Protein-coding Gene Sequences Research Articles

The complete mitochondrial genome of the freshwater fairy shrimp Branchinella kugenumaensis Ishikawa 1894 (Crustacea: Anostraca: Thamnocephalidae)

In this study, we determined and analyzed the complete mitochondrial genome of the freshwater fairy shrimp Branchinella kugenumaensis Ishikawa 1894 (Crustacea: Anostraca: Thamnocephalidae). The mitogenome is 15,127 bp in length, consisted of 37 genes that participate in protein production and energy metabolism of mitochondria. The gene order of the B. kugenumaensis mtDNA exhibits major rearrangements compared with the pancrustacean ancestral pattern or other known anostracan mitogenomes, representing a novel mitochondrial genomic organization within the Crustacea. A maximum-likelihood phylogenetic analysis based on concatenated nucleotide sequences of protein-coding genes places B. kugenumaensis next to Streptocephalus sirindhornae, inside the Anostraca clade. Our study will provide new evidence to the less sampled anostracan evolution and take a further step to the completion of the Branchiopoda tree of life.

Comparative analysis of the complete chloroplast genome sequences of six species of Pulsatilla Miller, Ranunculaceae

BackgroundBaitouweng is a traditional Chinese medicine with a long history of different applications. Although referred to as a single medicine, Baitouweng is actually comprised of many closely related species. It is therefore critically important to identify the different species that are utilized in these medicinal applications. Knowledge about their phylogenetic relationships can be derived from their chloroplast genomes and may provide additional insights into development of molecular markers.MethodsGenomic DNA was extracted from six species of Pulsatilla and then sequenced on an Illumina HiSeq 4000. Sequences were assembled into contigs by SOAPdenovo 2.04, aligned to the reference genome using BLAST, and then manually corrected. Genome annotation was performed by the online DOGMA tool. General characteristics of the cp genomes of the six species were analyzed and compared with closely related species. Additionally, phylogenetic trees were constructed, based on single nucleotide polymorphisms (SNPs) and 51 shared protein-coding gene sequences in the cp genome among all 31 species via maximum likelihood.ResultsThe size of cp genomes of P. chinensis (Bge.) Regel, P. chinensis (Bge.) Regel var. kissii (Mandl) S. H. Li et Y. H. Huang, P. cernua (Thunb.) Bercht. et Opiz f. plumbea J. X. Ji et Y. T. zhao, P. dahurica (Fisch.) Spreng, P. turczaninovii Kryl. et Serg, and P. cernua (Thunb.) Bercht. et Opiz. were 163,851 bp, 163,756 bp, 162,481 bp, 162,450 bp, 162,795 bp, and 162,924 bp, respectively. Each species included two inverted repeat regions, a small single-copy region, and a large single-copy region. A total of 134 genes were annotated, including 90 protein-coding genes, 36 tRNAs, and eight rRNAs across all species. In simple sequence repeat analysis, only P. dahurica was found to contain hexanucleotide repeats. A total of 26, 39, 32, 37, 32 and 43 large repeat sequences were identified in the genic regions of the six Pulsatilla species. Nucleotide diversity analysis revealed that the rpl36 gene and ccsA-ndhD region have the highest Pi value. In addition, two phylogenetic trees of the cp genomes were constructed, which laced all Pulsatilla species into one branch within Ranunculaceae.ConclusionsWe identified and analyzed the cp genome features of six species of P. Miller, with implications for species identification and phylogenetic analysis.

The complete mitochondrial genome of Harpago chiragra and Lambis lambis (Gastropoda: Stromboidea): implications on the Littorinimorpha phylogeny

