Transcript- and annotation-guided genome assembly of the European starling.

Autor: Stuart KC; Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, New South Wales, Australia., Edwards RJ; Evolution & Ecology Research Centre, School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia., Cheng Y; School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia., Warren WC; Department of Animal Sciences, Institute for Data Science and Informatics, The University of Missouri, Columbia, Missouri, USA., Burt DW; Office of the Deputy Vice-Chancellor (Research and Innovation), The University of Queensland, Brisbane, Australia., Sherwin WB; Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, New South Wales, Australia., Hofmeister NR; Department of Ecology and Evolutionary Biology, Cornell University, New York, USA.; Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, New York, USA., Werner SJ; United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, Colorado, USA., Ball GF; Department of Psychology, University of Maryland, Maryland, USA., Bateson M; Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK., Brandley MC; Section of Amphibians and Reptiles, Carnegie Museum of Natural History, Pittsburgh, Pennsylvania, USA., Buchanan KL; School of Life and Environmental Sciences, Deakin University, Waurn Ponds, Victoria, Australia., Cassey P; Invasion Science & Wildlife Ecology Lab, University of Adelaide, Adelaide, Australia., Clayton DF; Department of Genetics & Biochemistry, Clemson University, South Carolina, USA., De Meyer T; Department of Data Analysis & Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium., Meddle SL; The Roslin Institute, The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK., Rollins LA; Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, New South Wales, Australia.; School of Life and Environmental Sciences, Deakin University, Waurn Ponds, Victoria, Australia.
Jazyk: angličtina
Zdroj: Molecular ecology resources [Mol Ecol Resour] 2022 Nov; Vol. 22 (8), pp. 3141-3160. Date of Electronic Publication: 2022 Jul 18.
DOI: 10.1111/1755-0998.13679
Abstrakt: The European starling, Sturnus vulgaris, is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range. Here, we present the genome assembly and long-read transcriptome of an Australian-sourced European starling (S. vulgaris vAU), and a second, North American, short-read genome assembly (S. vulgaris vNA), as complementary reference genomes for population genetic and evolutionary characterization. S. vulgaris vAU combined 10× genomics linked-reads, low-coverage Nanopore sequencing, and PacBio Iso-Seq full-length transcript scaffolding to generate a 1050 Mb assembly on 6222 scaffolds (7.6 Mb scaffold N50, 94.6% busco completeness). Further scaffolding against the high-quality zebra finch (Taeniopygia guttata) genome assigned 98.6% of the assembly to 32 putative nuclear chromosome scaffolds. Species-specific transcript mapping and gene annotation revealed good gene-level assembly and high functional completeness. Using S. vulgaris vAU, we demonstrate how the multifunctional use of PacBio Iso-Seq transcript data and complementary homology-based annotation of sequential assembly steps (assessed using a new tool, saaga) can be used to assess, inform, and validate assembly workflow decisions. We also highlight some counterintuitive behaviour in traditional busco metrics, and present buscomp, a complementary tool for assembly comparison designed to be robust to differences in assembly size and base-calling quality. This work expands our knowledge of avian genomes and the available toolkit for assessing and improving genome quality. The new genomic resources presented will facilitate further global genomic and transcriptomic analysis on this ecologically important species.
(© 2022 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.)
Databáze: MEDLINE
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