EZmito: a simple and fast tool for multiple mitogenome analyses

Detailed characterization of the complete mitochondrial genome of the oceanic whitetip shark Carcharhinus longimanus (Poey, 1861)

BACKGROUND

The oceanic whitetip shark Carcharhinus longimanus (family Carcharhinidae) is one of the largest sharks inhabiting all tropical and subtropical oceanic regions. Due to their life history traits and mortality attributed to pelagic longline fishing practices, this species is experiencing substantial population decline. Currently, C. longimanus is considered by the IUCN Red List of Threatened Species as "vulnerable" throughout its range and "critically endangered" in the western north Atlantic. This study sequences and describes the complete mitochondrial genome of C. longimanus in detail.

METHODS AND RESULTS

The mitochondrial genome of C. longimanus was assembled through next-generation sequencing and then analyzed using specialized bioinformatics tools. The circular, double-stranded AT-rich mitogenome of C. longimanus is 16,704 bp long and contains 22 tRNA genes, 2 rRNA genes, 13 protein coding genes and a 1,065 bp long control region (CR). Out of the 22 tRNA genes, only one (tRNA-Ser1) lacked a typical 'cloverleaf' secondary structure. The prevalence of TTA (Leu), ATT (Ile) and CTA (Leu) codons in the PCGs likely contributes to the AT-rich nature of this mitogenome. In the CR, ten microsatellites were detected but no tandem repeats were found. Stem-and-loop secondary structures were common along the entire length of the CR. Ka/Ks values estimated for all PCGs were < 1, indicating that all the PCGs experience purifying selection. A phylomitogenomic analysis based on translated PCGs confirms the sister relationship between C. longimanus and C. obscurus. The analysis did not support the monophyly of the genus Carcharhinus.

CONCLUSIONS

The assembled mitochondrial genome of this pelagic shark can provide insight into the phylogenetic relationships in the genus Carcharhinus and aid conservation and management efforts in the Central Pacific Ocean.

Characterization of the mitochondrial genomes of the Mexican endemic bats Corynorhinus mexicanus and Corynorhinus leonpaniaguae (Chiroptera: Vespertilionidae)

BACKGROUND

The genus Corynorhinus is composed of four recognized species: C. rafinesquii, C. townsendii, C. mexicanus, and C. leonpaniaguae, the latter two being endemic to Mexico. According to the IUCN, C. mexicanus is considered "Near Threatened", as its populations are dwindling and habitats are affected by anthropogenic disturbance. Corynorhinus leonpaniaguae has not been assigned to an IUCN Red List risk category due to its recent description.

METHODS AND RESULTS

In this study, the mitochondrial genomes of C. mexicanus and C. leonpaniaguae were assembled and characterized in detail. The mitochondrial genomes (mtDNA) of C. mexicanus and C. leonpaniaguae have lengths of 16,470 and 16,581 bp respectively, with a predominant nucleotide usage of adenine (31.670% and 31.729%, respectively) and thymine (26.15% and 26.18%, respectively). The mtDNA of C. mexicanus and C. leonpaniaguae is composed of 37 coding and non-coding elements: 22 transfer RNAs (tRNA), 13 protein-coding genes (PCGs), two ribosomal RNAs and a non-coding region, the control region, which has a length of 933 bp and 1,149 bp, respectively. All tRNAs exhibited a cloverleaf secondary structure, with the exception of trn-Ser1 which showed a deletion of the dihydrouridine arm in the two species. All PCGs are subjected to purifying selection, with atp8 being the gene showing the highest Ka/Ks value.

CONCLUSIONS

These are the first whole mitogenomic resources developed for C. mexicanus and C. leonpaniaguae and enhance our knowledge of the ecology of these species and aid in their conservation.

