The genome of a globally invasive passerine, the common myna, <i>Acridotheres tristis</i>

Stuart, Katarina C; Johnson, Rebecca N; Major, Richard E; Atsawawaranunt, Kamolphat; Ewart, Kyle M; Rollins, Lee A; Santure, Anna W; Whibley, Annabel

doi:10.1093/dnares/dsae005

Cited by 3 publications

(1 citation statement)

References 120 publications

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“…Even the methods to compare and evaluate transcriptome annotations are subject to variation, exposing the subjective nature of qualitative transcript classifications. Most studies rely on either GFFcompare (Stuart et al 2024; Saha et al 2024) or SQANTI3 (Pardo-Palacios et al 2023b; Brooks et al 2024) to this avail. When comparing both methods on the same data, we observed surprisingly different assembly accuracies (c.f.…”

Section: Discussionmentioning

confidence: 99%

Assembly Arena: Benchmarking RNA isoform reconstruction algorithms for nanopore sequencing

Sagniez,

Budhraja,

Paré

et al. 2024

Preprint

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Resolving the transcriptomes of higher eukaryotes is more tangible with the advent of long read sequencing, which greatly facilitates the identification of new transcripts and their splicing isoforms. However, the computational analysis of long read RNA sequencing data remains challenging as it is difficult to disentangle technical artifacts frombona fidebiological information. To address this, we evaluated the performance of multiple leading transcriptome assembly algorithms on their ability to accurately reconstruct RNA transcript isoforms. We specifically focused on deep nanopore sequencing of synthetic RNA spike-in controls (Sequins™ and SIRVs) across different chemistries, including cDNA and direct RNA protocols. Our systematic comparative benchmarking exposes the strengths and limitations of the different surveyed strategies. We also highlight conceptual and technical challenges with the annotation of transcriptomes and the formalization of assembly quality metrics. Our results complement similar recent endeavors, helping forge a path towards a gold standard analytical pipeline for long read transcriptome assembly.

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Section: Discussionmentioning

confidence: 99%

Assembly Arena: Benchmarking RNA isoform reconstruction algorithms for nanopore sequencing

Sagniez,

Budhraja,

Paré

et al. 2024

Preprint

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Population Genetics and Invasion History of the European Starling Across Aotearoa New Zealand

Thompson,

Atsawawaranunt,

Nehmens

et al. 2024

Molecular Ecology

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The expansion of human settlements over the past few centuries is responsible for an unprecedented number of invasive species introductions globally. An important component of biological invasion management is understanding how introduction history and postintroduction processes have jointly shaped present‐day distributions and patterns of population structure, diversity and adaptation. One example of a successful invader is the European starling (Sturnus vulgaris), which was intentionally introduced to numerous countries in the 19th century, including Aotearoa New Zealand, where it has become firmly established. We used reduced representation sequencing to characterise the genetic population structure of the European starling in New Zealand, comparing it to that present in sampling locations in the native range and invasive Australian range. The population structure and genetic diversity patterns we found suggested restricted gene flow from the majority of New Zealand to the northmost sampling location (Auckland). We also profiled genetic bottlenecks and shared outlier genomic regions, which supported historical accounts of translocations between both Australian subpopulations and New Zealand, and provided evidence of which documented translocation events were more likely to have been successful. Using these results as well as historic demographic patterns, we demonstrate how genomic analysis complements even well‐documented invasion histories to better understand invasion processes, with direct implications for understanding contemporary gene flow and informing invasion management.

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Parallel Signatures of Diet Adaptation in the Invasive Common Myna Genome

Atsawawaranunt,

Stuart,

Whibley

et al. 2024

Molecular Ecology

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Invasive species offer uniquely replicated model systems to study rapid adaptation. The common myna (Acridotheres tristis) has been introduced to over a dozen countries and is classified as one of the most invasive birds in the world. Their multiple invasions provide an opportunity to identify repeated adaptation, as invasive populations originated from multiple source populations. We compared whole‐genome resequencing data from 80 individuals from four native and seven invasive populations, representing two independent introduction pathways. Results from two different selection scan methods were combined and identified a strongly selected region on chromosome 8 that spans two copies of AMY2A, part of the alpha‐amylase gene family, a putative ncRNA and an insertion–deletion structural variant (SV) that contains an ERVK transposable element (TE). Outlier SNPs and the SV are polymorphic in native populations, but fixed or close‐to‐fixed in the two invasive pathways, with the fixation of the same alleles in two independent lineages providing evidence for parallel selection on standing variation. Intriguingly, the second copy of AMY2A has a non‐conservative missense mutation at a phylogenetically conserved site. This mutation, alongside variation in the SV, TE and ncRNA, provide possible routes for changes to protein function or expression. AMY2A has been associated with human commensalism in house sparrows, and genes in this family have been linked to adaptation to high‐starch diets in humans and dogs. This study illustrates the value of replicated analyses within and across species to understand rapid adaptation at the molecular level.

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

Cited by 3 publications

References 120 publications

Assembly Arena: Benchmarking RNA isoform reconstruction algorithms for nanopore sequencing

Assembly Arena: Benchmarking RNA isoform reconstruction algorithms for nanopore sequencing

Population Genetics and Invasion History of the European Starling Across Aotearoa New Zealand

Parallel Signatures of Diet Adaptation in the Invasive Common Myna Genome

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