In a recent survey in Hexapoda, one of the most studied groups of metazoans, about 47% of mitogenomes were found rearranged with respect to the PanGO pattern, which is the prevalent GO in the class 32 . In non-branchiopod crustacean taxa, although much less studied, still several variations with respect to the PanGO pattern have been observed: for example, in Decapoda 26 , 28 , 29 , Amphipoda 23 , 31 , Copepoda 24 , 27 and Ostracoda 22 , 30 .…”

“…For example, the close evolutionary relationship between crustaceans and insects, which are in fact both included in the Pancrustacea clade 18 , 19 , has been further confirmed by the sharing of the same mitogenomic GO (the PanGO pattern), which differs from the so-called ancestral arthropod GO (AAGO pattern) by a single tRNA displacement 20 , 21 . Given the many examples of GO rearrangements in pancrustaceans at different taxonomic levels 22 – 31 , the analysis of GO synapomorphy, which may be particularly helpful in phylogenetic reconstruction, may be difficult 25 . In addition to this, several examples of GO parallel evolution have been reported in hexapods 32 .…”