The complete mitochondrial genomes of Harpago chiragra and Lambis lambis (Strombidae) were determined with the size of 15,460 bp and 15,481 bp, respectively, and both sequences contained 13 protein-coding genes, 22 tRNAs, and two rRNAs. H. chiragra and L. lambis have similar mitochondrial features, corresponding to typical gastropod mitochondrial genomes, such as the conserved gene order, a high A + T content (66.22% for H. chiragra and 66.10% for L. lambis), and preference for A + T-rich codons. The start or termination codon of same protein-coding gene in H. chiragra was consistent with that in L. lambis, except for the termination codon of cox1 gene (TAG for H. chiragra and TAA for L. lambis) and the start codon of nad4 (GTG for H. chiragra and ATG for L. lambis). Pairwise sequence alignments detected different degrees of variations in H. chiragra and L. lambis mitochondrial genomes; and the two species had lower levels of genetic distance (0.202 for nucleotide sequence) and closest relationships as compared to Strombus gigas and Oncomelania hupensis. The 13 partitioned nucleotide sequences of protein coding genes of H. chiragra and L. lambis were aligned with representatives of the main lineages of gastropods and their phylogenetic relationships were inferred. H. chiragra and L. lambis share the same gene order as Littorinimorpha species, except Vermetoidea, which demonstrate a gene rearrangement in species. The reconstructed phylogeny supports three major clades within Littorinimorpha: 1) Stromboidea, Tonnoidea, Littorinoidea, and Naticoidea, 2) Rissooidea and Truncatelloidea, and 3) Vermetoidea. In addition, a relaxed molecular clock calibrated with fossils dated the diversification of Strombidae near 112 (44–206) Mya and a possible radiation is detected to occur between 45–75 Mya, providing implications to understand the Cenozoic replacement event (65–135 Mya) of Aporrhaidae by Strombidae.

Phylogenetic placement of Paratrichaptum and reconsideration of Gloeophyllales.

Paratrichaptum accuratum is a large conspicuous polypore fungus growing on dead or living angiosperm trees in subtropical-boreal areas of China, Indonesia, Japan, and Taiwan. The present study places P. accuratum in the family Gloeophyllaceae that belongs to the order Gloeophyllales within Agaricomycetes (Basidiomycota), based on evidence derived from morphological and ecological characteristics, and phylogenetic analyses of sequences of nuclear rDNA regions (5.8S, nuc 18S, nuc 28S) and protein-coding genes (rpb1, rpb2, and tef1). The analyses presented in this study also give strong support for including Jaapia in Gloeophyllaceae and Gloeophyllales. Thus, the names Jaapiaceae and Jaapiales are considered here as synonyms of Gloeophyllaceae and Gloeophyllales. Since Paratrichaptum represents the earliest diverging lineage in Gloeophyllales, pileate basidiocarps and brown rot appear to be ancestral states of Gloeophyllales. Paratrichaptum accuratum may represent a relic species, according to its phylogenetic position, peculiar distribution pattern and rare occurrence.

The complete mitochondrial genome of Min pig (Hebao) and a phylogenetic analysis

The complete mitochondrial genomes of Min pig (Hebao) are published in this paper. The full length of mtDNA is 16,719 bp and contained 13 PCGs, 2 rRNA and 22 tRNA, and 1D-loop(MN258706). A phylogenetic tree with the 13 protein-coding genes sequences of Min pig (Hebao) together with 45 other Chinese pig breeds and 7 foreign pig breeds was constructed. The results can be subsequently used to provide information for pig phylogenetic and insights into the evolution of genomes. The result of phylogenetic analysis showed that the genetic relationship of Min pig (Hebao) is closer to that of Dapulian pigs.

The complete mitochondrial genome of click beetle Agrypnus sp. (Coleoptera: Elateridae) and phylogenetic analysis

Larvae of click beetles are the most important soil-dwelling agricultural pests and are abundant throughout the world. Agrypnus sp. belongs to the subfamily Agrypninae of Elateridae. Here, we sequenced and annotated the complete mitochondrial genome (mitogenome) of Agrypnus sp., the new representative of the mitogenome of the subfamily. This mitogenome was 16,056 bp long and encoded 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA unit genes (rRNAs). Gene order was conserved and identical to most other previously sequenced Elateridae. The nucleotide composition biases towards A and T, which together made up 70.8% of the entirety. Phylogenetic analysis based on 13 PCGs sequences showed that Agrypnus sp. got together with the same subfamily species Pyrophorus divergens, Pyrearinus termitilluminans, Ignelater luminosus, and Hapsodrilus ignifer with high support value.