Mitochondrial genome comparison and phylogenetic position of Fannia pusio among the Calyptratae flies

Fannia pusio, the chicken dung fly species, remains unexplored despite its forensic, sanitary, and veterinary importance in the Nearctic and Neotropical regions. In this study, we obtained the complete mitochondrial genome of Fannia pusio for the first time using next-generation sequencing. We compared it with previously published mitogenomes of the genus from the Palearctic region, and its phylogenetic position was studied based on the concatenated protein-coding genes (PCGs) dataset of Calyptratae flies. The circular mitochondrial genome of F. pusio is 16,176 bp in length, with a high A + T content (78.3%), whose gene synteny, codon usage analysis, and amino acid frequency are similar to previously reported Fannia mitogenomes. All PCGs underwent purifying selection except the nad2 gene. Interspecific K2P distances of PCGs of Fannia yielded an average of 12.4% (8.1%-21.1%). The Fannia genus is monophyletic and closely related to Muscidae based on molecular data. Further taxonomic sampling is required to deep into the phylogenetic relationships of the originally proposed species-groups and subgroups within the genus. These results provide a valuable dataset for studying the mitochondrial genome evolution and a resource for the taxonomy and systematics of Fannia.

Complete mitogenome of Lepidopygopsis typus, an evolutionarily-distinct, endangered cyprinid fish from the Western Ghats Biodiversity Hotspot: Phylogenetic relationships and implications for conservation

The mitogenome of Lepidopygopsis typus, an evolutionarily distinct, endangered, cyprinid fish from the Western Ghats Biodiversity Hotspot, was characterized. Total length of the mitogenome was 16,729 bp, and comprised of 13 protein coding, 22 tRNA and two rRNA genes. Thirteen protein coding genes contributed a total nucleotide length of 11,408 bp, which coded for a total of 3794 amino acids and accounting for 68.2 % of the mitogenome. A maximum likelihood phylogenetic tree based on mitogenomes of members of cyprinid subfamilies Torinae, Schizothoracinae and Schizopygopsinae, recovered L. typus in a well-resolved clade of Torinae with members of the Western Ghats endemic genus Hypselobarbus as sister taxa. Selection analysis suggested that the branch of L. typus and Hypselobarbus spp. was under intensified selection with reference to other members of Torinae. There were 19 codons under diversifying selection in L. typus, which could be the result of positive selection for adapting to high-altitude, upstream tributaries of Periyar River, where the species has a restricted distribution. With respect to Hypselobarbus spp., L. typus was under relaxed selection with about 68 % of codons experiencing neutral evolution. Restricted distribution, low population size and relaxation in selection can likely trigger extinction in L. typus, and therefore urgent conservation and monitoring plans are required to secure the future of this evolutionary distinct, and globally endangered species.

Insights into the nuclear and mitochondrial genome of the Lemon shark Negaprion brevirostris using low-coverage sequencing: Genome size, repetitive elements, mitochondrial genome, and phylogenetic placement

The Lemon shark Negaprion brevirostris is an important species experiencing conservation issues that is in need of genomic resources. Herein, we conducted a genome survey sequencing in N. brevirostris and determined genome size, explored repetitive elements, assembled and annotated the 45S rRNA DNA operon, and assembled and described in detail the mitochondrial genome. Lastly, the phylogenetic position of N. brevirostris in the family Carcharhinidae was examined using translated protein coding genes. The estimated haploid genome size ranged between 2.29 and 2.58 Gbp using a k-mer analysis, which is slightly below the genome size estimated for other sharks belonging to the family Carcharhinidae. Using a k-mer analysis, approx. 64-71 % of the genome of N. brevirostris was composed of repetitive elements. A relatively large proportion of the 'repeatome' could not be annotated. Taking into account only annotated repetitive elements, Class I - Long Interspersed Nuclear Element (LINE) were the most abundant repetitive elements followed by Class I - Penelope and Satellite DNA. The nuclear ribosomal operon was fully assembled. The AT-rich complete mitochondrial genome was 16,703 bp long and encoded 13 protein coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Negaprion brevirostris is closely related to the genera Carcharhinus, Glyphis and Lamiopsis in the family Carcharinidae. This new genomic resources will aid with the development of conservation plans for this large coastal shark.

