The complete mitochondrial genome of dhole Cuon alpinus: phylogenetic analysis and dating evolutionary divergence within Canidae

Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes

Technological advances have allowed improvements in genome reference sequence assemblies. Here, we combined long- and short-read sequence resources to assemble the genome of a female Great Dane dog. This assembly has improved continuity compared to the existing Boxer-derived (CanFam3.1) reference genome. Annotation of the Great Dane assembly identified 22,182 protein-coding gene models and 7,049 long noncoding RNAs, including 49 protein-coding genes not present in the CanFam3.1 reference. The Great Dane assembly spans the majority of sequence gaps in the CanFam3.1 reference and illustrates that 2,151 gaps overlap the transcription start site of a predicted protein-coding gene. Moreover, a subset of the resolved gaps, which have an 80.95% median GC content, localize to transcription start sites and recombination hotspots more often than expected by chance, suggesting the stable canine recombinational landscape has shaped genome architecture. Alignment of the Great Dane and CanFam3.1 assemblies identified 16,834 deletions and 15,621 insertions, as well as 2,665 deletions and 3,493 insertions located on secondary contigs. These structural variants are dominated by retrotransposon insertion/deletion polymorphisms and include 16,221 dimorphic canine short interspersed elements (SINECs) and 1,121 dimorphic long interspersed element-1 sequences (LINE-1_Cfs). Analysis of sequences flanking the 3' end of LINE-1_Cfs (i.e., LINE-1_Cf 3'-transductions) suggests multiple retrotransposition-competent LINE-1_Cfs segregate among dog populations. Consistent with this conclusion, we demonstrate that a canine LINE-1_Cf element with intact open reading frames can retrotranspose its own RNA and that of a SINEC_Cf consensus sequence in cultured human cells, implicating ongoing retrotransposon activity as a driver of canine genetic variation.

Ancient DNA from the Asiatic Wild Dog (Cuon alpinus) from Europe

The Asiatic wild dog (Cuon alpinus), restricted today largely to South and Southeast Asia, was widespread throughout Eurasia and even reached North America during the Pleistocene. Like many other species, it suffered from a huge range loss towards the end of the Pleistocene and went extinct in most of its former distribution. The fossil record of the dhole is scattered and the identification of fossils can be complicated by an overlap in size and a high morphological similarity between dholes and other canid species. We generated almost complete mitochondrial genomes for six putative dhole fossils from Europe. By using three lines of evidence, i.e., the number of reads mapping to various canid mitochondrial genomes, the evaluation and quantification of the mapping evenness along the reference genomes and phylogenetic analysis, we were able to identify two out of six samples as dhole, whereas four samples represent wolf fossils. This highlights the contribution genetic data can make when trying to identify the species affiliation of fossil specimens. The ancient dhole sequences are highly divergent when compared to modern dhole sequences, but the scarcity of dhole data for comparison impedes a more extensive analysis.

Structural variation during dog domestication: insights from gray wolf and dhole genomes

Several processes like phenotypic evolution, disease susceptibility and environmental adaptations, which fashion the domestication of animals, are largely attributable to structural variations (SVs) in the genome. Here, we present high-quality draft genomes of the gray wolf (Canis lupus) and dhole (Cuon alpinus) with scaffold N50 of 6.04 Mb and 3.96 Mb, respectively. Sequence alignment comprising genomes of three canid species reveals SVs specific to the dog, particularly 16 315 insertions, 2565 deletions, 443 repeats, 16 inversions and 15 translocations. Functional annotation of the dog SVs associated with genes indicates their enrichments in energy metabolisms, neurological processes and immune systems. Interestingly, we identify and verify at population level an insertion fully covering a copy of the AKR1B1 (Aldo-Keto Reductase Family 1 Member B) transcript. Transcriptome analysis reveals a high level of expression of the new AKR1B1 copy in the small intestine and liver, implying an increase in de novo fatty acid synthesis and antioxidant ability in dog compared to gray wolf, likely in response to dietary shifts during the agricultural revolution. For the first time, we report a comprehensive analysis of the evolutionary dynamics of SVs during the domestication step of dogs. Our findings demonstrate that retroposition can birth new genes to facilitate domestication, and affirm the importance of large-scale genomic variants in domestication studies.

