DNA Day 2023

Robert Macey et al. use deep sequencing to reveal two co-existing, deeply divergent, fully functional mitochondrial genomes in a single Tuatara from Lady Alice Island, New Zealand. This finding will stimulate further investigation, having profound implications for our understanding of mitochondrial evolution and function.

DNA methylation aging clocks are generated for several species of pinnipeds enabling the estimation of pinniped age from blood or skin samples.

Todd Robeck and Zhe Fei et al. use DNA methylation profiling to develop an epigenetic clock to measure age in odontocete species, including toothed whales and dolphins. The clocks were highly accurate and represent a valuable tool to help in wildlife conservation efforts.

Larison et al. report epigenetic aging models in plains zebras (Equus quagga) using the epigenetic clock and epigenetic pacemaker approaches. Their epigenetic clock allows age to be accurately estimated in endangered sister species, and the pacemaker model identifies an association between inbreeding and accelerating aging.

A chromosome-level genome assembly of the Xingguo gray goose enables deeper insight into Chinese indigenous geese genetic origins and evolution.

Jocelyn Colella et al. report whole-genome sequences of 10 stoats (Mustela erminea) from four regions of glacial refugia. They find evidence for two past introgressive events between lineages that coincide with interglacial periods, a pattern that may extend to other high–latitude species.

The genetic structure of modern-day brown bears mainly reflects contemporary population connectivity. Recent gene flow barriers have obscured the genomic signatures of postglacial recolonisation.

A highly-complete chromosome-scale genome assembly of the brown anole, Anolis sagrei, provides insight into the evolution of sex chromosomes and is a crucial resource for this model lizard species.

Robert R. Fitak et al. investigate the genetic basis for domestication in camels. They found that the positive selection of candidate domestication genes is consistent with neural crest deficiencies and altered thyroid hormone-based signaling. Their work provides insights to the evolutionary history of camels and genetics of domestication.

A chromosome-level genome assembly of the American mink (Neogale vison) provides a valuable genetic resource to guide mink breeding strategies and conservation efforts.

Integrated genomic, transcriptomic, and methylomic data from the endangered Drung cattle (Bos frontalis) provide further insight into its unique physiology and adaptation to alpine environments.

The Antarctic Weddell inhabits one of the most extreme environments on Earth. Comparative genomics with close relatives reveals the specific genetic adaptations for cardiovascular and fat metabolism that enable it to thrive.

Cai and colleagues sequence and annotate the genome of the yellowstripe goby at the chromosome level. Combining genome and transcriptome data, they infer key metabolic pathways for high lipid accumulation in the liver of this fish.

He, Li, and Lv et al. took a genomics approach to study innate feeding behavior in mandarin fish. They identify genes related to predatory feeding that underwent rapid adaptive evolution. They also functionally validate the role of bmp4-edar pathway in inducing predatory feeding in zebrafish.

Genome assembles for Northern three-toed jerboa, Siberian jerboa, Midday jird and Desert hamster and provides insights into similarities and differences in mechanisms for desert adaptation.

Olena Maiakovska et al. provide whole-genome sequencing of the parthenogenetic and invasive marbled crayfish and develop a computational framework for data analysis of monoclonal genomes. These data and methodology allow the authors to demonstrate genetic separation between two populations and provide the first size estimate for a marbled crayfish colony, which they used to model population growth patterns.

Sanchez, Rokhsar, and colleagues use genome skimming to generate DNA markers for phylogenomic analyses of bobtail and bottletail squid. The ancestral state of bioluminescence suggests that the Sepiolinae ancestor possessed a bilobed light organ with bacteriogenic luminescence. Also, analyses of divergence time suggest that major biogeographic events might have shaped the speciation of these animals.

Ming, Yuan et al. performed whole-genome sequencing on 128 wild and domesticated Bactrian camels across Asia. They show that wild and domestic Bactrian camels are genetically diverged from dromedaries, and that wild camels contributed little to domestic camel ancestry despite sharing a habitat in East Asia.

A genome-wide analysis in galloping racehorse breeds identifies protein-altering genetic variants in a core set of genes that appear to determine attributes for racing, including muscle, neurobiological, and metabolic advantages.

