Chromosomer: A Reference-Based Genome Arrangement Tool for Producing Draft Chromosome Sequences

Background: As the number of sequenced genomes rapidly increases, chromosome assembly is becoming an even more crucial step of any genome study. Since de novo chromosome assemblies are confounded by repeat-mediated artifacts, reference-assisted assemblies that use comparative inference have become widely used, prompting the development of several reference-assisted assembly programs for prokaryotic and eukaryotic genomes. Findings: We developed Chromosomer – a reference-based genome arrangement tool, which rapidly builds chromosomes from genome contigs or scaffolds using their alignments to a reference genome of a closely related species. Chromosomer does not require mate-pair libraries and it offers a number of auxiliary tools that implement common operations accompanying the genome assembly process. Conclusions: Despite implementing a straightforward alignment-based approach, Chromosomer is a useful tool for genomic analysis of species without chromosome maps. Putative chromosome assemblies by Chromosomer can be used in comparative genomic analysis, genomic variation assessment, potential linkage group inference and other kinds of analysis involving contig or scaffold mapping to a high-quality assembly

Population genomic analysis of North American eastern wolves (Canic lycaon) support their conservation priority status

The threatened eastern wolf is found predominantly in protected areas of central Ontario and has an evolutionary history obscured by interbreeding with coyotes and gray wolves, which challenges its conservation status and subsequent management. Here, we used a population genomics approach to uncover spatial patterns of variation in 281 canids in central Ontario and the Great Lakes region. This represents the first genome-wide single nucleotide polymorphism (SNP) dataset with substantial sample sizes of representative populations. Although they comprise their own genetic cluster, we found evidence of eastern wolf dispersal outside of the boundaries of protected areas, in that the frequency of eastern wolf genetic variation decreases with increasing distance from provincial parks. We detected eastern wolf alleles in admixed coyotes along the northeastern regions of Lake Huron and Lake Ontario. Our analyses confirm the unique genomic composition of eastern wolves, which are mostly restricted to small fragmented patches of protected habitat in central Ontario. We hope this work will encourage an innovative discussion regarding a plan for managed introgression, which could conserve eastern wolf genetic material in any genome regardless of their potential mosaic ancestry composition and the habitats that promote them

A Moving Landscape for Comparative Genomics in Mammals

Today we count some 62,000 species of vertebrates (half are fishes) including some 550 species of mammals on earth. The genome sequencing of non-laboratory species in recent years is expanding our breadth and understanding of genetic bases of adaptation and evolution in varied and amazing ways. Recent completion and inspection of whole genome sequence and assembly for over 200 species of mammals, from platypus to panda to human, offer the prospect of a better view of the patterns of changes within genome organization across the mammalian radiations. In 2009 my colleagues and I have created Genome-10K, an international consortium of scientist who have set a goal of gathering, sequencing, assembling, and annotating to high quality some 10,000 vertebrate genomes with 2nd and 3rd generation sequencing technology within the coming five years. These activities and advances provide an enormous Bioinformatics challenge whose solution will provide future zoologists of every persuasion a genome sequence resource for their favorite study animal. The applications and potential for the genome sequence in several research questions will be discussed

Genomics reveals complex population history and unexpected diversity of Eurasian otters (Lutra lutra) in Britain relative to genetic methods

Conservation genetic analyses of many endangered species have been based on genotyping of microsatellite loci and sequencing of short fragments of mtDNA. The increase in power and resolution afforded by whole genome approaches may challenge conclusions made on limited numbers of loci and maternally inherited haploid markers. Here we provide a matched comparison of whole genome sequencing versus microsatellite and control region genotyping for Eurasian otters (Lutra lutra). Previous work identified four genetically differentiated ‘stronghold’ populations of otter in Britain, derived from regional populations that survived the population crash of the 1950-80 s. Using whole genome resequencing data from 45 samples from across the British stronghold populations we confirmed some aspects of population structure derived from previous marker-driven studies. Importantly we showed that genomic signals of the population crash bottlenecks matched evidence from otter population surveys. Unexpectedly, two strongly divergent mitochondrial lineages were identified that were undetectable using control region fragments, and otters in the east of England were genetically distinct and surprisingly variable. We hypothesise that this previously unsuspected variability may derive from past releases of Eurasian otters from other, non-British source populations in England around the time of the population bottleneck. Our work highlights that even reasonably well studied species may harbour genetic surprises, if studied using modern high-throughput sequencing methods