Insights into the genome of the 'Loco' Concholepas concholepas (Gastropoda: Muricidae) from low-coverage short-read sequencing: genome size, ploidy, transposable elements, nuclear RNA gene operon, mitochondrial genome, and phylogenetic placement in the family Muricidae

BACKGROUND

The Peruvian 'chanque' or Chilean 'loco' Concholepas concholepas is an economically, ecologically, and culturally important muricid gastropod heavily exploited by artisanal fisheries in the temperate southeastern Pacific Ocean. In this study, we have profited from a set of bioinformatics tools to recover important biological information of C. concholepas from low-coverage short-read NGS datasets. Specifically, we calculated the size of the nuclear genome, ploidy, and estimated transposable elements content using an in silico k-mer approach, we discovered, annotated, and quantified those transposable elements, we assembled and annotated the 45S rDNA RNA operon and mitochondrial genome, and we confirmed the phylogenetic position of C. concholepas within the muricid subfamily Rapaninae based on translated protein coding genes.

RESULTS

Using a k-mer approach, the haploid genome size estimated for the predicted diploid genome of C. concholepas varied between 1.83 Gbp (with kmer = 24) and 2.32 Gbp (with kmer = 36). Between half and two thirds of the nuclear genome of C. concholepas was composed of transposable elements. The most common transposable elements were classified as Long Interspersed Nuclear Elements and Short Interspersed Nuclear Elements, which were more abundant than DNA transposons, simple repeats, and Long Terminal Repeats. Less abundant repeat elements included Helitron mobile elements, 45S rRNA DNA, and Satellite DNA, among a few others.The 45S rRNA DNA operon of C. concholepas that encodes for the ssrRNA, 5.8S rRNA, and lsrRNA genes was assembled into a single contig 8,090 bp long. The assembled mitochondrial genome of C. concholepas is 15,449 bp long and encodes 13 protein coding genes, two ribosomal genes, and 22 transfer RNAs.

CONCLUSION

The information gained by this study will inform the assembly of a high quality nuclear genome for C. concholepas and will support bioprospecting and biomonitoring using environmental DNA to advance development of conservation and management plans in this overexploited marine snail.

The complete mitochondrial genome of Octopus vulgaris

BACKGROUND

The Octopus vulgaris species complex consists of numerous morphologically similar but genetically distinct species. The current publicly available mitogenome of this species has been generated from a specimen collected from Tsukiji Fish Market, Tokyo, Japan. Octopus from the northwestern Pacific Ocean are now considered to be a separate species, Octopus sinensis. For this reason, we hypothesised that the current record of O. vulgaris was sequenced from a specimen of O. sinensis. Here, we sequenced the first complete mitogenome of a specimen of Octopus vulgaris sensu stricto that was collected from the species' confirmed distribution areas in northeastern Atlantic.

METHODS AND RESULTS

The complete mitogenome was assembled de novo and annotated using 250 bp paired-end sequences. A single circular contig 15,655 bp in length with a mean read coverage of 1089 reads was reconstructed. The annotation pipeline identified 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNA) and two ribosomal RNAs. A maximum likelihood phylogenetic tree recovered the assembled mitogenome as the sister taxon of a monophyletic group comprising O. sinensis and the previously published mitogenome of "O. vulgaris" from Japan. This confirms that the latter was a Japanese specimen of O. sinensis.

CONCLUSION

The mitogenome sequenced here is the first to be published for Octopus vulgaris sensu stricto. It represents an important first step in genetics-informed research on the evolution, conservation, and management of this commercially important species.

Phylomitogenomics elucidates the evolution of symbiosis in Thoracotremata (Decapoda: Cryptochiridae, Pinnotheridae, Varunidae)

Background

Thoracotremata belong to the large group of "true" crabs (infraorder Brachyura), and they exhibit a wide range of physiological and morphological adaptations to living in terrestrial, freshwater and marine habitats. Moreover, the clade comprises various symbiotic taxa (Aphanodactylidae, Cryptochiridae, Pinnotheridae, some Varunidae) that are specialised in living with invertebrate hosts, but the evolutionary history of these symbiotic crabs is still partially unresolved.