Comparison of the fecal microbiota of dholes high-throughput Illumina sequencing of the V3-V4 region of the 16S rRNA gene

Intestinal microbes are part of a complex ecosystem. They have a mutual relationship with the host and play an essential role in maintaining the host's health. To optimize the feeding strategies and improve the health status of the dhole, which is an endangered species, we analyzed the structure of fecal microbes in four captive dholes using high-throughput Illumina sequencing targeting the V3-V4 region of the 16S rRNA gene. The diversity indexes and rarefaction curves indicated high microbial diversity in the intestines of the four dholes. The average number of operational taxonomical units (OTUs) in the four samples was 1196, but the number of OTUs common to all libraries was 126, suggesting only a few dominant species. Phylogenetic analysis identified 19 prokaryotic phyla from the 16S rRNA gene sequences, of which only 5 phyla were core microbiota: Bacteroidetes (21.63-38.97 %), Firmicutes (20.97-44.01 %), Proteobacteria (9.33-17.60 %), Fusobacteria (9.11-17.90 %), and Actinobacteria (1.22-2.87 %). These five phyla accounted for 97 % of the bacteria in all the dholes apart from one, in which 78 % of the bacteria were from these phyla. The results of our study provide an effective theoretical basis from which to reach an understanding of the biological mechanisms relevant to the protection of this endangered species.

First report on the bacterial diversity in the distal gut of dholes (Cuon alpinus) by using 16S rRNA gene sequences analysis

The aim of this study was to investigate the bacterial community in the distal gut of dholes (Cuon alpinus) based on the analysis of bacterial 16S rRNA gene sequences. Fecal samples were collected from five healthy unrelated dholes captured from Qilian Mountain in Gansu province of China. The diversity of the fecal bacteria community was investigated by constructing a polymerase chain reaction (PCR)-amplified 16S rRNA gene clone library. Bacterial 16S rRNA gene was amplified by using universal bacterial primers 27F and 1492R. A total of 275 chimera-free near full length 16S rRNA gene sequences were collected, and 78 non-redundant bacteria phylotypes (operational taxonomical units, OTUs) were identified according to the 97 % sequence similarity. Forty-two OTUs (53.8 %) showed less than 98 % sequence similarity to 16S rRNA gene sequences reported previously. Phylogenetic analysis demonstrated that dhole bacterial community comprised five different phyla, with the majority of sequences being classified within the phylum Bacteroidetes (64.7 %), followed by Firmicutes (29.8 %), Fusobacteria (4.7 %),Proteobacteria (0.4 %), and Actinobacteria (0.4 %). The only order Bacteroidales in phylum Bacteroidetes was the most abundant bacterial group in the intestinal bacterial community of dholes. Firmicutes and Bacteroidetes were the two most diverse bacterial phyla with 46.2 and 44.9 % of OTUs contained, respectively. Bacteroidales and Clostridiales were the two most diverse bacterial orders that contained 44.9 and 39.7 % of OTUs, respectively.

The complete mitochondrial genome of Vespertilio sinensis from China

The complete mitogenome sequence of Vespertilio sinensis was determined using long PCR. The genome was 17,146 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 control region. The overall base composition of the heavy strand is A (32.73%), C (23.64%), T (29.72%), and G (13.91%). The base compositions present clearly the A-T skew, which is most obviously in the control region and protein-coding genes. The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of V. sinensis.

The complete mitochondrial genome sequence of the maned wolf (Chrysocyon brachyurus)

In this study, the complete mitochondrial genome of the maned wolf (Chrysocyon brachyurus), the unique species in Chrysocyon, was sequenced and reported for the first time using blood samples obtained from a female individual in Shanghai Zoo, China. Sequence analysis showed that the genome structure was in accordance with other Canidae species and it contained 12 S rRNA gene, 16 S rRNA gene, 22 tRNA genes, 13 protein-coding genes and 1 control region.

The complete mitochondrial genome sequence of the corsac fox (Vulpes corsac)

In this study, we sequenced and reported the complete mitochondrial genome of the corsac fox (Vulpes corsac) for the first time using blood samples obtained from a wild female corsac fox captured from Inner Mongolia, China. Sequence analysis showed it contains 12S rRNA gene, 16S rRNA gene, 22 tRNA genes, 13 protein-coding genes and 1 control region.

The complete mitochondrial genome sequence of the Tibetan red fox (Vulpes vulpes montana)

In this study, the complete mitochondrial genome of the Tibetan red fox (Vulpes Vulpes montana) was sequenced for the first time using blood samples obtained from a wild female red fox captured from Lhasa in Tibet, China. Qinghai--Tibet Plateau is the highest plateau in the world with an average elevation above 3500 m. Sequence analysis showed it contains 12S rRNA gene, 16S rRNA gene, 22 tRNA genes, 13 protein-coding genes and 1 control region (CR). The variable tandem repeats in CR is the main reason of the length variability of mitochondrial genome among canide animals.

