Samuel Sacco
A5077340196- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Genetic diversity and population structure
- Geology and Paleoclimatology Research
- Environmental DNA in Biodiversity Studies
- Climate change and permafrost
- Bat Biology and Ecology Studies
- Cancer Genomics and Diagnostics
- Identification and Quantification in Food
- Genomic variations and chromosomal abnormalities
- Genomics and Rare Diseases
- Wildlife Ecology and Conservation
- Genomics and Chromatin Dynamics
- Evolution and Genetic Dynamics
- Amphibian and Reptile Biology
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Geological formations and processes
- Aeolian processes and effects
- Primate Behavior and Ecology
- Genetic Mapping and Diversity in Plants and Animals
- Brain Tumor Detection and Classification
- Spider Taxonomy and Behavior Studies
- Nuts composition and effects
- Coral and Marine Ecosystems Studies
- Plant and Fungal Interactions Research
University of California, Santa Cruz
2022-2025
Institute of Arctic and Alpine Research
2023
University of Colorado Boulder
2023
University of Zurich
2023
Abstract Here the Human Pangenome Reference Consortium presents a first draft of human pangenome reference. The contains 47 phased, diploid assemblies from cohort genetically diverse individuals 1 . These cover more than 99% expected sequence in each genome and are accurate at structural base pair levels. Based on alignments assemblies, we generate that captures known variants haplotypes reveals new alleles structurally complex loci. We also add 119 million pairs euchromatic polymorphic...
Abstract The short arms of the human acrocentric chromosomes 13, 14, 15, 21 and 22 (SAACs) share large homologous regions, including ribosomal DNA repeats extended segmental duplications 1,2 . Although resolution these regions in first complete assembly a genome—the Telomere-to-Telomere Consortium’s CHM13 (T2T-CHM13)—provided model their homology 3 , it remained unclear whether patterns were ancestral or maintained by ongoing recombination exchange. Here we show that contain...
Abstract Apes possess two sex chromosomes—the male-specific Y chromosome and the X chromosome, which is present in both males females. The crucial for male reproduction, with deletions being linked to infertility 1 . vital reproduction cognition 2 Variation mating patterns brain function among apes suggests corresponding differences their chromosomes. However, owing repetitive nature incomplete reference assemblies, ape chromosomes have been challenging study. Here, using methodology...
We present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran siamang. achieve chromosome-level contiguity with unparalleled sequence accuracy (<1 error in 500,000 base pairs), completely sequencing 215 gapless chromosomes telomere-to-telomere. resolve challenging regions, such as the major histocompatibility complex immunoglobulin loci, providing more in-depth evolutionary insights. Comparative...
Abstract The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies 1–3 . Consequently, our understanding the evolution species is incomplete. Here we present haplotype-resolved reference analyses six species: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan siamang. We achieve chromosome-level contiguity with substantial sequence accuracy (<1 error in 2.7 megabases) completely 215 gapless chromosomes...
Dire wolves (Aenocyon dirus) are extinct predators of Pleistocene North America. Although phenotypically similar to living (Canis lupus), dire have yet be placed confidently in the canid family tree. We generated 3.4x and 12.8x paleogenomes from two well-preserved dating > 13,000 72,000 years ago, estimated consensus species trees for these 10 species. Our results revealed that ~2/3 wolf ancestry is derived a lineage sister clade comprising gray wolf, coyote, dhole, remaining ~1/3 near...
Abstract Most current studies rely on short-read sequencing to detect somatic structural variation (SV) in cancer genomes. Long-read offers the advantage of better mappability and long-range phasing, which results substantial improvements germline SV detection. However, long-read detection methods do not generalize well analysis SVs tumor genomes with complex rearrangements, heterogeneity, aneuploidy. Here, we present Severus: a method for accurate different types using phased breakpoint...
Abstract Apes possess two sex chromosomes—the male-specific Y and the X shared by males females. The chromosome is crucial for male reproduction, with deletions linked to infertility. carries genes vital reproduction cognition. Variation in mating patterns brain function among great apes suggests corresponding differences their structure evolution. However, due highly repetitive nature incomplete reference assemblies, ape chromosomes have been challenging study. Here, using state-of-the-art...
Somatic variant detection is an integral part of cancer genomics analysis. While most methods have focused on short-read sequencing, long-read technologies now offer potential advantages in terms repeat mapping and phasing. We present DeepSomatic, a deep learning method for detecting somatic SNVs insertions deletions (indels) from both data, with modes whole-genome exome able to run tumor-normal, tumor-only, FFPE-prepared samples. To help address the dearth publicly available training...
Abstract Most human cancers arise from somatic alterations, ranging single nucleotide variations to structural (SVs) that can alter the genomic organization. Pathogenic SVs are identified in various cancer types and subtypes, they play a crucial role diagnosis patient stratification. However, studies on have been limited due biological computational challenges, including tumor heterogeneity, aneuploidy, diverse spectrum of simpler deletions focal amplifications catastrophic events shuffling...
