Harris A. Lewin
A5007998668- Genetic and phenotypic traits in livestock
- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Phylogenetic Studies
- Animal Genetics and Reproduction
- Chromosomal and Genetic Variations
- T-cell and Retrovirus Studies
- Reproductive Biology and Fertility
- Cancer-related molecular mechanisms research
- Genetic diversity and population structure
- Animal Disease Management and Epidemiology
- Reproductive Physiology in Livestock
- Genomics and Chromatin Dynamics
- T-cell and B-cell Immunology
- Molecular Biology Techniques and Applications
- Immune Cell Function and Interaction
- Monoclonal and Polyclonal Antibodies Research
- Reproductive System and Pregnancy
- Wheat and Barley Genetics and Pathology
- Pluripotent Stem Cells Research
- Vector-Borne Animal Diseases
- Renal and related cancers
- Environmental DNA in Biodiversity Studies
- Microbial infections and disease research
- Toxin Mechanisms and Immunotoxins
- RNA and protein synthesis mechanisms
University of California, Davis
2014-2024
Arizona State University
2024
John Muir Health
2018-2023
University of Vienna
2022
Cornell University
1981-2021
University of California Division of Agriculture and Natural Resources
2021
Presbyterian Hospital
2021
Council of Science Editors
2020
Harefield Hospital
2020
Imperial College London
2020
For 10,000 years pigs and humans have shared a close complex relationship. From domestication to modern breeding practices, shaped the genomes of domestic pigs. Here we present assembly analysis genome sequence female Duroc pig (Sus scrofa) comparison with wild from Europe Asia. Wild emerged in South East Asia subsequently spread across Eurasia. Our results reveal deep phylogenetic split between European Asian boars ∼1 million ago, selective sweep indicates selection on genes involved RNA...
To understand the biology and evolution of ruminants, cattle genome was sequenced to about sevenfold coverage. The contains a minimum 22,000 genes, with core set 14,345 orthologs shared among seven mammalian species which 1217 are absent or undetected in noneutherian (marsupial monotreme) genomes. Cattle-specific evolutionary breakpoint regions chromosomes have higher density segmental duplications, enrichment repetitive elements, species-specific variations genes associated lactation immune...
Increasing our understanding of Earth’s biodiversity and responsibly stewarding its resources are among the most crucial scientific social challenges new millennium. These require fundamental knowledge organization, evolution, functions, interactions millions planet’s organisms. Herein, we present a perspective on Earth BioGenome Project (EBP), moonshot for biology that aims to sequence, catalog, characterize genomes all eukaryotic over period 10 years. The outcomes EBP will inform broad...
Jianquan Liu and colleagues report the draft genome sequence of domestic yak, Bos grunniens. Their comparative analyses with low-altitude cattle provide insights into high-altitude adaptation in yak. Domestic yaks (Bos grunniens) meat other necessities for Tibetans living at high altitude on Qinghai-Tibetan Plateau adjacent regions. Comparison between yak closely related taurus) is informative studying animal to altitude. Here, we present a female generated using Illumina-based technology...
Significance The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of COVID-19, a major pandemic that threatens millions human lives and global economy. We identified large number mammals can potentially be infected by SARS-CoV-2 via their ACE2 proteins. This assist identification intermediate hosts for hence reduce opportunity future outbreak COVID-19. Among species we found with highest risk infection are wildlife endangered species. These represent an...
The genome organizations of eight phylogenetically distinct species from five mammalian orders were compared in order to address fundamental questions relating chromosomal evolution. Rates chromosome evolution within found increase since the Cretaceous-Tertiary boundary. Nearly 20% breakpoint regions reused during evolution; these reuse sites are also enriched for centromeres. Analysis gene content and around evolutionary revealed increased density relative genome-wide average. We that...
The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs increase sequencing efficiency, with concomitant development improved annotation technology and, therefore, propose to create collection tissue DNA specimens 10 000 specifically designated the very near future. For this purpose, we, Genome 10K Community...
We previously localized a quantitative trait locus (QTL) on chromosome 6 affecting milk fat and protein concentration to 4-cM confidence interval, centered the microsatellite BM143 . characterized genes sequence variation in this region identified common haplotypes spanning five polymorphic sites IBSP, SPP1, PKD2 , ABCG2 for two sires heterozygous QTL. Expression of SPP1 bovine mammary gland increased from parturition through lactation. all coding exons were sequenced these sires. The single...
Phylogeny and characteristics of ruminants Ruminants are a diverse group mammals that includes families containing well-known taxa such as deer, cows, goats. However, their evolutionary relationships have been contentious, the origins distinctive digestive systems headgear, including antlers horns (see Perspective by Ker Yang). To understand among ruminants, L. Chen et al. sequenced 44 species representing 6 performed phylogenetic analysis. From this analysis, they were able to resolve...