The complete mitochondrial genome sequence of the Tibetan wolf (Canis lupus laniger)

In this study, the complete mitochondrial genome of the Tibetan wolf (Canis lupus laniger) was sequenced using blood samples obtained from a wild female Tibetan wolf captured from Lhasa in Tibet, China. Qinghai-Tibet Plateau, with an average elevation above 3500 m, is the highest plateau in the world. Sequence analysis showed that its structure is in accordance with other Canidae species, but GTG is used as the start codon in ND4L gene which is different from many canide animals.

The complete mitochondrial genome of Cuon alpinus lepturus

The complete mitochondrial genome of a female Chinese dhole (Cuon alpinus lepturus) was sequenced for the first time. It contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region.

Evolution of mammalian diving capacity traced by myoglobin net surface charge

Extended breath-hold endurance enables the exploitation of the aquatic niche by numerous mammalian lineages and is accomplished by elevated body oxygen stores and adaptations that promote their economical use. However, little is known regarding the molecular and evolutionary underpinnings of the high muscle myoglobin concentration phenotype of divers. We used ancestral sequence reconstruction to trace the evolution of this oxygen-storing protein across a 130-species mammalian phylogeny and reveal an adaptive molecular signature of elevated myoglobin net surface charge in diving species that is mechanistically linked with maximal myoglobin concentration. This observation provides insights into the tempo and routes to enhanced dive capacity evolution within the ancestors of each major mammalian aquatic lineage and infers amphibious ancestries of echidnas, moles, hyraxes, and elephants, offering a fresh perspective on the evolution of this iconic respiratory pigment.

Can long-range PCR be used to amplify genetically divergent mitochondrial genomes for comparative phylogenetics? A case study within spiders (Arthropoda: Araneae)

The development of second generation sequencing technology has resulted in the rapid production of large volumes of sequence data for relatively little cost, thereby substantially increasing the quantity of data available for phylogenetic studies. Despite these technological advances, assembling longer sequences, such as that of entire mitochondrial genomes, has not been straightforward. Existing studies have been limited to using only incomplete or nominally intra-specific datasets resulting in a bottleneck between mitogenome amplification and downstream high-throughput sequencing. Here we assess the effectiveness of a wide range of targeted long-range PCR strategies, encapsulating single and dual fragment primer design approaches to provide full mitogenomic coverage within the Araneae (Spiders). Despite extensive rounds of optimisation, full mitochondrial genome PCR amplifications were stochastic in most taxa, although 454 Roche sequencing confirmed the successful amplification of 10 mitochondrial genomes out of the 33 trialled species. The low success rates of amplification using long-Range PCR highlights the difficulties in consistently obtaining genomic amplifications using currently available DNA polymerases optimised for large genomic amplifications and suggests that there may be opportunities for the use of alternative amplification methods.

The complete mitochondrial genome of Martes flavigula

The complete mitogenome sequence of Martes flavigula was determined using long PCR. The genome was 16,549 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 control region. The overall base composition of the heavy strand is A (32.48%), C (26.89%), T (26.51%) and G (14.12%). The base compositions present clearly the A-C skew, which is most obvious in the control region and protein-coding genes. The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of M. flavigula.

Complete mitochondrial DNA sequence of Crassostrea nippona: comparative and phylogenomic studies on seven commercial Crassostrea species

The complete mitochondrial genome of Crassostrea nippona was determined and compared with six other Crassostrea mitogenomes from GenBank in an attempt to shed light on the evolutionary relatedness within Crassostrea. The total length of the mitogenome was 20,030 bp for C. nippona, which was the largest among seven Crassostrea mitogenomes. Among six Asian oysters, the gene order of mitochondrial DNA was identical except for C. nippona with a transposition of trnG. While the American oyster C. virginica and Asian oysters showed broad differences in gene order with relocation of most tRNA genes and indels of duplicated tRNAs and rrnS, indicating the relatively distant relationships between the American oyster and Asian oysters. Different from other six Crassostrea oysters, C. nippona had two repeats of 66 bp in non-coding regions. Pairwise divergence among the seven Crassostrea oysters based on DNA sequences of 12 protein-coding genes ranged from 3.1 to 44.4% (Kimura two-parameter distance, K2P). The close relationship between C. nippona and C. hongkongensis was revealed by K2P of 18.9%. Phylogenetic analyses robustly revealed Crassostrea monophyly, with C. virginica at the basal position. The results of phylogenetic analyses strongly supported C. gigas and C. angulata had the closest relationship, with C. sikamea being the sister taxon. These findings presented here provide a better insight into the relationships within Crassostrea and will be useful for further evolution studies of oysters.