Characterization Of Mitochondrial Genome Research Articles

An introduction to the Special Section on Crustacean Mitochondrial Genomics: Improving the assembly, annotation, and characterization of mitochondrial genomes using user-friendly and open-access bioinformatics tools, with decapod crustaceans as an example

Abstract The special section on crustacean mitochondrial genomics houses five articles focused on the characterization of mitochondrial genomes in different decapod crustaceans. In this introductory article, I highlight details and peculiarities of the workflow used in these articles with which mitochondrial genomes were de novo assembled, annotated, manually curated, and characterized. The workflows used in these studies improves the characterization of mitochondrial genomes and are expected to democratize and advance our knowledge on mitochondrial genomics in non-model crustaceans, while profiting from user-friendly and open access bioinformatics tools.

Characterization of the complete mitochondrial genome of Diplocheila zealandica Redtenbacher (Insecta: Coleoptera: Carabidae) from Henan province

Diplocheila zealandica Redtenbacher is a natural enemy of aphids and larva of lepidoptera worldwide. Here, we first report the characterization of mitochondrial genome of D. zealandica in Diplocheila and its phylogenetic position. The complete mitogenome (GenBank accession number: MN995217) of D. zealandica from Henan Province consisted of a circular DNA molecule of 16,190 bp (with 21.66% G + C content), which comprised 13 protein-coding genes (PCGs), and 22 tRNA, and two rRNA genes. PCGs had typical ATN (Met) initiation codons and were terminated by typical TAN stop codons.

Characterization of the complete mitochondrial genome of Plagiorchis maculosus (Digenea, Plagiorchiidae), Representative of a taxonomically complex digenean family

Despite the highly divergent morphology, pathogenicity and worldwide distribution of digenean parasites belonging to one of the largest families, the Plagiorchiidae, there are no complete mitochondrial (mt) genomes published to date for plagiorchiids. In this study, we obtained nuclear ribosomal DNA (ITS region and 28S rDNA) sequences and the complete mt genome sequences of Plagiorchis maculosus (Rudolphi 1802) Braun, 1902, and assessed its phylogenetic relationship with other xiphidiates, based on the mtDNA sequences. The obtained ITS and 28S rDNA sequences were identical to the corresponding sequences of P. maculosus available in GenBank. The complete mitochondrial genome of P. maculosus (14,124 bp) contained 36 genes (atp8 is absent) and a long non-coding region (NCR) with two sets of repeated sequences of 283 nucleotides each. The phylogenetic tree resulting from Bayesian inference (BI) analyses based on concatenated nucleotide sequences of all 36 genes of P. maculosus and other xiphidiates mitochondrial genomes, indicated that P. maculosus (and the Plagiorchiidae) is phylogenetically closest to the Brachycladiidae and Paragonimidae. The present study describes the first mitochondrial genome from the type genus of the family Plagiorchiidae. The overall gene arrangement, nucleotide composition, A + T contents, AT and GC skew and codon usage with relative synonymous codon usage (RSCU) for 12 PCGs are described. Characterization of mitochondrial genomes from additional plagiorchiid taxa is necessary to make further progress in phylogenetic and epidemiological studies of these digeneans as well as accurate diagnostics of these parasites including those parasitic in humans.

Complete mitochondrial genome of Black Soft-shell Turtle (Nilssonia nigricans) and comparative analysis with other Trionychidae

