The complete mitochondrial genome of the Mexican blind brotula Typhlias pearsei (Ophidiiformes: Dinematichthydae): an endemic and troglomorphic cavefish from the Yucatán Peninsula karst aquifer

The first complete mitochondrial genome sequence of Ailia coila from Bangladesh was determined by the bioinformatic assembly of the next generation sequencing (NGS) reads. The constructed circular mitogenome for A. coila was 16,565 bp in length which harbored the canonical 13 protein-coding genes, 22 tRNAs, 2 rRNAs. Two non-coding regions, control region, D-loop (927 bp), and origin of light strand replication, OL (30 bp) were also well conserved in the mitogenome. Among the currently reported mitochondrial genomes in the order Siluriformes, A. coila was most closely related to Eutropiichthys vacha (AB919123) with 85.63% sequence identity.

The first complete mitochondrial genome sequencing of Asiatic Water snake or Checkered Keelback or Fowlea piscator (=Xenochrophis piscator) was carried out using Next-Generation Sequencing technology. The complete mitochondrial genome of Asiatic Water snake is 16,999bp long with a base composition of 33% A, 28% T, 12% G and 27% C, with a GC content of 39%. Like the typical snake mitochondrial genome, F. piscator also shows relatively similar mitogenome arrangement comprising 37 genes including 13 protein-coding genes, 22 tRNA genes, two rRNA genes and two non-coding regions or a duplicated control region (D-Loop) along with an origin of replication. Nine genes including eight tRNAs and NAD6 were encoded on the Light or L-strand. Phylogenetic analyses using the complete mitochondrial genome of F. piscator demonstrate a close relationship with the family Colubridae and sub family Natricinae.

The complete mitochondrial genome of the large yellow croaker, Larimichthys crocea (Perciformes, Sciaenidae): Unusual features of its control region and the phylogenetic position of the Sciaenidae

BackgroundIn Metazoa, mitochondrial markers are the most commonly used targets for inferring species-level molecular phylogenies due to their extremely low rate of recombination, maternal inheritance, ease of use and fast substitution rate in comparison to nuclear DNA. The mitochondrial control region (CR) is the main non-coding area of the mitochondrial genome and contains the mitochondrial origin of replication and transcription.While sequences of the cytochrome oxidase subunit 1 (COI) and 16S rRNA genes are the prime mitochondrial markers in phylogenetic studies, the highly variable CR is typically ignored and not targeted in such analyses. However, the higher substitution rate of the CR can be harnessed to infer the phylogeny of closely related species, and the use of a non-coding region alleviates biases resulting from both directional and purifying selection. Additionally, complete mitochondrial genome assemblies utilizing next generation sequencing (NGS) data often show exceptionally low coverage at specific regions, including the CR. This can only be resolved by targeted sequencing of this region.ResultsHere we provide novel sequence data for the echinoid mitochondrial control region in over 40 species across the echinoid phylogenetic tree. We demonstrate the advantages of directly targeting the CR and adjacent tRNAs to facilitate complementing low coverage NGS data from complete mitochondrial genome assemblies. Finally, we test the performance of this region as a phylogenetic marker both in the lab and in phylogenetic analyses, and demonstrate its superior performance over the other available mitochondrial markers in echinoids.ConclusionsOur target region of the mitochondrial CR (1) facilitates the first thorough investigation of this region across a wide range of echinoid taxa, (2) provides a tool for complementing missing data in NGS experiments, and (3) identifies the CR as a powerful, novel marker for phylogenetic inference in echinoids due to its high variability, lack of selection, and high compatibility across the entire class, outperforming conventional mitochondrial markers.

A suite of polymorphic microsatellite markers and the complete mitochondrial genome sequence was developed by next generation sequencing (NGS) for the critically endangered orange-bellied parrot, Neophema chrysogaster. A total of 14 polymorphic loci were identified and characterized using DNA extractions representing 40 individuals from Melaleuca, Tasmania, sampled in 2002. We observed moderate genetic variation across most loci (mean number of alleles per locus = 2.79; mean expected heterozygosity = 0.53) with no evidence of individual loci deviating significantly from Hardy-Weinberg equilibrium. Marker independence was confirmed with tests for linkage disequilibrium, and analyses indicated no evidence of null alleles across loci. De novo and reference-based genome assemblies performed using MIRA were used to assemble the N. chrysogaster mitochondrial genome sequence with mean coverage of 116-fold (range 89 to 142-fold). The mitochondrial genome consists of 18,034 base pairs, and a typical metazoan mitochondrial gene content consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a single large non-coding region (control region). The arrangement of mitochondrial genes is also typical of Avian taxa. The annotation of the mitochondrial genome and the characterization of 14 microsatellite markers provide a valuable resource for future genetic monitoring of wild and captive N. chrysogaster populations. As found previously, NGS provides a rapid, low cost and reliable method for polymorphic nuclear genetic marker development and determining complete mitochondrial genome sequences when only a fraction of a genome is sequenced.

