Position Of Protein-coding Genes Research Articles

Comparative Mitogenomics and Phylogenetic Analyses of Pentatomoidea (Hemiptera: Heteroptera).

Pentatomoidea is the largest superfamily of Pentatomomorpha; however, the phylogenetic relationships among pentatomoid families have been debated for a long time. In the present study, we gathered the mitogenomes of 55 species from eight common families (Acanthosomatidae, Cydnidae, Dinidoridae, Scutelleridae, Tessaratomidae, Plataspidae, Urostylididae and Pentatomidae), including 20 newly sequenced mitogenomes, and conducted comparative mitogenomic studies with an emphasis on the structures of non-coding regions. Heterogeneity in the base composition, and contrasting evolutionary rates were encountered among the mitogenomes in Pentatomoidea, especially in Urostylididae, which may lead to unstable phylogenetic topologies. When the family Urostylididae is excluded in taxa sampling or the third codon positions of protein coding genes are removed, phylogenetic analyses under site-homogenous models could provide more stable tree topologies. However, the relationships between families remained the same in all PhyloBayes analyses under the site-heterogeneous mixture model CAT + GTR with different datasets and were recovered as (Cydnidae + (((Tessaratomidae + Dinidoridae) + (Plataspidae + Scutelleridae)) + ((Acanthosomatidae + Urostylididae) + Pentatomidae)))). Our study showed that data optimizing strategies after heterogeneity assessments based on denser sampling and the use of site-heterogeneous mixture models are essential for further analysis of the phylogenetic relationships of Pentatomoidea.

First mitogenome of subfamily Langiinae (Lepidoptera: Sphingidae) with its phylogenetic implications

To date, a relatively complete classification of Sphingidae (Lepidoptera) has been generated, but the phylogeny of the family remains need to be fully resolved. Some phylogenetic relationships within Sphingidae still remains uncertain, especially the taxonomic status of the subfamily Langiinae and its sole included genus and species, Langia zenzeroides. To begin to address this problem, we generated nine new complete mitochondrial genomes, including that of Langia, and together with that of Theretra oldenlandiae from our previous study and 25 other Sphingidae mitogenomes downloaded from GenBank, analyzed the phylogenetic relationships of Sphingidae and investigated the mitogenomic differences among members of the Langiinae, Sphinginae, Smerinthinae and Macroglossinae. The mitogenomes of Sphingidae varied from 14995bp to 15669bp in length. The gene order of all newly sequenced mitogenomes was identical, containing 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and the A+T-rich region. Nucleotide composition was A+T biased, and all the protein-coding genes exhibited a positive AT-skew, which was reflected in the nucleotide composition, codon, and amino acid usage. The A+T-rich region was comprised of nonrepetitive sequences, which contained regulatory elements related to the control of replication and transcription. We analyzed concatenated gene sequences, with third codon positions of protein coding genes and rRNAs excluded, using Maximum Likelihood and Bayesian Inference techniques. All four currently recognized subfamilies were recovered as monophyletic but in contrast to the most recent studies, our preferred tree placed Langiinae as the first subfamily to diverge within Sphingidae rather as sister to Smerinthinae+Sphinginae. Our results also support the removal of the genus Barbourion from the smerinthine tribe Ambulycini to an unresolved position in "Smerinthinae incertae sedis".

Plastid phylogenomics and biogeographic analysis support a trans-Tethyan origin and rapid early radiation of Cornales in the Mid-Cretaceous

