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Dryad

Data from: The genome of a globally invasive passerine, the common myna, Acridotheres tristis

Cite this dataset

Stuart, Katarina et al. (2024). Data from: The genome of a globally invasive passerine, the common myna, Acridotheres tristis [Dataset]. Dryad. https://doi.org/10.5061/dryad.tx95x6b69

Abstract

In an era of global climate change, biodiversity conservation is receiving increased attention. Conservation efforts are greatly aided by genetic tools and approaches, which seek to understand patterns of genetic diversity and how they impact species health and their ability to persist under future climate regimes. Invasive species offer vital model systems in which to investigate questions regarding adaptive potential, with a particular focus on how changes in genetic diversity and effective population size interact with novel selection regimes. The common myna (Acridotheres tristis) is a globally invasive passerine and is an excellent model species for research both into the persistence of low-diversity populations and the mechanisms of biological invasion. To underpin research on the invasion genetics of this species, we present the genome assembly of the common myna. We describe the genomic landscape of this species, including genome wide allelic diversity, methylation, repeats, and recombination rate, as well as an examination of gene family evolution. Finally, we use demographic analysis to identify that some native regions underwent a dramatic population increase between the two most recent periods of glaciation, and reveal artefactual impacts of genetic bottlenecks on demographic analysis.

README: The genome of a globally invasive passerine, the common myna, Acridotheres tristis

This dryad upload contains the genome files that were generated for the myna genome (https://doi.org/10.1093/dnares/dsae005).

Description of the data and file structure

List of uploaded files

Assembly:
AcTris_vAus2.0.fasta

Matching annotation file:
braker_gemoma_combined_katmanual_brakerforce_longestIsoform_transcripts.emapper.decorated.gff

Tissue specific transcripts (raw fasta files):
Heart.fa (heart tissue)
Liver.fa (liver tissue)
Test.fa (testies tissue)

Repeat libraries and annotation:
acridotheresTristis_combined_library.fasta (Earlgrey custom repeat library fasta file)
allLTR_rename.lib (Maker custom repeat library fasta file)
AcTris_vAus2.0.fasta.out (repeatmasker output of assembly repeat annotation)

SNP based recombination track:
recombination_rho_allchroms.txt

Methylation track:
AcTris_vAus_ALL_modbam2bed.out

Raw Data and NCBI uploads

BioProject PRJNA928557

NCBI assembly upload: GCA_037013685.1

Code/Software

The associated code is available at https://github.com/katarinastuart/At1_MynaGenome

Funding

Royal Society Te Apārangi, Award: UOA1911

Australian Museum Foundation

City of Sydney Environmental Grants Program

University of Auckland