Non-coding cis-element of Period2 is essential for maintaining organismal circadian behaviour and body temperature rhythmicity

Non-coding cis-regulatory elements are essential determinants of development, but their exact impacts on behavior and physiology in adults remain elusive. Cis-element-based transcriptional regulation is believed to be crucial for generating circadian rhythms in behavior and physiology. However, genetic evidence supporting this model is based on mutations in the protein-coding sequences of clock genes. Here, we report generation of mutant mice carrying a mutation only at the E′-box cis-element in the promoter region of the core clock gene Per2. The Per2 E′-box mutation abolishes sustainable molecular clock oscillations and renders circadian locomotor activity and body temperature rhythms unstable. Without the E′-box, Per2 messenger RNA and protein expression remain at mid-to-high levels. Our work delineates the Per2 E′-box as a critical nodal element for keeping sustainable cell-autonomous circadian oscillation and reveals the extent of the impact of the non-coding cis-element in daily maintenance of animal locomotor activity and body temperature rhythmicity.

IMKT: the integrative McDonald and Kreitman test.

The McDonald and Kreitman test (MKT) is one of the most powerful and widely used methods to detect and quantify recurrent natural selection using DNA sequence data. Here we present iMKT (acronym for integrative McDonald and Kreitman test), a novel web-based service performing four distinct MKT types. It allows the detection and estimation of four different selection regimes −adaptive, neutral, strongly deleterious and weakly deleterious− acting on any genomic sequence. iMKT can analyze both user's own population genomic data and pre-loaded Drosophila melanogaster and human sequences of protein-coding genes obtained from the largest population genomic datasets to date. Advanced options in the website allow testing complex hypotheses such as the application example showed here: do genes located in high recombination regions undergo higher rates of adaptation? We aim that iMKT will become a reference site tool for the study of evolutionary adaptation in massive population genomics datasets, especially in Drosophila and humans. iMKT is a free resource online at https://imkt.uab.cat.

Septonema lohmanii G. Delgado & O. Koukol, sp. nov., a New Species in Mytilinidiales (Dothideomycetes) and the Phylogenetic Position of S. fasciculare (Corda) S. Hughes

During independent surveys of microfungi associated with Pinus spp. in the United States and the Czech Republic, a distinct fungus matching the generic concept of Septonema Corda was collected. It is characterized by distinctly ornamented conidiophores, branches, conidia and hyphae, ranging from verruculose to strongly verrucose with prominent rounded warts, yellowish brown to brown or reddish brown in color and forming densely floccose, dark brown or dark reddish brown colonies on pine wood and bark. Conidia are cylindrical or subcylindrical and produced in short, simple or branched acropetal chains. Multigene phylogenetic analyses including nuclear ribosomal (LSU) and protein coding gene (EF1-α) sequence data suggest that both collections are conspecific and belong to the order Mytilinidiales (Dothideomycetes, Ascomycota) where they group distant from other mytilinidiaceous fungi with known septonema-like anamorphs. To provide a proper name based on phylogenetic placement and to possibly circumscribe Septonema sensu stricto, a non-sporulating, putative strain belonging to S. secedens Corda, the generic type, was included in the analyses. DNA sequence data placed this strain within the family Venturiaceae (Venturiales, Dothideomycetes) but morphological examination of the corresponding herbarium specimen revealed that it belongs instead to S. fasciculare (Corda) S. Hughes. Because of the polyphyletic nature of the genus and the unknown phylogenetic position of its type species, our fungus is accommodated in Septonema as a new species named S. lohmanii G. Delgado & Koukol, sp. nov.

The complete chloroplast genome sequence of traditional medical herb, Plantago depressa Willd. (Plantaginaceae)

Plantago depressa Willd. (Plantaginaceae) belonging to the section Mesembrynia and subgenus Plantago has been used as a traditional medicine. Here, we presented the complete chloroplast genome of P. depressa which is 164,617 bp long and has four subregions: 82,933 bp of large single copy (LSC) and 4,908 bp of small single copy (SSC) regions are separated by 38,388 bp of inverted repeat (IR) regions including 139 genes (93 protein-coding genes, eight rRNAs, and 38 tRNAs). The overall GC contents of the chloroplast genome were 38.0% and in the LSC, SSC, and IR regions were 36.6%, 30.6%, and 39.9%, respectively. Phylogenetic tree constructed with concatenated 79 protein-coding genes sequences of the chloroplast genomes in Plantaginaceae from APG group presents the phylogenetic position of P. depressa.