Mitochondrial genome-based synthesis and timeline of Eurasian otter (Lutra lutra) phylogeography

Eurasian otters (Lutra lutra) have a broad distribution across Eurasia, but biogeographic data outside of western Europe is limited to disconnected pockets. Based on current subspecies designations, Asia appears to harbour a large proportion of the species’ diversity, with 10 of 12 Eurasian otter subspecies found in Asia. Here we provide a range-wide synthesis of mitochondrial data, inferring a timeline and pattern of phylogeographic signals. Whole mitochondrial genomes of 27 Eurasian otters across 4 subspecies are presented from newly generated data (n = 6; 4 from Korea, 1 from Hong Kong and 2 from UK), assembled from the Sequence Read Archive (n = 4), and sourced from GenBank (n = 17). We then combined whole mitochondrial genome results with cytochrome b data to increase the sample size and contextualise our results with prior studies. We identified five distinct lineages that were discordant with current subspecies classification. Phylogenetic dating revealed that the earliest diverging lineage was the Japanese lineage, with remaining lineages diverging ≥0.08 million years ago. Mitochondrial diversity calculated by sample locations seemed mainly driven by the presence of multiple lineages. When grouping samples by lineage, genetic diversity was highest in Lineage 1 (primarily found in China and Laos), followed by Lineage 2 (primarily found in Korea), and lowest diversity identified in Lineage 3 (primarily found in Europe). Our findings highlight previously undetected lineage diversity within Eurasian otters, but also the need for further taxonomic and genomic evaluation of the species in Asia. The identified unique, distinct lineages of Eurasian otters also warrant urgent conservation attention

Are Pangolins Scapegoats of the COVID-19 Outbreak-CoV Transmission and Pathology Evidence?

The COVID‐19 outbreak has infected over 6 million people across the world. The origin of COVID‐19 coronavirus (CoV) remains unknown, although pangolins have been suggested as potential hosts. We investigated two pangolins seized in Guangdong Province, China. Molecular screening revealed CoV in one pangolin (“Dahu”), while another (“Meidong”) was infected by Ehrlichia ruminantium. Dahu exhibited difficulty breathing, infections of lung, intestines, and nostrils, as revealed by computed tomography imaging and necropsy. Previous phylogenetic analyses showed bat coronavirus RaTG13 is closer to COVID‐19 CoV compared to pangolin coronavirus. Over 20 caregivers have had close physical contact with CoV‐positive Dahu, but none became infected with CoV. Our data suggest that pangolins are unlikely the natural reservoir or secondary hosts of COVID‐19 CoV. Pangolins seems to be victims infected by CoV carried by a not yet unidentified natural reservoir host species, perhaps due to their weakened immune system

Diversity and Paleodemography of the Addax (Addax nasomaculatus), a Saharan Antelope on the Verge of Extinction.

Since the 19th century, the addax (Addax nasomaculatus) has lost approximately 99% of its former range. Along with its close relatives, the blue antelope (Hippotragus leucophaeus) and the scimitar-horned oryx (Oryx dammah), the addax may be the third large African mammal species to go extinct in the wild in recent times. Despite this, the evolutionary history of this critically endangered species remains virtually unknown. To gain insight into the population history of the addax, we used hybridization capture to generate ten complete mitochondrial genomes from historical samples and assembled a nuclear genome. We found that both mitochondrial and nuclear diversity are low compared to other African bovids. Analysis of mitochondrial genomes revealed a most recent common ancestor ~32 kya (95% CI 11-58 kya) and weak phylogeographic structure, indicating that the addax likely existed as a highly mobile, panmictic population across its Sahelo-Saharan range in the past. PSMC analysis revealed a continuous decline in effective population size since ~2 Ma, with short intermediate increases at ~500 and ~44 kya. Our results suggest that the addax went through a major bottleneck in the Late Pleistocene, remaining at low population size prior to the human disturbances of the last few centuries