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

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 BUSCOMP, 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.