The complete mitochondrial genome and phylogenetic analysis of Nerita yoldii (Gastropoda: Neritidae)

The complete mitochondrial genome of Nerita yoldii has been determined. The whole sequence was 15,719 bp in length and included 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes (12S rRNA and 16S rRNA). The overall base composition is A 29.5%, C 13.8%, G 21.5%, and T 35.2%. In 13 protein-coding genes, the nad2, nad5, and nad6 gene start with ATT, whereas nad4 started with ATA, the other nine genes start with ATG. For the stop codon, COX1, COX3, nad3, and atp8 end with TAG, other nine genes end with TAA. Phylogenetic tree was constructed based on 13 protein-coding genes sequences of Archaeogastropoda species, and the result showed that N. yoldii is most closely related to Clithon retropictus. These mitogenome sequence data will be useful for population genetics and phylogenetic analysis of the family Neritidae.

The complete mitochondrial genome of Onustus exutus(Gastropoda: Xenophoridae)

Complete mitochondrial genome of Onustus exutus has been sequenced and phylogenetic relationships were evaluated. The circular mitochondrial genome is 16,043 bp in length consisting of 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes. The nucleotide composition of the complete mitochondrial genome of O. exutus is 30.46% A, 14.32% C, 15.83% G, and 39.38% T. With the exception of eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. Thirteen protein-coding genes start with ATG. For the stop codon, CYTB, ND6, ND4L, and ND4 end with TAG, other 9 genes end with TAA. Phylogenetic tree was constructed based on 13 protein-coding gene sequences of 11 species using the neighbor-joining method, and the result showed that O. exutus is most closely related to Conomurex luhuanus. This is the first record of complete mitochondrial genome from the genus in the Onustus. The present study provides additional data for Mesogastropoda phylogeny.

The complete mitochondrial genome of Thryssa vitrirostris (Engraulinae, Engranlidae, Clupeoidei) and phylogenetic studies of Clupeoidei

The complete mitochondrial genome of T. vitrirostris was 16,975bp in length, and it contained a typically conserved structure including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region (D-loop). Except ND6 and 8 tRNA genes, all other mitochondrial genes are encoded on the heavy strand, the gene arrangement was consistent with other Engraulidae mitochondrial genomes. The overall base composition is A 30.56%, C 28.40%, G 16.01%, T 25.03%. Additionally, phylogenetic tree was constructed based on 13 protein-coding genes sequences of 21 Clupeoidei species, and Chirocentrus dorab (belongs to Clupeiformes) as outgroup, the result showed that T. vitrirostris is most closely related to T. dussumieri. These results would be useful for the investigation of phylogenetic relationship, taxonomic classification, and phylogeography of the Clupeoidei.

Complete mitochondrial genome of the leaf-rolling-weevil, Apoderus jekelii Roelofs, 1874 (Coleoptera: Attelabidae)

We sequenced 15,803 bp of the leaf-rolling-weevil, Apoderus jekelii (Coleoptera: Attelabidae) mitochondrial genome (mitogenome) that lacked ∼8000 bp of the A + T-rich region for the completion of the genomic sequence. The A. jekelii mitogenome, which includes 1169 bp of A + T-rich region, possesses typical sets of genes [13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes] and gene arrangement of the species was identical to that commonly found in the majority of the insects. The start codon for ND1 was a rare TTG instead of typical ATN. Nearly, all PCGs ended with complete stop codons, TAA or TAG, except for ND5 which ended with an incomplete T. Phylogenetic analyses using the eight concatenated PCG sequences, which are commonly available for the mitogenome sequences of Curculionoidea, revealed Attelabidae as monophyletic, as well as the sister relationship between current A. jekelii and congeneric species A. coryli in Attelabidae, with the highest nodal supports both in Bayesian inference and maximum likelihood methods. In order to gain a more comprehensive picture of the phylogenetic relationships among the lineages of Attelabidae, an extended analysis with more taxonomic sampling will be necessary.

Complete mitochondrial genome sequence of flathead fish Platycephalus sp.1 (Scorpaeniformes: Platycephalidae)

In this study, the complete mitochondrial genome (mitogenome) sequence of Platycephalus sp.1 was sequenced by long polymerase chain (PCR) reaction and primer walking method. The mitogenome was total 16552 base pairs (bp) in length and contained 2 ribosomal RNA (rRNA), 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA), and 1 non-coding region (control region) as those found in other vertebrates. The overall base composition was displayed as 25.8% T, 30.0% C, 27.0% A, and 17.2% G. The neighbour-joining tree was reconstructed based on the 13 PCGs sequences of Platycephalus sp.1 and other six species. The mitogenome data would provide useful information for further studies on the taxonomy and phylogenetic analysis of Platycephalidae.