Dairy cows are highly susceptible after parturition to developing liver lipidosis and ketosis, which costly diseases farmers. A bovine microarray platform consisting of 13,257-annotated oligonucleotides was used study hepatic gene networks underlying nutrition-induced ketosis. On day 5 postpartum, 14 Holstein were randomly assigned ketosis-induction (n = 7) or control groups. Cows in the group fed at 50% 4 intake until they developed signs clinical ad libitum throughout treatment period....
The Tibetan antelope (Pantholops hodgsonii) is endemic to the extremely inhospitable high-altitude environment of Qinghai-Tibetan Plateau, a region that has low partial pressure oxygen and high ultraviolet radiation. Here we generate draft genome this artiodactyl use it detect potential genetic bases highland adaptation. Compared with other plain-dwelling mammals, shows signals adaptive evolution gene-family expansion in genes associated energy metabolism transmission. Both American pika,...
November 2020 marked 2 y since the launch of Earth BioGenome Project (EBP), which aims to sequence all known eukaryotic species in a 10-y timeframe. Since then, significant progress has been made across aspects EBP roadmap, as outlined 2018 article describing project’s goals, strategies, and challenges (1). The phase ended clock started on reaching EBP’s major milestones. This Special Feature explores many facets EBP, including review progress, description scientific exemplar projects,...
The kākāpō is a flightless parrot endemic to New Zealand. Once common in the archipelago, only 201 individuals remain today, most of them descending from an isolated island population. We report first genome-wide analyses species, including high-quality genome assembly for kākāpō, one chromosome-level reference genomes sequenced by Vertebrate Genomes Project (VGP). also and analyzed 35 modern sole surviving population 14 extinct mainland While theory suggests that such small likely have...
Abstract Background The gemsbok (Oryx gazella) is one of the largest antelopes in Africa. Gemsbok are heterothermic and thus highly adapted to live desert, changing their feeding behavior when faced with extreme drought heat. A high-quality genome sequence this species will assist efforts elucidate these other important traits facilitate research on conservation efforts. Findings Using 180 Gbp Illumina paired-end mate-pair reads, a 2.9 assembly scaffold N50 1.48 Mbp was generated using...
Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes 240 species, we identify bases that, when mutated, are likely affect fitness and alter disease risk. At least 332 million (~10.7%) in human genome unusually conserved across species (evolutionarily constrained) relative neutrally evolving repeats, 4552 ultraconserved elements nearly perfectly conserved. Of 101 significantly constrained single bases, 80% outside protein-coding exons half...
Abstract Egg-laying mammals (monotremes) are the only extant mammalian outgroup to therians (marsupial and eutherian animals) provide key insights into evolution 1,2 . Here we generate analyse reference genomes of platypus ( Ornithorhynchus anatinus ) echidna Tachyglossus aculeatus ), which represent two monotreme lineages. The nearly complete genome assembly has anchored almost entire onto chromosomes, markedly improving continuity gene annotation. Together with our sequence, species allow...
Annotating coding genes and inferring orthologs are two classical challenges in genomics evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method integrates structural gene annotation orthology inference. implements different paradigm orthologous loci, improves ortholog detection of conserved compared with state-of-the-art methods, handles even highly fragmented assemblies. scales...
Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How these innovations come about what constraints are there origins of novelty continuing maintenance biodiversity Earth? The history life code for working parts cells systems written genome. BioGenome Project proposed that genomes all extant, named...
The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis genetic variation across an alignment 241 mammal genome assemblies, addressing prior concerns regarding limited genomic sampling species. compared neutral genome-wide phylogenomic signals using concatenation coalescent-based approaches, interrogated chromosomes, analyzed extensive catalogs structural variants. Interordinal...
Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability discern which positions functionally important. Evolutionary constraint is a powerful predictor function, agnostic cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% the genome as significantly constrained and likely functional. We compared annotation, association studies, copy-number variation,...
We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. found that although mammals resemble one another total and diversity, they show substantial differences with regard recent accumulation. This includes multiple expansion quiescence events across mammalian tree. Young TEs, particularly long interspersed elements, drive increases size, whereas DNA transposons are associated smaller genomes....
Human accelerated regions (HARs) are conserved genomic loci that evolved at an rate in the human lineage and may underlie human-specific traits. We generated HARs chimpanzee with automated pipeline alignment of 241 mammalian genomes. Combining deep learning chromatin capture experiments neural progenitor cells, we discovered a significant enrichment topologically associating domains containing variants change three-dimensional (3D) genome organization. Differential gene expression between...
Understanding the regulatory landscape of human genome is a long-standing objective modern biology. Using reference-free alignment across 241 mammalian genomes produced by Zoonomia Consortium, we charted evolutionary trajectories for 0.92 million candidate cis-regulatory elements (cCREs) and 15.6 transcription factor binding sites (TFBSs). We identified 439,461 cCREs 2,024,062 TFBSs under constraint. Genes near constrained perform fundamental cellular processes, whereas genes...