Xiang et al. developed an Effect Direction Meta-analysis (EDME) approach to identify true pleiotropy. They used Cholesky-transformation to decorrelate the traits and identified many pleiotropic variants that consistently predicted phenotypic differences in cattle.

Genomic data presented in this study provide clues about why previous attempts to eradicate the invasive Sitka black-tailed deer from the Haida Gwaii archipelago in Canada have been incomplete. The authors find substantial gene flow between islands, with the exception of the remote island of SGang Gwaay, which they argue is a viable option for near-term eradication efforts.

Kersten et al. sequence a draft genome for the Atlantic puffin and report its population structure, genetic diversity and gene flow among four main clusters of populations across the northern Atlantic. These results identify a secondary contact zone between the puffins from the High Arctic and other colonies and proposes a new population structure from the currently recognized three subspecies.

Katherine Grabek et al. use genotype-by-sequencing to characterize genetic variation in 153 ground squirrels, finding high heritability for hibernation onset. They find 14 loci associated with hibernation onset, and a putative causal variant in the promoter of FAM204A.

An investigation of genetic variants that exist across human and livestock species supports the clear potential of livestock models in providing insights into the mechanisms driving human diseases and traits.

Metagenomes from 359 steers demonstrate a strong relationship between host genomics and microbial gene abundances, particularly those correlated with bovine emissions of methane.

Lingzhao Fang et al. studied the paternal genetic variants that affect gestational length in cattle. They found that paternal genes from pathways involved in embryonic development were associated with gestation length, and that these were often found in differentially methylated regions of the genome.

Using SNP-association analysis and genetic mapping, a SNP and an insertion in and close to HOXB13 associated with short tail length is identified in Merino sheep, which may be a target for safely selecting shorter tails and improving sheep welfare.

Xiang and colleagues infer mutant alleles in 113,000 cattle to quantify the effect of these mutations on complex traits including body size, fertility and milk production, and compare these mutation sites across 100 species of vertebrates. Some sites show long term selective pressure, are heavily conserved and demonstrate hybrid vigour, whereas sites selected over shorter time periods are biased towards undesirable mutation.

Pingxian Wu and Kai Wang et al. perform single-locus and haplotype-based GWAS in Yorkshire pigs to evaluate genetic factors involved in socially affected traits, like feed intake and weight gain. These results indicate several genetic factors that may ultimately be targeted to improve livestock breeding.

Yuzhe Wang, Xuemin Cao et al. report the fine-mapping of a major growth trait QTL in chicken using genome-wide association and haplotype association analyses. They discover multiple mutations cumulatively contribute to the previously-reported QTL and identify one of a regulatory mutation that contributes to the variation in the measured traits.

Yurtman, Özer, Yüncü et al. provide an ancient DNA data set to demonstrate the impact of human activity on the demographic history of domestic sheep. The authors demonstrate that there may have been multiple domestication events with notable changes to the gene pool of European and Anatolian sheep since the Neolithic.

Recent findings implicating homeobox B13 (HOXB13) as a regulator of sheep tail length and their impact on sheep breeding via selection-based strategies and molecular genetics-based tools are discussed.

Forutan et al. measure RNA expression and map transcription start sites (TSSs) between two sub-species of cattle in adult and fetal tissues and demonstrate translocation and changes in TSS distribution between the sub-species. This study provides insight into cattle adaptation and provides support of rapidly evolving TSS between two recently diverged subspecies.

Kadri and colleagues present the evolutionary constraints of the branch point motifs in the bovine and human genome. The functional role of these predicted branch points sequences in the bovine genome is inferred using splicing quantitative trait loci analyses.

Sara Lado et al. report a fine-scale analysis of genetic diversity in dromedary species across Asia and Africa. Using a genome-wide approach, the authors are able to infer patterns of migration following domestication, which follow known historic caravan routes, and identify major population expansions and bottlenecks through history.

Raddatz, Lyko and colleagues use whole-genome bisulfite sequencing data to generate a methylation clock for chicken. This clock was able to detect age acceleration in broiler chickens under experimentally induced inflammation.