The Cornales is a relatively small but morphologically diverse order in the basal position of the Asterids clade. Previous study hypothesized that the order might have undergone ancient rapid radiation during the Cretaceous when major angiosperm lineages were established. We conducted the phylogenomic analysis of Cornales using 81 plastid genome sequences with 67 newly generated in this study to test the hypothesis. This sampling represents all the families and 31 out of 48 genera in the order. Phylogenetic analyses were conducted using different datasets to examine the effects of different coding positions and character coding methods. We further conducted divergence time, diversification rate, and biogeographic analyses to understand the early evolutionary history of Cornales in space and time. Our phylogenetic analyses of four datasets (the amino acid characters, the 1st and 2nd codon positions of protein coding genes, nucleotide characters with degenerated coding method, and noncoding regions) resulted in a robust phylogeny congruent with results of previous studies, showing (((Cornaceae-Alangiaceae)-(Curtisiaceae-Grubbiaceae))-(((Nyssaceae-Davidiaceae)-Mastixiaceae)-((Hydrostachyaceae-(Hydrangeaceae-Loasaceae)))). Phylogenetic relationships within families were also well resolved. Conflicts in the placement of Hydrostachyaceae were found from analyses of two datasets, the nucleotide characters of all codon position and the 3rd codon positions, where the family was united with Loasaceae, but not strongly supported. Results from divergence time analyses suggested a mid-Cretaceous origin of Cornales followed by rapid early diversification into major clades/families within 10 million years. The early diversification of Cornales may have been facilitated by divergence in habitat and morphology following geographic dispersals. The ancestral distribution of the order was inferred as a widespread range covering Asia, Europe, North America, and Africa when including fossils in the analyses, suggesting an origin of the order likely along the Tethys Seaway where the areas were connected in the mid-Cretaceous. Inferred geographic origins of each family differed to some extent between analyses including fossils vs excluding fossils. In the analysis with extant and fossil species, the origins of the African Hydrostachyaceae and Grubbiaceae-Curtisiaceae clade were inferred to have involved two independent events, an intercontinental dispersal from the northern hemisphere to Africa and an intercontinental vicariance between the northern hemisphere and Africa, respectively. Other families were inferred to have evolved in the northern hemisphere with subsequent intercontinental dispersal(s) to other areas including to Central and South America, during their subsequent diversification. Net diversification rate analysis based on treePL dated phylogeny using MEDUSA detected a nearly 5-fold decrease in the African endemic Curtisiaceae-Grubbiaceae (CuG) clade and an increase of rate in the Hydrangeaceae-Loasaceae (HL) clade. Within HL, a decrease in the Fendlera-Jamesia clade and an increase in the Philadelphus clade were also detected. The findings are also consistent with the level of present species diversity in these lineages. Our study demonstrated the value of plastid genome in phylogenomic study, but posed an old challenge of biogeographic study with fossil data and raised caution for the synonymous substitution sites of plastid genome in phylogenomics studies.

Molecular phylogenetic analysis of Acridoidea (Orthoptera: Caelifera) based on mitochondrial cytochrome oxidase subunit sequences.

Phylogenetic relationships of Acridoidea were examined using mitochondrial cytochrome oxidase subunit sequences (COI, COII and COIII, total 2970bp). Fourteen grasshopper species of thirteen genera from seven families were sequenced to obtain mitochondrial genes data, along with twenty-two grasshopper species were obtained from the GenBank nucleotide database. The purpose of this study is to infer the phylogenetic relationships among families within Acridoidea and testing the monophyly of Acridoidea and each families of it. Phylogenic trees were reconstructed using Maximum Likelihood (ML) and Maximum Parsimony (MP) methods with Tettigonioidea and Gryllotalpoidea as outgroups. The putative initiation codon for COI is CCG in thirteen studied species and ATC in Bryodema luctuosum luctuosum. The 2970 bp concatenated sequences included 1431 conserved sites, 1539 variable sites, and 1216 parsimony-informative sites, the nucleotide compositions were significantly biased toward A and T (68.8%). The resulted phylogenetic trees supported the monophyly of Acridoidea, but did not entirely agree with the traditional morphology-based taxonomic system of grasshoppers within Acridoidea. The monophyly of three families of Acrididae, Catantopidae and Arcypteridae were not supported; Gomphoceridae and Arcypteridae were recovered together as a monophyletic group because of closer phylogenetic relationships; Pyrgomorphidae and Chrotogonidae have the same closer relationships; Pneumoridae, Pyrgomorphidae and Chrotogonidae were the most basal groups; while the taxonomic status of Pamphagidae, which was revealed as a monophyletic group, was not clear in this analysis. Moreover, the results indicate that a phylogeny inferred from the combination of several genes is more reliable than that from only a single gene sequence, and the third codon positions of protein coding genes can improve the topology and node supports of the phylogenetic trees.

The complete mitochondrial genome of the Hwanghae Rockfish Sebastes koreanus (Scorpaenidae, Scorpaeniformes)

The complete mitochondrial genome sequence of Sebastes koreanus was determined by next-generation sequencing. The total genome was 16,499 bp in length, comprising two rRNA, 22 tRNA and 13 protein-coding genes (PCGs), as well as the mtDNA control region. The genome constitutes 27.9% A, 26.6% T, 17.1% G and 28.4% C, showing a slight AT bias (54.5%). Of the 13 mitochondrial PCGs, 12 have an ATG start codon while COX1 had a GTG start codon; the incomplete stop codon (T) was present in the ND3, ND4 and Cytb genes. The anti-G bias was considerably lower at the third codon position of PCGs (8.8%). The complete mitogenome sequence of S. koreanus will contribute to molecular phylogenetic and evolutionary analyses of Sebastinae and to the identification of its genetic populations in the Yellow Sea.