Methods

Here we assembled and characterised the complete mitochondrial genomes (hereafter mitogenomes) of three gall crab species (Cryptochiridae): Kroppcarcinus siderastreicola, Opecarcinus hypostegus and Troglocarcinus corallicola. A phylogenetic tree of the Thoracotremata was reconstructed using 13 protein-coding genes and two ribosomal RNA genes retrieved from three new gall crab mitogenomes and a further 72 available thoracotreme mitogenomes. Furthermore, we applied a comparative analysis to characterise mitochondrial gene order arrangement, and performed a selection analysis to test for selective pressure of the protein-coding genes in symbiotic Cryptochiridae, Pinnotheridae, and Varunidae (Asthenognathus inaequipes and Tritodynamia horvathi).

Results

The results of the phylogenetic reconstruction confirm the monophyly of Cryptochiridae, which clustered separately from the Pinnotheridae. The latter clustered at the base of the tree with robust branch values. The symbiotic varunids A. inaequipes and T. horvathi clustered together in a clade with free-living Varunidae species, highlighting that symbiosis in the Thoracotremata evolved independently on multiple occasions. Different gene orders were detected in symbionts and free-living species when compared with the ancestral brachyuran gene order. Lastly, the selective pressure analysis detected two positively selected sites in the nad6 gene of Cryptochiridae, but the evidence for positive selection in Pinnotheridae and A. inaequipes and T. horvathi was weak. Adaptive evolution of mitochondrial protein-coding genes is perhaps related to the presumably higher energetic demands of a symbiotic lifestyle.

The mitochondrial genome of the mountain wooly tapir, Tapirus pinchaque and a formal test of the effect of altitude on the adaptive evolution of mitochondrial protein coding genes in odd-toed ungulates

BACKGROUND

The harsh conditions of high-altitude environments are known to drive the evolution of physiological and morphological traits in endothermic animals. These conditions are expected to result in the adaptive evolution of protein coding genes encoded in mitochondrial genomes that are vital for the oxidative phosphorylation pathway. In this study, we formally tested for signatures of adaptive evolution on mitochondrial protein coding genes in Tapirus pinchaque and other odd-toed ungulates inhabiting high-elevation environments.

RESULTS

The AT-rich mitochondrial genome of T. pinchaque is 16,750 bp long. A phylomitogenomic analysis supports the monophyly of the genus Tapirus and families in the Perissodactyla. The ratio of non-synonymous to synonymous substitutions demonstrated that all mitochondrial genes undergo purifying selection in T. pinchaque and other odd ungulates living at high elevations. Over this negative background selection, Branch Models suggested that cox3 and nad6 might be undergoing stronger purifying selection than other mitochondrial protein coding genes. Furthermore, Site Models suggested that one and four sites in nad2 and nad5, respectively, could be experiencing positive selection. However, these results were supported by Likelihood Ratio Tests but not Bayesian Empirical Bayes posterior probabilities. Additional analyses (in DataMonkey) indicated a relaxation of selection strength in nad6, evidence of episodic diversifying selection in cob, and revealed episodic positive/diversifying selection signatures for two sites in nad1, and one site each in nad2 and nad4.

CONCLUSION

The mitochondrial genome of T. pinchaque is an important genomic resource for conservation of this species and this study contributes to the understanding of adaptive evolution of mitochondrial protein coding genes in odd-toed ungulates inhabiting high-altitude environments.

The mitochondrial genome of the pentastome parasite Raillietiella orientalis Hett, 1915 (Raillietiellida; Raillietiellidae) with notes on its phylogenetic position

In this study we sequenced and annotated the complete mitochondrial genome of the invasive reptile parasite Raillietiella orientalis using Illumina DNA sequencing. The length of the mitogenome was 15,320 bp and had a GC content of 33.1%. The mitogenome contained 13 protein-coding genes, two ribosomal RNA genes, and 22 tRNA genes, the order of which was diagnostic of Pancrustacean mitogenomes. A phylogenetic tree constructed from the 13 protein-coding genes of R. orientalis and 26 other Pancrustacean mitogenomes supported the placement of R. orientalis as part of the monophyletic subclass Pentastomida within the Maxillopoda and sister to the subclass Branchiura.

