The mitochondrial genome and phylogenetic analysis of the tick Haemaphysalis qinghaiensis Teng, 1980 (Acari:Ixodidae)

Haemaphysalis qinghaiensis is an endemic species and mainly inhabiting in the northwestern plateau of China, which can transmit many zoonotic pathogens and cause great harm to animals. In this study, the complete mitochondrial genome (mitogenome) of H. qinghaiensis was assembled through the Illumina HiSeq platform. The mitogenome was 14,533 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and 3 noncoding regions (NCRs). The bias towards a high A+T content with 77.65% in mitogenome of H. qinghaiensis. The rearrangement of mitochondrial genes in H. qinghaiensis was consistent with other hard ticks. The phylogenetic analysis based on the concatenation of 13 PCGs from 65 tick mitogenomes showed that the H. qinghaiensis was clustered into a well-supported clade within the Haemaphysalis genus. This is the first complete mitogenome sequence of H. qinghaiensis, which provides a useful reference for understanding of the taxonomic and genetics of ticks.

Mitochondrial Genome Resource of a grapevine strain of Trichoderma harzianum, a potential biological control agent for fungal canker diseases

Trichoderma spp. are commonly used as bioremediation agents, biological controls, and for making biofuels. Herein, a Trichoderma harzianum strain PAR3 was isolated from grapevine roots in central California, USA. As part of a larger whole genome sequencing effort, the mitochondrial genome (mitogenome) sequence was obtained for the PAR3 strain. The mitogenome is 27,631 bp containing genes of 14 core mitochondrial proteins, 25 tRNA, and two rRNAs and a GC% content of 27.55%. BLAST search using the PAR3 mitogenome as query against GenBank sequence database showed mitogenome MUT3171 (29,791 bp) of Trichoderma lixii was the most similar (Query Coverage = 99%; Percentage Identity=100.00%) with two major deletions, 1,339 bp and 821 bp. The PAR3 mitogenome sequence will provide a useful reference for comparing different Trichoderma strains from US and around the world.

The first complete mitochondrial genome sequence of Cynopterus brachyotis (Müller, 1838) from the Philippines

The technical limitations of capillary sequencing in providing insights on phylogeny have been greatly aided in recent years by the implementation of next generation sequencing platforms which can generate whole mitochondrial genome (mitogenome) sequences. In this study, enriched mitochondrial DNA of Cynopterus brachyotis from Mindanao, Philippines was sequenced using the Illumina MiSeq platform. A total of 653,967 clean paired-end reads was assembled using a MIRA-MITObim pipeline, resulting to a consensus mitogenome sequence length of 17,382 bases and a GC content of 41.48%, which is consistent with other published mitogenomes in fruit bats. The assembled C. brachyotis mitogenome was annotated using the MITOS online server and was able to resolve all mitochondrial genes, except for one transfer RNA gene (trnT) which may be further resolved by additional capillary sequencing of the region. Sequence analysis showed that the Philippine C. brachyotis is only 90%-91% homologous with other Cynopterus spp. based on its full mitogenome sequence. Phylogenetic analysis of fruit bat mitogenomes deposited in online repositories revealed that the Philippine C. brachyotis in this study has diverged from Asian Cynopterus, namely Cynopterus brachyotis and Cynopterus sphinx from other parts of Asia (100% bootstrap support) with the latter two forming a separate clade. This divergence at the species level was consistent with phylogentic inference using cytochrome oxidase 1 (CO1) and cytochrome B (cytb) gene markers. Our results strengthen the previously reported hypothesis that the C. brachyotis in the Philippines is distinct from its Asian counterparts and should be therefore elevated to a new species.

The phylogeny of the Anderson’s White-bellied Rat (Niviventer andersoni) based on complete mitochondrial genomes provides insight into its evolutionary history

Anderson’s White-bellied Rat, Niviventer andersoni (Thomas, 1911) (Muridae, Niviventer) is an species endemic to China. In the present study, we have sequenced the first complete mitochondrial genome of N. andersoni using next-generation sequencing. The 16,291 bp mitochondrial genome consists of 22 transfer RNA genes, 13 protein-coding genes (PCGs), two ribosomal RNA genes, and one non-coding control region (D-Loop). Phylogenetic analyses of the nucleotide sequences of all 13 PCGs, PCGs minus ND6 and the entire mitogenome sequence except for the D-loop, produce nearly identical, well-resolved topologies. Our results support that N. andersoni clustered with N. excelsior and form a sister group with N. confucianus, and they statistically reject the hypothesis from one cytochrome b (cytb) gene tree that N. confucianus is sister to N. fulvescens. Our research may be helpful to further reconsideration of clearer taxonomy and improve our understanding of mitogenomic evolution in the genus Niviventer.