In order to fully comprehend the evolution and kinship of fishes in the family of Loricariidae, the complete mitochondrial genome of the Loricariidae fish Ancistrus temmincki was firstly characterized in the present study. The whole mitogenome was 16,657 bp in size and consisted of 13 protein-coding genes, 22 tRNAs, 2 rRNAs genes, a control region and origin of light-strand replication. The proportion of coding sequences with a total length of 11,473 bp was 68.88%, which encoded 3,813 amino acids. The genome composition was highly A + T biased (56.29%), and exhibited AT-skew (0.0661) and a negative GC-skew (–0.2740). All protein-coding genes were started with ATG except for GTG in CO1, while stopped with the standard TAN codons or a single T. The control region (D-loop) ranging from 15,635 bp to 16,657 bp was 1023 bp in size. Until now, there is hardly any studies on the complete mitochondrial sequence in the genus of Ancistrus, phylogenetic analysis showed that A. temmincki was most closely related to Ancistrus cryptophthalmus in the genus of Ancistrus. The complete mitochondrial genome sequence has provided a new insight into the taxonomic classification, and a more complex picture of the species diversity within the family of Loricariidae.

The classification of Badidae family based on morphology has been revised several times, but data on complete mitogenome are scarce, the complete mitochondrial genome of the Badidae fish Dario dario was characterized for the first time in the present study. The whole mitogenome was 16,830 bp in size and consisted of 13 protein-coding genes, 22 tRNAs, two rRNAs genes, a control region and origin of light-strand replication. The proportion of coding sequences with a total length of 11,431 bp was 67.92%, which encoded 3800 amino acids. The genome composition was highly A + T biased (58.12%), and exhibited a negative AT-skew (–0.0045) and GC-skew (–0.2347). All protein-coding genes started with ATG except for GTG in CO1, while stopped with the standard TAN codons or a single T. The control region (D-loop) ranging from 15,658 bp to 16,830 bp was 1173 bp in size. Phylogenetic analysis showed that D. dario was most closely related to Badis badis. The complete mitochondrial genome sequence provided new insight into taxonomic classification, and a more complex picture of species diversity within the Anabantiformes.

In this study, we sequenced the complete mitochondrial genome of Pampus cinereus (Bloch, 1795). This mitochondrial genome, consisting of 16,540 base pairs (bp), contains 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and two mainly noncoding regions (control region and origin of light-strand replication) as those found in other vertebrates. Control region with 846 bp in length, is located between tRNAPro and tRNAPhe. The overall base composition of the heavy strand shows 27.4% of T, 27.5% of C, 30.0% of A, and 15.2% of G, with a slight A + T rich bias (57.4%). The complete mitochondrial genome data will provide useful genetic markers for the studies on the molecular identification, population genetics, phylogenetic analysis and conservation genetics.

In this study, we used next-generation sequencing to obtain the complete mitochondrial genome of Jaydia lineata. This mitochondrial genome, consisting of 16,510 base pairs (bp), contains 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and 2 noncoding control regions (control region and origin of light-strand replication) as those found in other vertebrates. Control region, of 848 bp in length, is located between tRNAPro and tRNAPhe. Within the control region, typical conserved domains, such as the termination-associated sequence, central and conserved sequence blocks domains were identified. The overall base composition shows 26.71% of T, 28.46% of C, 27.24% of A and 17.58% of G, with a slight A + T rich feature (53.95%). The complete mitogenome data provides useful genetic markers for the studies on the molecular identification, population genetics, phylogenetic analysis and conservation genetics.

The complete mitochondrial genome sequence of Lagocephalus sceleratus was determined. The complete mitochondrial genome was 16,444 bp in length and contained 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and two non-coding region (the control region and the origin of light strand replication). The overall base composition was A 27.59%, C 31.43%, G 17.12%, T 23.85%. All protein-coding genes started with an ATG initiation codon, except COI used GTG. With the exception of ND6 and eight tRNA genes, all other genes were encoded on the heavy strand. Additionally, the phylogenetic relationship of 37 Tetraodontidae species based on the complete genome was analyzed, and the result showed that L. sceleratus was clustered with other Lagocephalus species. These results would be useful for the investigation of phylogenetic relationship, taxonomic classification and phylogeography of the Tetraodontidae.

The complete mitochondrial genome sequences of two species of the family Trichonotidae, Trichonotus elegans (Shimada and Yoshino 1984) and Trichonotus filamentosus (Steindachner 1867), were determined using a polymerase chain reaction-based method. The genomes ranged from 16,517 to 17,235 bp in length and included 37 genes (13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes) and two non-coding regions (control region and origin of the light strand replication) as in other vertebrates. However, they shared a unique gene order among vertebrates with multiple gene switching and insertions. Phylogenetic analysis showed that Trichonotidae and Apogonidae are sister groups, which together with Kurtidae are placed as a closely related clade of Gobioidei. These results would be useful for analyzing the evolutionary relationships of Gobiiformes and the evolutionary study of fish mitogenomes.