Second generation DNA sequencing of the mitogenome of the Chinstrap penguin and comparative genomics of Antarctic penguins

The complete mitochondrial genome of the Chinstrap penguin (Pygoscelis antarcticus) was sequenced and compared with other penguin mitogenomes. The genome is 15,972 bp in length with the number and order of protein coding genes and RNAs being very similar to that of other known penguin mitogenomes. Comparative nucleotide analysis showed the Chinstrap mitogenome shares 94% homology with the mitogenome of its sister species, Pygoscelis adelie (Adélie penguin). Divergence at nonsynonymous nucleotide positions was found to be up to 23 times less than that observed in synonymous positions of protein coding genes, suggesting high selection constraints. The complete mitogenome data will be useful for genetic and evolutionary studies of penguins.

Complete mitochondrial genome of the anadromous river pufferfish, Takifugu obscurus (Tetraodontiformes:Tetraodontidae)

The complete mitochondrial genome was sequenced from the anadromous river pufferfish, Takifugu obscurus. The genome sequence was 16,446 bp in size, and the gene order and contents were identical with those of congeneric species in the genus Takifugu. Of 13 protein-coding genes (PGCs), 2 genes (CO2 and ND4) had incomplete stop codons as shown in T. obscurus. Furthermore, the stop codon of CO1 and ND6 genes was AGG. The base composition of T. obscurus mitogenome showed anti-G bias (13.2% and 6.4%) on the second and third positions of protein-coding genes (PCGs), respectively.

Complete mitochondrial genome of the sand lamprey, Lampetra reissneri (Petromyzontiformes, Petromyzontidae)

The complete mitochondrial genome was sequenced from the river lamprey, Lampetra reissneri. The genome sequence was 16,197 bp in size, and the gene order and contents were identical to those of the congeneric species Lampetra japonica. However, L. reissneri had two incomplete control regions with a rearrangement of mitochondrial genomic organization compared with other fish mitochondrial genomes. Of 13 protein-coding genes (PCGs), only one gene (CO1) had an incomplete stop codon. The base composition of L. reissneri showed anti-G bias (12.99% and 4.49%) on the 2nd and 3rd position of PCGs, respectively.

Complete mitochondrial genome of the monogonont rotifer, Brachionus koreanus (Rotifera, Brachionidae)

The complete mitochondrial genome was obtained from the assembled genome data sequenced by next generation sequencing (NGS) technology from the monogonont rotifer Brachionus koreanus. The mitochondrial genome of B. koreanus was composed of two circular chromosomes designated as mtDNA-I (10,421 bp) and mtDNA-II (11,923 bp). The gene contents of B. koreanus were identical with previously reported B. plicatilis mitochondrial genomes. However, gene orders of B. koreanus showed one rearrangement between the two species. Of 12 protein-coding genes (PCGs), 3 genes (ATP6, ND1, and ND3) had an incomplete stop codon. The A + T base composition of B. koreanus mitochondrial genome was high (68.81%). They also showed anti-G bias (12.03% and 10.97%) on the second and third position of PCGs as well as slight anti-C bias (15.96% and 14.31%) on the first and third position of PCGs.

Complete mitochondrial genome of the jellyfish, Chrysaora quinquecirrha (Cnidaria, Scyphozoa)

We sequenced 16,775 bp of the linear mitochondrial DNA of the jellyfish Chrysaora quinquecirrha and characterized them. C. quinquecirrha has 13 protein-coding genes (PCGs), 16S rRNA and 12S rRNA with 3 tRNAs (tRNA-Leu, tRNA-Ser(TGA), tRNA-Met) as shown in Aurelia sp. nov. Both have another two PCGs such as helicase and orf363 with telomeres at both ends. The PCGs of C. quinquecirrha shows anti-G bias on 2nd and 3rd positions of PCGs as well as anti-C bias on 1st and 3rd positions of PCGs.

Complete mitochondrial genome of the striped bittering Acheilognathus yamatsutae (Cypriniformes; Cyprinidae)

The complete mitochondrial genome was sequenced from the striped bittering Acheilognathus yamatsutae. The genome sequence was 16,703 bp in size, and the gene order and contents were identical tot those of the congeneric species Acheilognathus signifer and other previously reported fish mitochondrial genomes. Of 13 protein-coding genes (PCGs), three genes (CO2, CO3, and Cytb) had incomplete stop codons. The base composition of A. yamatsutae showed anti-G bias (13.50% and 9.72%) on the 2nd and 3rd position of PCGs.

Complete mitochondrial genome of the freshwater sculpin Cottus koreanus (Scorpaeniformes, Cottidae)

The complete mitochondrial genome was sequenced from the freshwater sculpin Cottus koreanus. The genome sequence was 16,560 bp in size, and the gene order and contents were identical with those of previously reported fish mitochondrial genomes. Of 13 protein-coding genes (PCGs), 3 genes (CO2, ND4, Cytb) had incomplete stop codons. The base composition of C. koreanus mitogenome showed anti-G bias (13.94% and 12.73%) on the second and third positions of PCGs, respectively.

