Complete mitochondrial genome of Odontobutis haifengensis (Perciformes, Odontobutiae): A unique rearrangement of tRNAs and additional non-coding regions identified in the genus Odontobutis

Lee

et al. 2020

Sci Rep

Taiwanofungus camphoratus is a highly valued medicinal mushroom that is endemic to Taiwan, China. In the present study, the mitogenome of T. camphoratus was assembled and compared with other published Polyporales mitogenomes. The T. camphoratus mitogenome was composed of circular DNA molecules, with a total size of 114,922 bp. Genome collinearity analysis revealed large-scale gene rearrangements between the mitogenomes of Polyporales, and T. camphoratus contained a unique gene order. The number and classes of introns were highly variable in 12 Polyporales species we examined, which proved that numerous intron loss or gain events occurred in the evolution of Polyporales. The Ka/Ks values for most core protein coding genes in Polyporales species were less than 1, indicating that these genes were subject to purifying selection. However, the rps3 gene was found under positive or relaxed selection between some Polyporales species. Phylogenetic analysis based on the combined mitochondrial gene set obtained a well-supported topology, and T. camphoratus was identified as a sister species to Laetiporus sulphureus. This study served as the first report on the mitogenome in the Taiwanofungus genus, which will provide a basis for understanding the phylogeny and evolution of this important fungus.

Section: Discussionmentioning

confidence: 99%

“…The arrangement of mitochondrial genes can also serve as an important reference for revealing phylogenetic relationships among species 68 – 70 . In this study, we found that the arrangement of mitochondrial genes was highly variable in Polyporales .…”

Section: Discussionmentioning

confidence: 99%

The complete mitochondrial genome of medicinal fungus Taiwanofungus camphoratus reveals gene rearrangements and intron dynamics of Polyporales

Lee

et al. 2020

Sci Rep

“…The first step was to obtain the sequences of the 16S rRNA, COI and Cyt b genes by PCR with universal primers [ 5 , 22 , 23 ], and the sequence gaps in these mitochondrial genes can then be obtained by the specific primers designed based on the known sequences listed above; the resulting fragments of the PCR products, obtained with only seven sets of PCR primers, are shorter than 3000 bp and can be sequenced by Sanger sequencing. Compared to other sequencing methods, such as PCR amplification with multiple PCR primer pairs (> 15) [ 21 , 24 ] and next-generation sequencing [ 13 , 19 ], our strategy can avoid nonspecific amplification or other problems resulting from sequence assembly.…”

Section: Discussionmentioning

confidence: 99%

Complete mitochondrial genome of Iniistius trivittatus and unique variation in two observed inserts between rRNA and tRNA genes in wrasses

Liu¹,

Zhang²,

Zhang

et al. 2020

BMC Evol Biol

Background The family Labridae made up of 519 species in the world. The functional evolution of the feeding-related jaws leaded to differentiation of species, and the pharyngeal jaw apparatus evolved independently, but evolutionary mechanism still remain unaddressed in wrasses. Mitogenomes data can be used to infer genetic diversification and investigate evolutionary history of wrasses, whereas only eight complete mitogenomes in this family have been sequenced to date. Here, we sequenced the complete mitogenomes of Iniistius trivittatus to investigate genetic differentiation among wrasse species. Results We sequenced the complete mitogenomes of I. trivittatus using a novel PCR strategy. The I. trivittatus mitogenomes is 16,820 bp in length and includes 13 protein -coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region. Compared to eight known mitochondrial genome, 2 additional noncoding regions (lengths of 121 and 107 bp), or so-called inserts, are found in the intergenic regions 12S rRNA - tRNAVal - 16S rRNA. The presumed origin of the two rare inserts is from tRNA- related retrotransposons. Compared with cytochrome b gene, the two insert sequences are highly conserved at the intraspecies level, but they showed significant variation and low similarity (< 70%) at the interspecies level. The insert events were only observed in I. trivittatus by checking the phylogenetic trees based on the complete mitogenomes of Labrida species. This finding provides evidence that in the mitogenomes, retrotransposon inserts result in intraspecific homoplasmy and interspecific heteroplasmy by natural selection and adaptation to various environments. Conclusions This study found additional mitogenome inserts limited in wrasse species. The rRNA genes with inserts might have experienced a selective pressure for adaptation to feeding modes. Such knowledge can enable a better understanding of molecular mechanism underlying morphological evolution in wrasses.

“…To test the utility of selected markers for studies at the species level, we reconstructed a species tree of four species of freshwater sleepers ( Odontobutis , Gobiiformes), whose relationships are unresolved (Ren & Zhang, ; Zhong et al, ). The species tree was reconstructed based on exon capture data of the chosen markers, including five individuals of each species of Odontobutis sinensis , O. potamophila, and O. yaluensis and one individual of O. haifengensis .…”

Section: Methodsmentioning

confidence: 99%

“…To test the utility of selected markers for studies at the species level, we reconstructed a species tree of four species of freshwater sleepers (Odontobutis, Gobiiformes), whose relationships are unresolved (Ren & Zhang, 2007;Zhong et al, 2017). ASTRAL v4.11.1 (Mirarab & Warnow, 2015) was used to infer the species tree.…”

Section: Testing Phylogenetic Usefulness Of the Markers Selected Anmentioning

confidence: 99%

Gene markers for exon capture and phylogenomics in ray‐finned fishes

Jiang

Yuan

Zheng

et al. 2019

Ecology and Evolution

Gene capture coupled with the next‐generation sequencing has become one of the preferred methods of subsampling genomes for phylogenomic studies. Many exon markers have been developed in plants, sharks, frogs, reptiles, fishes, and others, but no universal exon markers have been tested in ray‐finned fishes. Here, we identified a suite of “single‐copy” protein‐coding sequence (CDS) markers through comparing eight fish genomes, and tested them empirically in 83 species (33 families and nine orders or higher clades: Acipenseriformes, Lepisosteiformes, Elopomorpha, Osteoglossomorpha, Clupeiformes, Cypriniformes, Gobiaria, Carangaria, and Eupercaria; sensu Betancur et al. 2013). Sorting the markers according to their completeness and phylogenetic decisiveness in taxa tested resulted in a selection of 4,434 markers, which were proven to be useful in reconstructing phylogenies of the ray‐finned fishes at different taxonomic levels. We also proposed a strategy of refining baits (probes) design a posteriori based on empirical data. The markers that we have developed may greatly enrich the batteries of exon markers for phylogenomic study in ray‐finned fishes.