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Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation

https://doi.org/10.1101/720797

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Global variation in copy number in the human genome

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Genome-wide detection and characterization of positive selection in human populations

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De novo assembly of a haplotype-resolved human genome

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De novo assembly of haplotype-resolved genomes with trio binning

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Fast and accurate short read alignment with Burrows–Wheeler transform

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The Sequence Alignment/Map format and SAMtools

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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

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Assemblytics: a web analytics tool for the detection of variants from an assembly

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The Ensembl gene annotation system

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PAML 4: Phylogenetic Analysis by Maximum Likelihood

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MUSCLE: multiple sequence alignment with high accuracy and high throughput

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PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments

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ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

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Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era

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Phosphatidylcholine and Sphingomyelin Profiles Vary in Bos taurus indicus and Bos taurus taurus In Vitro- and In Vivo-Produced Blastocysts1

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Ribbon: Visualizing complex genome alignments and structural variation

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Copy number variation of individual cattle genomes using next-generation sequencing

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SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification

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PANTHER: A Library of Protein Families and Subfamilies Indexed by Function

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The IGF 1 pathway genes and their association with age of puberty in cattle

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Ancient cattle genomics, origins, and rapid turnover in the Fertile Crescent

inferredcites →https://doi.org/10.1152/ajpcell.00038.2012openalex-snapshot

Arachidonic acid supplementation enhances in vitro skeletal muscle cell growth via a COX-2-dependent pathway

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Complete mitochondrial genomes of Bos taurus and Bos indicus provide new insights into intra-species variation, taxonomy and domestication

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A whole-genome assembly of the domestic cow, Bos taurus

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LUMPY: a probabilistic framework for structural variant discovery

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Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle

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Repbase Update, a database of repetitive elements in eukaryotic genomes

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AdapterRemoval v2: rapid adapter trimming, identification, and read merging

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Using diverse U.S. beef cattle genomes to identify missense mutations in EPAS1, a gene associated with high-altitude pulmonary hypertension

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MUMmer4: A fast and versatile genome alignment system

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Integrating Hi-C links with assembly graphs for chromosome-scale assembly

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Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis

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Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

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Primary structures of different isoforms of buffalo pregnancy-associated glycoproteins (BuPAGs) during early pregnancy and elucidation of the 3-dimensional structure of the most abundant isoform BuPAG 7

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Rapid birth-death evolution and positive selection in detoxification-type glutathione S-transferases in mammals

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Thyroid hormones in fetal growth and prepartum maturation

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Metabolic characteristics of multiparous Angus and Brahman cows grazing in the Chihuahuan Desert

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Reproductive Rates, Birth Weight, Calving Ease and 24-h Calf Survival in a Four-Breed Diallel among Simmental, Limousin, Polled Hereford and Brahman Beef Cattle

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Association of Bovine Fatty Acid Desaturase 2 Gene Single-Nucleotide Polymorphisms with Intramuscular Fatty Acid Composition in Japanese Black Steers

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An end-to-end assembly of the Aedes aegypti genome

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Advances in optical mapping for genomic research

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The structural variation landscape in 492 Atlantic salmon genomes

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Ensembl 2020

inferred← citeshttps://doi.org/10.1111/age.13298openalex-snapshot

Assessment of copy number variants in three Brazilian locally adapted cattle breeds using whole‐genome re‐sequencing data

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Comparative analyses of copy number variations between Bos taurus and Bos indicus

inferred← citeshttps://doi.org/10.1186/s12864-024-11021-7openalex-snapshot

Proteomic identification of potential biomarkers for heat tolerance in Caracu beef cattle using high and low thermotolerant groups

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Genomics in animal breeding from the perspectives of matrices and molecules

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Symposium review: Advances in sequencing technology herald a new frontier in cattle genomics and genome-enabled selection

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380. Investigation of genes associated with maternal weaning weight in South African Bonsmara beef cattle

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