Comparative mitochondrial genomics of American nectar-feeding long-nosed bats Leptonycteris spp. with insights into the phylogeny of the family Phyllostomidae

Among leaf-nosed bats (family Phyllostomidae), the genus Leptonycteris (subfamily Glossophaginae), contains three migratory and obligate nectar-dwelling species of great ecological and economic importance; the greater long-nosed bat L. nivalis, the lesser long-nosed bat L. yerbabuenae, and the southern long-nosed bat L. curasoae. According to the IUCN, the three species are categorized as 'vulnerable', 'endangered', and 'near threatened', respectively. In this study, we assembled and characterized in detail the mitochondrial genome of Leptonycteris spp. and examined the phylogenetic position of this genus in the family Phyllostomidae based on protein coding genes (PCGs). The mitogenomes of L. nivalis, L. curasoae, and L. yerbabuenae are 16,708, 16,758, and 16,729 bp in length and each encode 13 PCGs, 22 transfer RNA genes, 2 rRNA genes, and a putative control region (CR). Mitochondrial gene order is identical to that reported before for the family Phyllostomidae. All tRNAs exhibit a 'cloverleaf' secondary structure, except tRNA-Serine-1 that is missing the DHU arm in the three species. All PCGs are exposed to purifying selection with atp8 experiencing the most relaxed purifying selection as the ω ratio was higher for this gene compared to the other PCGs in each species. The CR of each species contains three functional domains: extended termination associated sequence (ETAS), Central, and conserved sequence block domain (CSB). A phylomitogenomic analysis revealed that Leptonycteris is monophyletic and most closely related to the genus Glossophaga. The analysis also supported the monophyly of the family Glossophaginae in the speciose family Phyllostomidae. The mitochondria characterization of these species provides relevant information to develop molecular markers for conservation purposes.

Low coverage sequencing provides insights into the key features of the nuclear and mitochondrial genomes of the Alligator Snapping Turtle Macrochelys temminckii

The alligator snapping turtle Macrochelys temminckii is a culturally, ecologically, and evolutionary relevant species of conservation concern. In this study, we conducted a genome survey of M. temminckii. Using a low-coverage short read sequencing strategy, this study estimated the genome size, repetitive genome content, annotated and quantified repetitive elements, assembled the 45S rRNA DNA operon, and characterized in detail the mitochondrial genome of M. temminckii. Using a k-mer strategy, the estimated haploid genome size varied between 3.77 and 3.19 Gbp, which is within the range previously reported for other representatives of the family Chelydridae. Repetitive genome content estimates using different k-mers (21 to 51) indicated that more than 75% of the genome of M. temminckii comprised repetitive elements. Taking into account only annotated repetitive elements, the most common repetitive elements were classified as Class I - Long Interspersed Nuclear Element (LINE) which were more abundant than Class I - Penelope and Class I - Long Terminal Repeat (LTR) Ty3-gypsy mobile elements. Less abundant repeat element families in the nuclear genome of M. temminckii included Class I - DIRS mobile elements and Satellite DNA. The nuclear ribosomal operon was partially assembled into two contigs, one encoding the complete ssrDNA and a second comprising the full lsrDNA. The AT-rich complete mitochondrial genome was 16,570 bp long. These new genomic resources are of utmost importance to aid in the development of conservation plans for this freshwater turtle.

First description of the mitochondrial genomes of the Central American brocket deer Mazama temama (Kerr, 1792) and the Yucatán Peninsula brocket deer Odocoileus pandora Merriam, 1901

BACKGROUND

The Central American (Mazama temama) and the Yucatán Peninsula brocket deer (Odocoileus pandora) are deer species with cryptic habits, and little is known about their biology. Odocoileus pandora is listed as Vulnerable on the 2015 IUCN Red List of Threatened Species, while M. temama is considered Data Deficient; however, it currently faces a decreasing population trend.

