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bioRxiv · 10.1101/2021.04.07.438753

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

Stuart, K. C.·Edwards, R. J.·Cheng, Y.·Warren, W. C.·Burt, D. W.·Sherwin, W. B.·Hofmeister, N. R.·Werner, S. J.·Ball, G. F.·Bateson, M.·Brandley, M. C.·Buchanan, K. L.·Cassey, P.·Clayton, D. F.·De Meyer, T.·Meddle, S. L.·Rollins, L. A.
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Abstract

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 genome (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 1,628 scaffolds (72.5 Mb scaffold N50). Species-specific transcript mapping and gene annotation revealed high structural and functional completeness (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. Rapid, recent advances in sequencing technologies and bioinformatics software have highlighted the need for evidence-based assessment of assembly decisions on a case-by-case basis. 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 BO_SCPLOWUSCOMPC_SCPLOW, a complementary tool for assembly comparison designed to be robust to differences in assembly size and base-calling quality. Finally, we present a second starling assembly, S. vulgaris vNA, to facilitate comparative analysis and global genomic research on this ecologically important species.

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Stuart, K. C., Edwards, R. J., Cheng, Y., Warren, W. C., Burt, D. W., Sherwin, W. B., Hofmeister, N. R., Werner, S. J., Ball, G. F., Bateson, M., Brandley, M. C., Buchanan, K. L., Cassey, P., Clayton, D. F., De Meyer, T., Meddle, S. L., Rollins, L. A.. 2021-04-08. Transcript- and annotation-guided genome assembly of the European starling. https://doi.org/10.1101/2021.04.07.438753

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