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The complete sequence and comparative analysis of ape sex chromosomes

Apes possess two sex chromosomes—the male-specific Y chromosome and the X chromosome, which is present in both males and females. The Y chromosome is crucial for male reproduction, with deletions being linked to infertility1. The X chromosome is vital for reproduction and cognition2. Variation in mating patterns and brain function among apes suggests corresponding differences in their sex chromosomes. However, owing to their repetitive nature and incomplete reference assemblies, ape sex chromosomes have been challenging to study. Here, using the methodology developed for the telomere-to-telomere (T2T) human genome, we produced gapless assemblies of the X and Y chromosomes for five great apes (bonobo (Pan paniscus), chimpanzee (Pan troglodytes), western lowland gorilla (Gorilla gorilla gorilla), Bornean orangutan (Pongo pygmaeus) and Sumatran orangutan (Pongo abelii)) and a lesser ape (the siamang gibbon (Symphalangus syndactylus)), and untangled the intricacies of their ....

United States , Wilson Sayres , Iturralde Martinez , Hylobates Symphalangus , Mc Cartney , Mpa Assembly , Repbase Update , Cell Genet , Integrative Genomics , Cancer Res , Improved Pairwise Alignment , Penn State , Acids Res , Annotation Toolkit , Cell Biol , Kosakovsky Pond , Genome Analysis Toolkit ,

The complete sequence of a human Y chromosome

The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications1–3. As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished4,5. Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, showing the complete ampliconic structures of gene families TSPY, DAZ and RBMY; 41 additional protein-coding genes, mostly from the TSPY family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a previous assembly of the CHM13 genome4 and mapped available population variation, clinical ....

United States , Sri Lanka , Mc Cartney , Auwera Ga Oconnor , Svetec Mikleni , European Molecular Biology Open Software Suite , Mpa Assembly , Jt Organization , Human Pangenome Project , Acids Res , Simons Genome Diversity Project , Genome Res , Genome Biol , Human Genome Browser , Identifyingy Chromosome , Hierarchy Finder , Improved Pairwise Alignmnet , Pennsylvania State Univ , Annotation Toolkit , Biol Evol , Graphpad Prism , European Molecular Biology Open Software , Trends Genet , Genome Analysis Toolkit , Data Science Analysis , Cell Genomics ,

Early Release - Hepatitis C Virus Transmission Clusters in Public Health and Correctional Settings, Wisconsin, USA, 2016–2017 - Volume 27, Number 2—February 2021 - Emerging Infectious Diseases journal

18) and quality trimmed by using Trimmomatic version 0.36 (
19). Viral contigs were generated by using default settings with Vicuna version 1.1 (
20), and a de novo consensus assembly was generated by using Viral Finishing and Annotation Toolkit (V-FAT) version 1.1 (https://www.broadinstitute.org/viral-genomics/v-fat). Read data are available from the National Center for Biotechnology Information Read Archive (https://www.ncbi.nlm.nih.gov) under BioProject accession no. PRJNA661611.
Phylogenetic Reconstruction
21) and IQ-TREE version 1.6 (
22). We then constructed a maximum-likelihood phylogenetic tree with 1,000 ultrafast bootstrap replicates (
HCV Transmission Network Analyses
We uploaded Illumina paired-end reads to GHOST and subjected them to automatic quality control criteria. In brief, read pairs were filtered out if a read had 3 Ns (N indicates that software was not able to make a basecall for this base) or a length 185 bp. Each identifier on f ....

United States , New York , United Kingdom , British Columbia , University Of Wisconsin , Columbia University , Bioanalyzer Agilent , Harvard Cambridge , Wisconsin Division Of Public Health , Centers For Disease , National Center , Ragon Institute , University Of Wisconsin School Medicine , Surveillance Technology , Public Health In Madison , Wisconsin State Laboratory Of Hygiene , Columbia University School Of Social Work , Transmission Network Analyses , Disease Control , Global Hepatitis Outbreak , Wisconsin Electronic Disease Surveillance System , Wisconsin Division , Public Health , Wisconsin State Laboratory , Acid Extraction , Platinum Taq High Fidelity ,