The characterization of mitochondrial genome has been evidenced as an efficient field of study for phylogenetic and evolutionary analysis in vertebrates including turtles. The aim of this study was to distinguish the structure and variability of the Trionychidae species mitogenomes through comparative analysis. The complete mitogenome (16796 bp) of an endangered freshwater turtle, Nilssonia nigricans was sequenced and annotated. The mitogenome encoded for 37 genes and a major non-coding control region (CR). The mitogenome was A + T biased (62.16%) and included six overlapping and 19 intergenic spacer regions. The Relative synonymous codon usage (RSCU) value was consistent among all the Trionychidae species; with the exception of significant reduction of Serine (TCG) frequency in N. nigricans, N. formosa, and R. swinhoei. In N. nigricans, most of the transfer RNAs (tRNAs) were folded into classic clover-leaf secondary structures with Watson-Crick base pairing except for trnS1 (GCT). The comparative analysis revealed that most of the tRNAs were structurally different, except for trnE (TTC), trnQ (TTG), and trnM (CAT). The structural features of tRNAs resulted ≥ 10 mismatched or wobble base pairings in 12 tRNAs, which reflects the nucleotide composition in both H- and L-strands. The mitogenome of N. nigricans also revealed two unique tandem repeats (ATTAT)8, and (TATTA)20 in the CR. Further, the conserved motif 5′-GACATA-3′ and stable stem-loop structure was detected in the CRs of all Trionychidae species, which play an significant role in regulating transcription and replication in the mitochondrial genome. Further, the comparative analysis of Ka/Ks indicated negative selection in most of the protein coding genes (PCGs). The constructed Maximum Likelihood (ML) phylogeny using all PCGs showed clustering of N. nigricans with N. formosa. The resulting phylogeny illustrated the similar topology as described previously and consistent with the taxonomic classification. However, more sampling from different taxonomic groups of Testudines and studies on their mitogenomics are desirable for better understanding of the phylogenetic and evolutionary relationships.

Complete sequence and characterization of mitochondrial genome in the swimming crab Portunus sanguinolentus (Herbst, 1783) (Decapoda, Brachyura, Portunidae)

The three-spot swimming crab Portunus sanguinolentus (Herbst, 1783) is a commercially important fishery species, widely distributed in the Indo-Pacific region. In this study, we present the complete mitochondrial genome of P. sanguinolentus. The genome is 16 027 bp in length with circular organization, encoding the standard set of 13 protein-coding genes, 22 tRNA genes, and two rRNA genes. The overall A + T content is 65.60%, which is lower than that of its congeneric species Portunus pelagicus and Portunus trituberculatus. The mitogenome carries 1254 bp of intergenic region constituting 7.82% of the genome, and six pairs of overlapping genes with the overlap size from 1 to 7 bp. The complete mitogenome sequence information of P. sanguinolentus would provide useful data for further studies on population genetics and molecular systematics.

Complete sequence and characterization of mitochondrial genome in great snakehead, Channa marulius (Hamilton, 1822)

The complete nucleotide sequence of mitogenome of the great snakehead, Channa marulius (Channidae), was determined and found to be 16,569 base pairs in length. The content and arrangement of different genes on the mitogenome was found similar to other typical teleosts. The overall base composition of the L-strand was found to be T (19.1%), C (31.5%), A (34.8%) and G (14.6%). The control region was 915 nt long and without any repetitive region. The mitogenome sequence data would be useful for studying phylogenetic relationship of C. marulius with other perciform species.

Molecular Characterization of Mitochondrial Genomes of Rice Lines Containing Wild Abortive (WA) Male Sterile and Fertile Cytoplasms

Indian rice breeders have developed hybrid rice using primarily the wild abortive (WA) type cytoplasm for the male sterile parent. In this communication, we report our studies on the molecular characterization of the mitochondrial genomes of male sterile lines possessing this cytoplasm as also the respective maintainer, restorer and restored lines using 16 mitochondrial gene probes. The results show polymorphism in the location of several genes and expression of one of the genes, namely orf 156. Polymorphism in five genes namely coxl, cob, atp 6, rrn18 and orf156 differentiates the sterile cytoplasm from the fertile ones while the RFLPs in coxIII and rps14 can differentiate maintainers and restores from each other. The WA cytoplasm is very different from the Chinsurah boro II cytoplasm as is evident from the transcription patterns of atp6. Of the genes studied, only orf156, which encodes a membrane bound 156 amino acid long polypeptide showed differences In the transcript pattern between the male sterile and fertile cytoplasms. However, it is not clear whether this gene is associated with the CMS trait in WA type of cytoplasm. These studies show the utility of mitochondrial RFLPs to distinguish different cytoplasms existing in the rice lines.