Complete mitochondrial genome of the Korean bitterling Acheilognathus intermedia (Cypriniformes; Cyprinidae)

The complete mitochondrial genome was sequenced from the Korean bitterling Acheilognathus intermedia. The genome sequence was 16,610 bp in size, and the gene order and contents were identical with the congeneric Acheilognathus signifier and other previously reported fish mitochondrial genomes. Of 13 protein-coding genes (PCGs), three genes (CO2, CO3, and Cytochrome b) had incomplete stop codons. The base composition of A. intermedia showed anti-G bias (12.48%) on the third position of PCGs.

Complete mitochondrial genome of the Korean bitterling Acheilognathus koreensis (Cypriniformes; Cyprinidae)

The complete mitochondrial genome was sequenced from the Korean bitterling Acheilognathus koreensis. The genome sequence was 16,563 bp in size, and the gene order and contents were identical with the same genera Acheilognathus signifier and other previously reported fish mitochondrial genomes. Of 13 protein-coding genes (PCGs), four genes (CO2, CO3, ND4, and Cytochrome b) had incomplete stop codons. The base composition of A. koreensis showed anti-G bias (13.69%) on the third position of PCGs.

Complete mitochondrial genome of the river lamprey, Lampetra japonica (Petromyzontiformes, Petromyzonidae)

The complete mitochondrial genome was sequenced from the river lamprey, Lampetra japonica. The genome sequence was 16,267 bp in size, and the gene order and contents were identical with the genera Lampetra reissneri. However, L. japonica has two control regions with different mitochondrial genomic organization compared to other previously reported fish mitochondrial genomes. Of 13 protein-coding genes (PCGs), 1 gene (CO1) had incomplete stop codon. The base composition of L. japonica showed anti-G bias (4.65%) on the third position of PCGs.

Complete mitochondrial genome of the freshwater gudgeon, Gobiobotia nakdongensis (Cypriniformes, Gobioninae)

The complete mitochondrial genome was sequenced from the freshwater gudgeon, Gobiobotia nakdongensis. The genome sequence was 16,609 bp in size, and the gene order and contents were identical with other previously reported fish mitochondrial genomes. Of the 13 protein-coding genes (PCGs), 3 genes (CO2, CO3, and Cytb) had incomplete stop codons. The base composition of G. nakdongensis showed anti-G bias (9.93%) on the third position of PCGs.

Complete mitochondrial genome of the Arctic green sea urchin Strongylocentrotus droebachiensis (Strongylocentrotidae, Echinoidea)

The complete mitochondrial genome was obtained from the assembled genome data sequenced by next-generation sequencing technology from the Arctic green sea urchin Strongylocentrotus droebachiensis. The mitochondrial genome sequence was 15,710 bp in size, and the gene order and contents were identical with previously reported sea urchin mitochondrial genomes. Of 13 protein-coding genes (PCGs), 1 gene (Cytb) had an incomplete stop codon. The base composition of the mitogenome of Arctic S. droebachiensis showed high A+T (58.36%) and anti-G bias (14.86%) on the third position of PCGs.

Complete mitochondrial genome of the Amur stickleback Pungitius kaibarae (Gasterosteiformes, Gasterosteidae)

The complete mitochondrial genome was sequenced from the Amur stickleback Pungitius kaibarae. The genome sequence was 16,505 bp in size, and the gene order and contents were identical with the same genera Pungitius sinensis and other previously reported fish mitochondrial genomes. Of 13 protein-coding genes (PCGs), 3 genes (CO2, ND4, and Cytb) had incomplete stop codons. The base composition of P. kaibarae showed anti-G bias (8.86%) on the third position of PCGs.

Complete mitochondrial genome of the marine medaka Oryzias melastigma (Beloniformes, Adrianichthyidae)

The complete mitochondrial genome was obtained from the assembled genome data sequenced by next-generation sequencer from the marine medaka Oryzias melastigma. The mitochondrial genome sequence was 16,864 bp in size, and the gene order and contents were identical with those of previously reported fish mitochondrial genomes. Of 13 protein-coding genes (PCGs), 4 genes (CO3, ND3, ND4, and Cytb) had incomplete stop codons. The base composition of O. melastigma mitogenome showed high A+T (59.65%) and anti-G bias (8.73%) on the 3rd position of PCGs.

Complete mitochondrial genome of the Amur stickleback Pungitius sinensis (Gasterosteiformes, Gasterosteidae)

The complete mitochondrial genome was sequenced from the Amur stickleback Pungitius sinensis. The genome sequence was 16,581 bp in size, and the gene order and contents were identical with those of previously reported fish mitochondrial genomes. Of 13 protein-coding genes (PCGs), four genes (ND2, CO2, ND4, Cytb) had incomplete stop codons. The base composition of P. sinensis showed anti-G bias (9.53%) on the third position of PCGs.