METHODS AND RESULTS

We assembled the complete mitochondrial genome for two M. temama specimens and one complete and one partial for O. pandora from Illumina 150 bp paired-end reads. The mitogenomes of M. temama and O. pandora have a length of 16,479-16,480 and 16,419 bp, respectively, AT-biased; they consist of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one non-coding control region, most of them follow a transcription direction in the heavy strand of the molecule. The mitochondrial genome of O. pandora shows some particularities compared to other deer species, like a shorter control region of 987-990 bp and a cytochrome b gene with a length of 1,143 bp. Our phylogenetic analyses confirm the close affinity of M. temama to South American M. americana and the nested position of the genus Odocoileus, including O. pandora, into the genus Mazama.

CONCLUSIONS

Here, we described for the first time the complete mitochondrial genome for these two species. While our study provides additional information about the taxonomic status of the northern neotropical brocket deer, further research is needed to solve the complicated taxonomy of neotropical deer.

First genomic resource for an endangered neotropical mega-herbivore: the complete mitochondrial genome of the forest-dweller (Baird's) tapir (Tapirus bairdii)

Baird's tapir, or the Central American Tapir Tapirus bairdii (family Tapiridae), is one of the largest mammals native to the forests and wetlands of southern North America and Central America, and is categorized as 'endangered' on the 2014 IUCN Red List of Threatened Species. This study reports, for the first time, the complete mitochondrial genome of T. bairdii and examines the phylogenetic position of T. bairdii amongst closely related species in the same family and order to which it belongs using mitochondrial protein-coding genes (PCG's). The circular, double-stranded, A-T rich mitochondrial genome of T. bairdii is 16,697 bp in length consisting of 13 protein-coding genes (PCG's), two ribosomal RNA genes (rrnS (12s ribosomal RNA and rrnL (16s ribosomal RNA)), and 22 transfer RNA (tRNA) genes. A 33 bp long region was identified to be the origin of replication for the light strand (O_L), and a 1,247 bp long control region (CR) contains the origin of replication for the heavy strand (O_H). A majority of the PCG's and tRNA genes are encoded on the positive, or heavy, strand. The gene order in T. baiirdi is identical to that of T. indicus and T. terrestris, the only two other species of extant tapirs with assembled mitochondrial genomes. An analysis of Ka/Ks ratios for all the PCG's show values <1, suggesting that all these PCGs experience strong purifying selection. A maximum-likelihood phylogenetic analysis supports the monophyly of the genus Tapirus and the order Perissodactyla. The complete annotation and analysis of the mitochondrial genome of T. bairdii will contribute to a better understanding of the population genomic diversity and structure of this species, and it will assist in the conservation and protection of its dwindling populations.

The mitogenome of the true bug Nysius cymoides (Insecta, Heteroptera) and the phylogeny of Lygaeoidea

The complete mitochondrial genome of the true bug (Homoptera) Nysius cymoides (Spinola, 1837) is herein described and used for phylogenetic comparison with other species of Lygaeoidea. The mtDNA has a gene order and other molecular features typically observed in hexapods, and a long A + T-rich region, due to the occurrence of several repeat units. The phylogenetic analyses support the monophyly of all families except Rhyparochromidae.

The complete mitochondrial genome of Trissolcus japonicus (Hymenoptera: Scelionidae), the candidate for the biological control of Halyomorpha halys (Hemiptera: Pentatomidae)

The samurai wasp Trissolcus japonicus (Ashmead, 1904) is a parasitoid hymenopteran that came into the limelight as the natural enemy of Halyomorpha halys. Here, we present the complete sequence of the mitochondrial genome of the CREATJ laboratory strain, naturally recovered in Italy in 2018. The molecule conforms to the typical model of animal mitochondrial genomes. Gene order is identical to that of its congeneric Trissolcus basalis. Phylogenetic analysis confirms its placement within monophyletic Scelionidae and Telenominae as the sister group of T. basalis.