As the Arctic continues to warm, woody shrubs are expected expand northward. This process, known as ‘shrubification,’ has important implications for regional biodiversity, food web structure, and high-latitude temperature amplification. While future rate of shrubification remains poorly constrained, past records plant immigration newly deglaciated landscapes in may serve useful analogs. We provide one new postglacial Holocene sedimentary ancient DNA ( sed aDNA) record vascular plants from...
Abstract Island oak (Quercus tomentella) is a rare relictual island tree species that exists only on six islands off the coast of California and Mexico, but was once widespread throughout mainland California. Currently, this endangered by threats such as non-native plants, grazing animals, human removal. Efforts for conservation restoration currently underway could benefit from information about its range-wide genetic structure evolutionary history. Here we present high-quality genome...
The Pacific banana slug, Ariolimax columbianus, is endemic to the forests of Northern West. Found throughout coastal foothills and mountains California, hermaphroditic molluscs spp. are niche-constrained, hyper-localized, phenotypically diverse. evolutionary history more recent population environmental conditions leading their phenotypic genetic variation not understood. To facilitate such research, we present first high-quality de novo genome assembly A. columbianus as part California...
Summary Recombination is central to genetics and evolution of sexually reproducing organisms. However, obtaining accurate estimates recombination rates, how they vary along chromosomes, continues be challenging. To advance our ability estimate we present Hi-reComb , a new method software for estimation maps from bulk gamete chromosome conformation capture sequencing (Hi-C). Simulations show that produces robust, landscapes. With empirical data sperm five fish species the advantages this...
Abstract DeepVariant is a highly accurate germline variant caller that applies deep dearning to classify variants with high accuracy. Here, we present DeepSomatic, which DeepVariant’s convolutional neural network (CNN) accurately call somatic mutations from paired tumor-normal sequencing and tumor-only sequencing. To develop adapted the input pipeline accommodate pairs. model inputs consist of set pileup images, also referred as “channels”, represent features extracted sequence data at...
Abstract Several methods exist for detecting genetic relatedness or identity by comparing DNA information. These generally require genotype calls, either single-nucleotide polymorphisms short tandem repeats, at the sites used comparison. For some samples, like those obtained from bone fragments single rootless hairs, there is often not enough present to generate calls that are accurate and complete these comparisons. Here, we describe IBDGem, a fast robust computational procedure genomic...
The human pangenome, a new reference sequence, addresses many limitations of the current GRCh38 reference. first release is based on 94 high-quality haploid assemblies from individuals with diverse backgrounds. We employed k-mer indexing strategy for comparative analysis across multiple assemblies, including pangenome reference, GRCh38, and CHM13, telomere-to-telomere assembly. Our approach enabled us to identify valuable collection universally conserved sequences all referred as...
Abstract The jaguar (Panthera onca) is the largest living cat species native to Americas and one of few large American carnivorans have survived into Holocene. However, extent which diversity declined during end-Pleistocene extinction event remains unclear. For example, Pleistocene fossils from North America are notably larger than average extant jaguar, leading hypotheses that jaguars this continent represent a now-extinct subspecies onca augusta) or augusta). Here, we used hybridization...
Abstract Climate-driven changes in hydrological regimes are of global importance and particularly significant riparian ecosystems. Riparian ecosystems California provide refuge to many native vulnerable species within a xeric landscape. Tetragnatha spiders play key role ecosystems, serving as link between terrestrial aquatic elements. Their tight reliance on water paired with the widespread distributions make them ideal candidates better understand relative waterways versus geographic...
Abstract Juglans californica, California walnut, is a vulnerable small tree that locally abundant but restricted to woodland and chaparral habitats of Southern threatened by urbanization land use change. This species the dominant in unique ecosystem California. It one 2 endemic walnut (family Juglandaceae). The other species, Northern black (J. hindsii), has been suggested controversially be variety J. californica. Here, we report new, chromosome-level assembly californica as part...
Abstract The Yuma myotis bat (Myotis yumanensis) is a small vespertilionid and one of 52 species new world Myotis bats in the subgenus Pizonyx. While M. yumanensis populations currently appear relatively stable, it 12 known or suspected to be susceptible white-nose syndrome, fungal disease causing declines across North America. Only two these have genome resources available, which limits ability resource managers use genomic techniques track responses syndrome generally. Here we present...
The glossy snake (Arizona elegans) is a polytypic species broadly distributed across southwestern North America. occupies habitats ranging from California's coastal chaparral to the shortgrass prairies of Texas and southeastern Nebraska, extensive arid scrublands central México. Three subspecies are currently recognized in California, one which afforded state-level protection based on loss modification its preferred alluvial scrub inland desert habitat. We report first genome assembly A....
Abstract Genome assemblies are increasingly being used to identify adaptive genetic variation that can help prioritize the population management of protected species. This approach may be particularly relevant species like Blainville’s horned lizard, Phrynosoma blainvillii, due its specialized diet on noxious harvester ants, numerous adaptative traits for avoiding predation (e.g. cranial horns, dorsoventrally compressed body, cryptic coloration, and blood squirting from orbital sinuses),...