Comparative mitogenome analyses uncover mitogenome features and phylogenetic implications of the subfamily Cobitinae

Background Loaches of Cobitinae, widely distributed in Eurasian continent, have high economic, ornamental and scientific value. However, the phylogeny of Cobitinae fishes within genera or family level remains complex and controversial. Up to now, about 60 Cobitinae mitogenomes had been deposited in GenBank, but their integrated characteristics were not elaborated. Results In this study, we sequenced and analyzed the complete mitogenomes of a female Cobits macrostigma. Then we conducted a comparative mitogenome analysis and revealed the conserved and unique characteristics of 58 Cobitinae mitogenomes, including C. macrostigma. Cobitinae mitogenomes display highly conserved tRNA secondary structure, overlaps and non-coding intergenic spacers. In addition, distinct base compositions were observed among different genus and significantly negative linear correlation between AT% and AT-skew were found among Cobitinae, genus Cobitis and Pangio mitogenomes, respectively. A specific 3 bp insertion (GCA) in the atp8-atp6 overlap was identified as a unique feature of loaches, compared to other Cypriniformes fish. Additionally, all protein coding genes underwent a strong purifying selection. Phylogenetic analysis strongly supported the paraphyly of Cobitis and polyphyly of Misgurnus. The strict molecular clock predicted that Cobitinae might have split into northern and southern lineages in the late Eocene (42.11 Ma), furthermore, mtDNA introgression might occur (14.40 Ma) between ancestral species of Cobitis and ancestral species of Misgurnus. Conclusions The current study represents the first comparative mitogenomic and phylogenetic analyses within Cobitinae and provides new insights into the mitogenome features and evolution of fishes belonging to the cobitinae family.

Structural Features and Phylogenetic Implications of Two New Mitogenomes of Erythroneurine Leafhoppers (Hemiptera: Cicadellidae: Typhlocybinae)

Background: Complete mitochondrial genome sequences facilitate species identification and analyses of phylogenetic relationships. However, the available data are limited for the diverse and widespread insect familiy Cicadellidae. In this study, we sequenced complete mitochondrial genomes of two species of Erythroneurini. Results: The mitogenomes of Empoascanara wengangensis and E. gracilis were 14,830 and 14,627 bp in length, respectively, and similar to other published leafhopper mitogenomes in terms of gene size, base composition, gene order, PCGs codon usage, and tRNA secondary structure. Most protein coding genes start with ATN and end with TAA or TAG. Two rRNA genes are highly conserved and encoded on the minority strand, and the AT content in 16S is higher than that of 12S. The control regions in the genus Empoascanara are highly variable and contain various numbers of repeat sequences. Conclusions: The mitogenomes of these two species closely resemble those of most other sequenced leafhoppers in various structural and compositional aspects. Phylogenetic analysis of 13 PCGs yielded a well-supported topology with most branches receiving maximum support and most relationships agreeing with those of other recent phylogenetic studies. Nucleotide diversity analysis show that nad4 and nad5 can be evaluated as potential DNA markers that define the Cicadellidae insect species. Like other studies, the main evolutionary event of leafhoppers occurred in the Tertiary, and its divergence time is estimated to be 10.03~122.48 Ma. This study confirms results of previous studies indicating that mitochondrial genome sequences are informative of leafhopper phylogeny.

Mytilus Mitochondrial DNA Contains a Functional Gene for a tRNASer(UCN) With a Dihydrouridine Arm-Replacement Loop and a pseudo-tRNASer(UCN) Gene

A 2500-nucleotide pair (ntp) sequence of F-type mitochondrial (mt) DNA of the Pacific Rim mussel Mytilus californianus (class Bivalvia, phylum Mollusca) that contains two complete (ND2 and ND3) and two partial (COI and COIII) protein genes and nine tRNA genes is presented. Seven of the encoded tRNAs (Ala, Arg, His, Met(AUA), Pro, Ser(UCN), and Trp) have the potential to fold into the orthodox four-armed tRNA secondary structure, while two [tRNASer(AGN) and a second tRNASer(UCN)] will fold only into tRNAs with a dihydrouridine (DHU) arm-replacement loop. Comparison of these mt-tRNA gene sequences with previously published, corresponding M. edulis F-type mtDNA indicates that similarity between the four-armed tRNASer(UCN) genes is only 63.8% compared with an average of 92.1% (range 86.2-98.5%) for the remaining eight tRNA genes. Northern blot analysis indicated that mature tRNAs encoded by the DHU arm-replacement loop-containing tRNASer(UCN), tRNASer(AGN), tRNAMet(AUA), tRNATrp, and tRNAPro genes occur in M. californianus mitochondria, strengthening the view that all of these genes are functional. However, Northern blot and 5′ RACE (rapid amplification of cDNA ends) analyses indicated that the four-armed tRNASer(UCN) gene is transcribed into a stable RNA that includes the downstream COI sequence and is not processed into a mature tRNA. On the basis of these observations the M. californianus and M. edulis four-armed tRNASer(UCN) sequences are interpreted as pseudo-tRNASer(UCN) genes.