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

Area of Science:

• Genomics
• Avian Biology
• Bioinformatics

Background:

• The European starling (Sturnus vulgaris) is a globally invasive species facing population declines in its native range.
• Understanding its genome is crucial for ecological and evolutionary research.

Purpose of the Study:

• To generate high-quality reference genome assemblies for the European starling.
• To provide genomic resources for population genetic and evolutionary characterization.
• To introduce new bioinformatic tools for assessing genome assembly quality.

Main Methods:

• Generated a long-read genome assembly (S. vulgaris vAU) using linked-reads, Nanopore sequencing, and PacBio Iso-Seq.
• Created a short-read genome assembly (S. vulgaris vNA).
• Scaffolded the vAU assembly using the zebra finch genome and annotated genes using species-specific transcripts.

Main Results:

• Produced a 1050 Mb European starling genome assembly (vAU) with high contiguity and completeness (94.6% BUSCO).
• Successfully assigned 98.6% of the assembly to 32 putative chromosomes.
• Demonstrated the utility of PacBio Iso-Seq data and introduced new tools (saaga, buscomp) for assembly validation and comparison.

Conclusions:

• The new genomic resources significantly enhance the study of European starling populations and evolution.
• The developed bioinformatic tools improve genome assembly assessment and quality control.
• These advancements facilitate future global genomic and transcriptomic analyses of this ecologically significant species.