The complete mitochondrial genome of the Alpine musk deer (Moschus chrysogaster)

A brighter shade of future climate on Himalayan musk deer Moschus leucogaster

Himalayan musk deer (Moschus leucogaster) is classified as an endangered species by IUCN with a historically misunderstood distribution due to misidentification with other species of musk deer, Moschus spp. Taking advantage of recent genetic analyses confirming the species of various populations in Nepal and China, we produced an accurate estimate of the species' current and future distribution under multiple climate change scenarios. We collected high-quality occurrence data using systematic surveys of various protected areas of Nepal to train species distribution models. The most influential determinants of the distribution of Himalayan musk deer were precipitation of the driest quarter, temperature seasonality, and annual mean temperature. These variables, and precipitation in particular, determine the vegetation type and structure in the Himalaya, which is strongly correlated with the distribution of Himalayan musk deer. We predicted suitable habitats between the Annapurna and Kanchenjunga region of Nepal Himalaya as well as the adjacent Himalaya in China. Under multiple climate change scenarios, the vast majority (85-89%) of current suitable sites are likely to remain suitable and many new areas of suitable habitat may emerge to the west and north of the current species range in Nepal and China. Two-thirds of current and one-third of future suitable habitats are protected by the extensive network of protected areas in Nepal. The projected large gains in suitable sites may lead to population expansion and conservation gains, only when the threat of overexploitation and population decline is under control.

Mitochondrial genome of captive Alpine musk deer, Moschus chrysogaster (Moschidae), and phylogenetic analyses with its coordinal species

Alpine musk deer, Moschus chrysogaster, a solitary, primitive ungulate inhabiting high elevation areas (3000–4500 m) is an endangered species facing threat of extinction globally due to excessive hunting for its musk. In this study, we determined the complete mitochondrial genome of M. chrysogaster, which was 16,354 bp in length, and revealed the same gene order and genomic organization as typical Moschidae mitochondrial DNA. Start codons in 13 protein-coding genes (PCGs) were all typical ATGs except ATA for ND2 and ND3 and ATT for ND5. Stop codons were all typical types except an incomplete stop codon T for COX3, ND2, ND3, and ND4. Secondary structures in 22 transfer RNA genes all showed typical cloverleaf except tRNA-Ser (AGY), in which the dihydrouridine arm formed a simple loop. No repeat units were found in the control region. The topology structure indicated that M. cupreus was primitive and located at the root of the Moschidae clade. Phylogenetic reconstruction placed M. chrysogaster as a distinct lineage, closely related to the branch of M. leucogaster, M. berezovskii (wild) and predicted a sister relationship with M. moschiferus, M. anhuiensis, and M. berezovskii (captive). However, we suggested that the genetic resources of M. chrysogaster_JQ608470 should be further investigated.

Next generation sequencing yields the complete mitogenome of captive forest musk deer, Moschus berezovskii (Ruminantia: Moschidae)

Moschus berezovskii is an endangered species, but its captive populations are valuable on musk secretions in traditional Chinese medicine and perfume manufacture. The mitogenome of M. berezovskii was 16,353 bp in size. Stop codons in 13 PCGs were all typical types except incomplete stop codon T for COX3, ND2 and ND4, and TA for ND3. No tandem repeat was found in control region. Phylogenetic analysis indicated that Moschidae has the closest relationship with Bovidae. We supported that M. berezovskii should be categorized into two subspecies, and suggested that the status of M. chrysogaster JQ608470 should be further investigated.

Characterization of the complete mitogenome of Indian Mouse Deer, Moschiola indica (Artiodactyla: Tragulidae) and its evolutionary significance

The mitochondrial genome of Indian mouse deer (Moschiola indica) was sequenced, assembled and characterized for the first time using 22 pairs of polymerase chain reaction (PCR) primers. The mitogenome of M. indica which is 16,444 bp in size was found very similar to most vertebrates in organisation that harbours 13 protein-coding genes, 22 transfer RNA, 2 ribosomal RNA and 1A + T-rich region. Its comparison with over 52 mitogenomes of the order Artiodactyla, showed a conserved nature of gene organisation, codon usage, gene orientation and evolutionary rates of proteins except that M. indica possesses an extra copy of trnF. The complete mitogenome and protein-coding genes of M. indica were found to be highly A + T biased. Rate of protein evolution was highest in atp8 and lowest in cox3. Further, a higher purifying selection pressure was found to be acting on family Tragulidae compared to Bovidae and Cervidae. The phylogenetic analysis of M. indica placed the Tragulidae as sister-group of all other ruminants, similar to previous analyses. Moschiola forms the sister-group to the other two tragulid genera Tragulus (from Asia) and Hyemoschus (from Africa), which is unexpected as usually the Asian species are thought to form a monophyletic group.

Mitogenome metadata: current trends and proposed standards

Mitogenome metadata are descriptive terms about the sequence, and its specimen description that allow both to be digitally discoverable and interoperable. Here, we review a sampling of mitogenome metadata published in the journal Mitochondrial DNA between 2005 and 2014. Specifically, we have focused on a subset of metadata fields that are available for GenBank records, and specified by the Genomics Standards Consortium (GSC) and other biodiversity metadata standards; and we assessed their presence across three main categories: collection, biological and taxonomic information. To do this we reviewed 146 mitogenome manuscripts, and their associated GenBank records, and scored them for 13 metadata fields. We also explored the potential for mitogenome misidentification using their sequence diversity, and taxonomic metadata on the Barcode of Life Datasystems (BOLD). For this, we focused on all Lepidoptera and Perciformes mitogenomes included in the review, along with additional mitogenome sequence data mined from Genbank. Overall, we found that none of 146 mitogenome projects provided all the metadata we looked for; and only 17 projects provided at least one category of metadata across the three main categories. Comparisons using mtDNA sequences from BOLD, suggest that some mitogenomes may be misidentified. Lastly, we appreciate the research potential of mitogenomes announced through this journal; and we conclude with a suggestion of 13 metadata fields, available on GenBank, that if provided in a mitogenomes's GenBank record, would increase their research value.