The complete mitochondrial genome of Triplophysa cuneicephala (Cypriniformes: Balitoridae) with phylogenetic consideration

The complete mitogenome of Triplophysa cuneicephala is 16,571 bp in length with the A + T contents of 56.12%, containing 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a putative control region. All PCGs employed ATG as the start codon, except for COI which utilized GTG as start codon. Four stop codons were observed in the PCGs, including TAA, TAG, TA and T. Phylogenetic analysis based on concatenated PCG sequences revealed that T. cuneicephala is closely related to T. robusta and T. minxianensis. This study would provide useful genetic information for future studies on phylogeny, evolutionary, and taxonomic classification in Triplophysa species.

The complete mitochondrial genome of Triplophysa sellaefer (Cypriniformes: Balitoridae)

The complete mitochondrial genome of Triplophysa sellaefer is a circular molecule of 16,571 bp in length with the A + T contents of 56.84%, containing 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a putative control region. Six gene overlaps and 10 intergenic spacers were observed, with the total length of 26 bp and 34 bp, respectively. The phylogenetic analysis based on the concatenated PCG sequences revealed that T. sellaefer is closely related to T. alticeps. This study would provide useful information on phylogenetic and evolutionary studies in Triplophysa.

Complete mitochondrial DNA genome of Thryssa dussumieri (Valenciennes, 1848)

In this study, the complete mitochondrial genome (mitogenome) sequence of Thryssa dussumieri was determined by long polymerase chain reaction and primer walking methods. The mitogenome was a circular molecule of 16,883 base pairs (bp) in length and contained 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA), 22 transfer RNA (tRNA), and a control region similar to those found in other bony fishes. The overall nucleotide composition was estimated to be 32.1% A, 26.1% C, 23.7% T, and 18.1% G. The neighbor-joining tree was reconstructed based on the 13 PCGs sequences of T. dussumieri and other 10 Engraulidae species. The mitogenome data will provide useful information for further studies on the phylogenetic analysis and population genetics.

Overview of inactivating mutations in the protein-coding genome of the mouse reference strain C57BL/6J.

Mice are extremely important as the premier model organism in human biomedical and mammalian genetic research. The genomes of several tens of mouse inbred strains have been sequenced. They have been compared to the genome of C57BL/6J, considered by convention as the reference genome. Based on a comparison of this reference genome with 36 other sequenced mouse strains, we generated an overview of all protein-coding genes that are deviant in this reference genome, compared with consensus protein-coding mouse gene sequences. We provide PROVEAN scores, reflecting the likelihood that these C57BL/6J proteins have lost function. We thus identified numerous abnormal proteins, and biological pathways, specifically present in C57BL/6J, suggesting the important caveats of this reference mouse strain, and linking candidate genes to some of the best-known phenotypes of this strain.

Codon Usage Pattern of Genes Involved in Central Nervous System.

Codon usage bias (CUB) is the non-uniform usage of synonymous codons in which some codons are more preferred to others in the transcript. Analysis of codon usage bias has applications in understanding the basics of molecular biology, genetics, gene expression, and molecular evolution. To understand the patterns of codon usage in genes involved in the central nervous system (CNS), we used bioinformatic approaches to analyze the protein-coding sequences of genes involved in the CNS. The improved effective number of codons (ENC) suggested that the overall codon usage bias was low. The relative synonymous codon usage (RSCU) revealed that the most frequently occurring codons had a G or C at the third codon position. The codons namely TCC, AGC, CTG, CAG, CGC, ATC, ACC, GTG, GCC, GGC, and CGG (average RSCU > 1.6) were over-represented. Both mutation pressure and natural selection might affect the codon usage pattern as evident from correspondence and parity plot analyses. The overall GC content (59.93) was higher than AT content, i.e., genes were GC-rich. The correlation of GC12 with GC3 suggested that mutation pressure might affect the codon usage pattern.