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

Lookup NU author(s): Dr Richard Edwards, Professor Melissa BatesonORCiD

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This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).


Abstract

© 2022 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd. 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.


Publication metadata

Author(s): Stuart KC, Edwards RJ, Cheng Y, Warren WC, Burt DW, Sherwin WB, Hofmeister NR, Werner SJ, Ball GF, Bateson M, Brandley MC, Buchanan KL, Cassey P, Clayton DF, De Meyer T, Meddle SL, Rollins LA

Publication type: Article

Publication status: Published

Journal: Molecular Ecology Resources

Year: 2022

Pages: Epub ahead of print

Online publication date: 28/06/2022

Acceptance date: 10/06/2022

Date deposited: 12/08/2022

ISSN (print): 1755-098X

ISSN (electronic): 1755-0998

Publisher: John Wiley and Sons Inc.

URL: https://doi.org/10.1111/1755-0998.13679

DOI: 10.1111/1755-0998.13679


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Funding

Funder referenceFunder name
BB/P013759/1
LP160100610
LP18010072
RGP0030/2015
UNSW

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