Long-read Sequencing Data Reveals Dynamic Evolution of Mitochondrial Genome Size and the Phylogenetic Utility of Mitochondrial DNA in Hercules Beetles (Dynastes; Scarabaeidae). | LitMetric
The evolutionary dynamics and phylogenetic utility of mitochondrial genomes (mitogenomes) have been of particular interest to systematists and evolutionary biologists. However, certain mitochondrial features, such as the molecular evolution of the control region in insects, remain poorly explored due to technological constraints. Using a combination of long- and short-read sequencing data, we assembled ten complete mitogenomes from ten Hercules beetles. We found large-sized mitogenomes (from 24 to 28 kb), which are among the largest in insects. The variation in genome size can be attributed to copy-number evolution of tandem repeats in the control region. Furthermore, one type of tandem repeat was found flanking the conserved sequence block in the control region. Importantly, such variation, which made up around 30% of the size of the mitogenome, may only become detectable should long-read sequencing technology be applied. We also found that, although different mitochondrial loci often inferred different phylogenetic histories, none of the mitochondrial loci statistically reject a concatenated mitochondrial phylogeny, supporting the hypothesis that all mitochondrial loci share a single genealogical history. We on the other hand reported statistical support for mito-nuclear phylogenetic discordance in 50% of mitochondrial loci. We argue that long-read DNA sequencing should become a standard application in the rapidly growing field of mitogenome sequencing. Furthermore, mitochondrial gene trees may differ even though they share a common genealogical history, and ND loci could be better candidates for phylogenetics than the commonly used COX1.
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA. Electronic address:
Interactions between distal loci, including those involving enhancers and promoters, are a central mechanism of gene regulation in mammals, yet the protein regulators of these interactions remain largely undetermined. The zinc-finger transcription factor (TF) ZNF143/ZFP143 has been strongly implicated as a regulator of chromatin interactions, functioning either with or without CTCF. However, how ZNF143/ZFP143 functions as a looping factor is not well understood.
Effective conservation strategies inherently depend on preserving populations, which in turn requires accurate tools for their detection. Beluga whales () inhabit the circumpolar Arctic and form discrete summer aggregations. Previous genetic studies using mitochondrial and microsatellite loci have delineated distinct populations associated to summer aggregations but the extent of dispersal and interbreeding among these populations remains largely unknown.
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
is a cosmopolitan aquatic plant genus that includes species with widespread global distributions. In previous studies, a revised molecular phylogeny was inferred using seven plastid loci from nine species across different geographic regions. By utilizing complete organellar genomes, we aim to provide a more comprehensive dataset that offers a robust phylogenetic signal for resolving species evolutionary relationships.
Background: The salmon louse (Lepeophtheirus salmonis) is a parasite of wild and farmed salmonid fish, causing huge economic damage to the commercial farming of Atlantic salmon (Salmo salar) in the northern hemisphere. The avermectin emamectin benzoate (EMB) is widely used for salmon delousing. While resistance to EMB is widespread in Atlantic populations of L.
Molecular genetic analyses are effective in revealing the origin, kinship, and genetic diversity of zoo animals. In this study, we carried out the genetic characterization of captive founder individuals of the South American fur seal (Arctocephalus australis) in Japanese zoos and aquariums based on analyses of mitochondrial sequences and nuclear microsatellite loci. In mitochondrial DNA analysis, the haplotype diversity and nucleotide diversity of the overall population were 0.
