Genomic signatures of mitonuclear coevolution across populations of Tigriopus californicus

Abstract

The copepod Tigriopus californicus shows extensive population divergence and is becoming a model for understanding allopatric differentiation and the early stages of speciation. Here, we report a high-quality reference genome for one population (~190 megabases across 12 scaffolds, and ~15,500 protein-coding genes). Comparison with other arthropods reveals 2,526 genes presumed to be specific to T. californicus, with an apparent proliferation of genes involved in ion transport and receptor activity. Beyond the reference population, we report re-sequenced genomes of seven additional populations, spanning the continuum of reproductive isolation. Populations show extreme mitochondrial DNA divergence, with higher levels of amino acid differentiation than observed in other taxa. Across the nuclear genome, we find elevated protein evolutionary rates and positive selection in genes predicted to interact with mitochondrial DNA and the proteins and RNA it encodes in multiple pathways. Together, these results support the hypothesis that rapid mitochondrial evolution drives compensatory nuclear evolution within isolated populations, thereby providing a potentially important mechanism for causing intrinsic reproductive isolation.

The genome and mRNA transcriptome of the cosmopolitan calanoid copepod Acartia tonsa Dana improve the understanding of copepod genome size evolution

“…We chose eight complete genes for analysis, as these eight genes aligned across the database and our A. tonsa resource. Extreme mitochondrial DNA divergence has previously been reported even within the copepod species T. californicus, why it is not surprising that not all copepod mitochondrial genes align across orders [7]. The genes used for phylogenetic placement of A. tonsa can be found in Table 2 between Calanoida and the other Copepod orders correlates closely with recent phylogenetic work on copepod orders where the calanoid species form the superorder Gymnoplea while the other copepods form the superorder Podoplea [33,34].…”

“…Yet, only five copepod genomes have hitherto been published. The five species are the calanoid Eurytemora affinis [5], the cyclopoid Oithona nana [6], the harpacticoid Tigriopus californicus [7] and Caligus rogercresseyi and Lepeophtheirus salmonis, which both belong to the order Siphonostomatoida and are important pests in salmon aquaculture [8].…”

Genomic scans reveal multiple mito‐nuclear incompatibilities in population crosses of the copepod Tigriopus californicus

“…We followed the same procedure to create consensus reference genomes for CAT and SC by extracting the consensus sequences from the BAM files (CAT and SC reads mapped to the SD reference) using the Samtools and Bcftools pipeline Li 2011). We then compared the references between each pair of populations used in the three crosses, and made them equivalent by adding "Ns" to any position where either the AB or the alternative populations also had an "N." This maintains the length of the references, but makes them comparable in terms of where reads can map, which is particularly important when the SD reference is considered (this population was de novo assembled, using diverse sequence sets, into a high-quality assembly; Barreto et al 2018). The purpose of creating these references is to allow the mapping of reads from both parental populations as well as hybrids, to identify SNPs that are fixed between populations in each cross.…”

CyMIRA: The Cytonuclear Molecular Interactions Reference forArabidopsis

“…For example, classic studies in animals have taken advantage of OXPHOS complex II (succinate dehydrogenase), which is entirely nuclear-encoded, in order to make comparisons with the other OXPHOS complexes, which are all chimeric (Ellison and Burton 2006). In the current genomic era, it has become increasingly popular for evolutionary studies to partition nuclear gene content into categories based on whether they are targeted to mitochondria/plastids and whether they are involved in direct molecular interactions with cytoplasmic genomes and gene products within these organelles Rogell, et al 2014;Pett and Lavrov 2015;Zhang, et al 2015;Adrion, et al 2016;Rockenbach, et al 2016;Zhang, et al 2016;Eslamieh, et al 2017;Barreto, et al 2018;Forsythe, et al 2018;Morales, et al 2018;Ferreira, et al 2019;Li, et al 2019;Yan, et al 2019;Zaidi and Makova 2019). Such approaches are an effective means to investigate the evolutionary effect of organelle targeting and molecular interactions.…”