Comparative mitogenomic analysis of three species of periwinkles: Littorina fabalis, L. obtusata and L. saxatilis

Abstract

The flat periwinkles, Littorina fabalis and L. obtusata, offer an interesting system for local adaptation and ecological speciation studies. In order to provide genomic resources for these species, we sequenced their mitogenomes together with that of the rough periwinkle L. saxatilis by means of next-generation sequencing technologies. The three mitogenomes present the typical repertoire of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a putative control region. Although the latter could not be fully recovered in flat periwinkles using short-reads due to a highly repetitive fragment, in L. saxatilis this problem was overcome with additional long-reads and we were able to assemble the complete mitogenome. Both gene order and nucleotide composition are similar between the three species as well as compared to other Littorinimorpha. A large variance in divergence was observed across mitochondrial regions, with six- to ten-fold difference between the highest and the lowest divergence rates. Based on nucleotide changes on the whole molecule and assuming a molecular clock, L. fabalis and L. obtusata started to diverge around 0.8 Mya (0.4-1.1 Mya). The evolution of the mitochondrial protein-coding genes in the three Littorina species appears mainly influenced by purifying selection as revealed by phylogenetic tests based on d/d ratios that did not detect any evidence for positive selection, although some caution is required given the limited power of the dataset and the implemented approaches.

Phylogeographic history of flat periwinkles, Littorina fabalis and L. obtusata

“…The previously proposed monophyly of flat periwinkles [39] was confirmed here. Our results suggest that the TMRCA of the two species is around 0.85 My ago, in agreement with previous estimates based on the entire mitogenome (0.8 My [40]). However, we need to take into account that both estimates are derived from mtDNA data and assume a molecular clock.…”

Relation between mitochondrial DNA hyperdiversity, mutation rate and mitochondrial genome evolution in Melarhaphe neritoides (Gastropoda: Littorinidae) and other Caenogastropoda

“…To this end, we conduct a comparative mitogenomic analysis of M. neritoides and the three other littorinid species whose mitogenomes have been sequenced, viz. Littorina fabalis , Littorina obtusata and Littorina saxatilis (hereafter referred to as “ Littorina sp.”) 25 , and extend this analysis to other Caenogastropoda. Melarhaphe neritoides is a caenogastropod that belongs to non-latrogastropod Hypsogastropoda, within which the family Naticidae is the closest phylogenetic relative, Hydrobiidae, Pomatiopsidae and Provannidae are more distant, and Cassidae, Cypraeidae, Ranellidae and Strombidae are the most distant relatives 26,27 .…”

Complete mitogenome of the noble volute Cymbiola nobilis from the Vietnamese Island of Phú Quốc

“…The control region of the C. nobilis mitogenome, located between cox3 and trnF, displays two copies of an inverted repeat sequence of about 500 bp that are separated by an AT-rich DNA segment. Long control regions with a similar structure have been observed in a few other Gastropoda mitogenomes where they account for their large size: for example, in the 16,887-bp mitogenome of Littorina saxatilis (Marques et al 2017) and in the 16,430-bp genome of Conus quercinus (Gao et al 2018). A phylogeny was inferred using the mitogenome sequences of 3 other taxa of the Volutidae, the Olividae Amalda northlandica and the Buccinidae Babylonia areolata as an outgroup.…”