Rapid advances in DNA sequencing technologies have made it increasingly cost-effective to obtain accurate and timely large-scale genomic sequence data on individuals (short read massively parallel or next generation [next-gen]). A next-gen molecular diagnostic approach that has seen rapid deployment in the clinic over the last year is exome sequencing. Whole exome sequencing covers all protein-coding genes in the genome (≈1.1% of genome), and an exome test for a single patient generates ≈6 gigabases (109 bp) of DNA sequence data. A key challenge facing routine use of next-gen data in patient diagnosis and management is data interpretation. What sequence variant findings are relevant to diagnosis (pathogenic mutations)? What sequence variant findings are relevant to clinical care but not necessarily to patient diagnosis (clinically actionable incidental data)? What sequence information should be stored, and where can it be stored? This review provides a tutorial on current approaches to answering these questions. A recent landmark study showed that application of next-gen sequencing to a large cohort of idiopathic dilated cardiomyopathy patients found ≈27% of patients to show mutations of the titin gene, the most complex gene in the genome (363 exons). We use titin in cardiomyopathy as an exemplar for explaining next-gen sequencing approaches and data interpretation. Decreasing sequencing costs and broad dissemination of next-generation (next-gen) equipment and expertise are increasing availability of massively parallel sequencing of patient DNA samples (short read massively parallel or next-gen sequencing).1,2 Most rapidly expanding is exome sequencing, where all protein-coding sequences (exons) are selected from total genomic DNA and selectively sequenced.3 Alternative approaches to next-gen sequencing include targeted sequencing (TS) and whole genome (complete genome) sequencing. Currently, marketed targeted Sanger sequencing panels using traditional individual exon-by-exon sequencing remain expensive and time consuming, and massively parallel next-gen approaches are beginning to supplant …

The complete mitochondrial genome of Sirembo imberbis was determined by the bioinformatic assembly of the next generation sequencing (NGS) reads. Total length of the mitogenome was 16,717 bp, which harbors the conserved 13 protein-coding genes (PCGs), 2 ribosomal RNAs (12S and 16S), 22 tRNAs, and two non-coding region (the control region and the origin of light-strand replication). Among 13 protein-coding genes, unusual start codon (GTG) was exclusively identified in COX1, while the incomplete stop codons (TA- or T–) were detected in COX2, COX3, ND2, ND3, ND4 and CytB. As a result of phylogenetic tree, S. imberbis formed a cluster of the family Ophidiidae together with Bassozetus zenkevitchi and Lamprogrammus niger.

Characterising mitochondrial genomes is a key to studying evolution in vertebrates including turtles. This study employed Next-Generation Sequencing (NGS) to characterise mitochondrial DNA sequences in Batagur borneoensis (Schlegel & Muller, 1844). We reported the nearly complete mitogenome to clearly characterise the gene sequence of B. borneoensis which has been deposited in GenBank under the accession number PP228865. Phylogenetic analyses using Maximum Likelihood (ML) on the 13 protein-coding genes were conducted with MEGA X Version 11 software. This study presents the second in-depth analysis of the B. borneoensis mitochondrial genome, spanning 16,397 base pairs and containing 13 protein-coding genes, 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and a major non-coding region, two non-coding regions: L-strand origin replication (OL) and control region (OH). The sequence length and organisation of this species' mitochondrial genome fall within the typical range and gene arrangement found in vertebrate species. Most genes, except for seven tRNAs and nad6, were encoded on the primary DNA strand. All protein-coding genes (PCGs) began with an ATG initiation codon, except for cox1 and trnF which started with GTG codon, and nad3_0, started with a TTA codon. These findings enhanced our understanding of nucleotide composition and molecular evolution in the genus Batagur. Phylogenetic analyses identified vulnerable and ecologically important species, aiding biodiversity and ecosystem protection. They also expanded the dataset for comparative studies within the Geoemydidae family. Additionally, this research may help develop primers and conservation strategies for future studies.

Human Genome Project had been completed in 2003. It provides gigantic resources for biological research. In recent years, next generation sequencing technique dramatically reduces the sequencing cost and time. Thus, completely sequencing new organisms will be popular and universal, and the genomes of these organisms also include huge research resources. The demands of comprehensive genomic annotation will be more urgent and necessary. Thus, it is necessary a computational pipeline. In order to assembly complete genome sequences, this pipeline uses several assembly tools which designed for assembling traditional sequencing and next generate sequencing raw data. It also integrates ab initio and evidence-based gene prediction approaches to predict genes. In addition, this pipeline can reconstruct metabolic pathways from the gene annotation results. This computational pipeline can assemble sequencing data from various platforms and provide the service of genomic annotation including: gene annotation and metabolic pathway reconstruction. This computational pipeline can be a crucial part of pipeline in the high throughput genomic annotation.