Population dynamics in the Japanese Archipelago since the Pleistocene revealed by the complete mitochondrial genome sequences

The Japanese Archipelago is widely covered with acidic soil made of volcanic ash, an environment which is detrimental to the preservation of ancient biomolecules. More than 10,000 Palaeolithic and Neolithic sites have been discovered nationwide, but few skeletal remains exist and preservation of DNA is poor. Despite these challenging circumstances, we succeeded in obtaining a complete mitogenome (mitochondrial genome) sequence from Palaeolithic human remains. We also obtained those of Neolithic (the hunting-gathering Jomon and the farming Yayoi cultures) remains, and over 2,000 present-day Japanese. The Palaeolithic mitogenome sequence was not found to be a direct ancestor of any of Jomon, Yayoi, and present-day Japanese people. However, it was an ancestral type of haplogroup M, a basal group of the haplogroup M. Therefore, our results indicate continuity in the maternal gene pool from the Palaeolithic to present-day Japanese. We also found that a vast increase of population size happened and has continued since the Yayoi period, characterized with paddy rice farming. It means that the cultural transition, i.e. rice agriculture, had significant impact on the demographic history of Japanese population.

The Complete Mitochondrial Genome of Critically Endangered Hangul (Cervus Hanglu Hanglu) and Its Comparison With the Other Red Deer

Background: Hangul (Cervus hanglu hanglu) or Kashmiri stag belongs to the family Cervidae and is only surviving red deer in the Indian subcontinent. Its complete mitogenome sequence is lacking in the open database for further phylogenetic inferences.Methods and results: We sequenced and characterized the first complete mitogenome of Hangul, which was 16,354 bp in length. It was compared with other red deer subspecies. We observed eight pairs of overlapping genes and 15 intergenic spacers in between the mitochondrial regions. Relative synonymous codon usage (RSCU) for the 13 PCGs of Hangul was consisting of 3597 codons (excluding stop codons). We observed a highest frequency for leucine (11.75%) and the lowest for tryptophan amino acid (1.12%) in 13 PCGs of Hangul. All the tRNA genes showed a typical secondary cloverleaf arrangement, excluding tRNA-Ser in which dihydrouridine arm did not form a stable structure. Conclusions: The Bayesian inference phylogenetic tree indicated that Hangul clustered within the Tarim deer group (C. h. yarkandensis) and closed to C. e. hippelaphus, which formed the western clade. Besides, the subspecies of C. nippon and C. canadensis clustered together and formed an eastern clade. The finding was supported by the mean pairwise genetic distance based on both complete mitogenome and 13 PCGs. The comparative study of the Hangul mitogenome with other red deer provides crucial information for understanding the evolutionary relationships. It offers a valuable resource for conserving this critically endangered cervid with a limited distribution range.

Structural Mutations in the Organellar Genomes of Valeriana sambucifolia f. dageletiana (Nakai. ex Maekawa) Hara Show Dynamic Gene Transfer

Valeriana sambucifolia f. dageletiana (Nakai. ex Maekawa) Hara is a broad-leaved valerian endemic to Ulleung Island, a noted hot spot of endemism in Korea. However, despite its widespread pharmacological use, this plant remains comparatively understudied. Plant cells generally contain two types of organellar genomes (the plastome and the mitogenome) that have undergone independent evolution, which accordingly can provide valuable information for elucidating the phylogenetic relationships and evolutionary histories of terrestrial plants. Moreover, the extensive mega-data available for plant genomes, particularly those of plastomes, can enable researchers to gain an in-depth understanding of the transfer of genes between different types of genomes. In this study, we analyzed two organellar genomes (the 155,179 bp plastome and the 1,187,459 bp mitogenome) of V. sambucifolia f. dageletiana and detected extensive changes throughout the plastome sequence, including rapid structural mutations associated with inverted repeat (IR) contraction and genetic variation. We also described features characterizing the first reported mitogenome sequence obtained for a plant in the order Dipsacales and confirmed frequent gene transfer in this mitogenome. We identified eight non-plastome-originated regions (NPRs) distributed within the plastome of this endemic plant, for six of which there were no corresponding sequences in the current nucleotide sequence databases. Indeed, one of these unidentified NPRs unexpectedly showed certain similarities to sequences from bony fish. Although this is ostensibly difficult to explain, we suggest that this surprising association may conceivably reflect the occurrence of gene transfer from a bony fish to the plastome of an ancestor of V. sambucifolia f. dageletiana mediated by either fungi or bacteria.

Population dynamics in the Japanese Archipelago since the Pleistocene

The Japanese Archipelago is widely covered with acidic soil made of volcanic ash, an environment which is detrimental to the preservation of ancient biomolecules. More than 10,000 Palaeolithic and Neolithic sites have been discovered nationwide, but few skeletal remains exist and preservation of DNA is poor. Despite these challenging circumstances, we succeeded in obtaining a complete mitogenome sequence from Palaeolithic human remains. We also obtained those of Neolithic (hunting-gathering Jomon and the farming Yayoi cultures) remains, and over 2,000 present-day Japanese. The Palaeolithic mitogenome is potentially an ancestral type of haplogroup M, suggesting it is not only connected to present-day Japanese but also present-day East Asians. There were no changes in the gene pool from the hunting-gathering (Jomon) to the farming cultures (Yayoi), and this is different from in Europe, where there was no genetic continuity between hunter-gatherers and farmers. We also found that a vast increase of population size happened and has continued since the Yayoi period, characterized with paddy rice farming. It means that the cultural transition, i.e. rice agriculture, had significant impact on the demographic history of Japanese population.