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

Katarina Stuart, Richard Edwards, Yuanyuan Cheng, Wesley Warren, Dave Burt, William Sherwin, Natalie Hofmeister, Scott Werner, Gregory F Ball, Melissa Bateson, Matthew Brandley, Katherine L Buchanan, Phillip Cassey, David F Clayton, Tim De Meyer, Simone Meddle, Lee Rollins

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

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 characterisation. S. vulgaris vAU combined 10x Genomics linked-reads, low-coverage Nanopore sequencing, and PacBio Iso-Seq full-length transcript scaffolding to generate a 1050 Mb assembly on 6,222 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 counter-intuitive 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.
Original languageEnglish
Pages (from-to)3141-3160
JournalMolecular Ecology Resources
Issue number8
Early online date28 Jun 2022
Publication statusPublished - Nov 2022

Keywords / Materials (for Non-textual outputs)

  • Sturnus vulgaris
  • full-length transcripts
  • genome annotation
  • genome assembly
  • genome assessment


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