Migrators within migrators: exploring transposable element dynamics in the monarch butterfly, <i>Danaus plexippus</i>

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Abstract

Background

Lepidoptera (butterflies and moths) are an important model system in ecology and evolution. A high-quality chromosomal genome assembly is available for the monarch butterfly ( Danaus plexippus), but it lacks an in-depth transposable element (TE) annotation, presenting an opportunity to explore monarch TE dynamics and the impact of TEs on shaping the monarch genome.

Results

We find 6.21% of the monarch genome is comprised of TEs, a reduction of 6.85% compared to the original TE annotation performed on the draft genome assembly. Monarch TE content is low compared to two closely related species with available genomes, Danaus chrysippus (33.97% TE) and Danaus melanippus (11.87% TE). The biggest TE contributions to genome size in the monarch are LINEs and Penelope-like elements, and three newly identified families, r2-hero_dPle (LINE), penelope-1_dPle ( Penelope-like), and hase2-1_dPle (SINE), collectively contribute 34.92% of total TE content. We find evidence of recent TE activity, with two novel Tc1 families rapidly expanding over recent timescales ( tc1-1_dPle, tc1-2_dPle). LINE fragments show signatures of genomic deletions indicating a high rate of TE turnover. We investigate associations between TEs and wing colouration and immune genes and identify a three-fold increase in TE content around immune genes compared to other host genes.

Conclusions

We provide a detailed TE annotation and analysis for the monarch genome, revealing a considerably smaller TE contribution to genome content compared to two closely related Danaus species with available genome assemblies. We identify highly successful novel DNA TE families rapidly expanding over recent timescales, and ongoing signatures of both TE expansion and removal highlight the dynamic nature of repeat content in the monarch genome. Our findings also suggest that insect immune genes are promising candidates for future interrogation of TE-mediated host adaptation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13100-022-00263-5.

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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh, Daron Standley (2013)

We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.

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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen, Heiko Schmidt, Arndt von Haeseler … (2014)

Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.

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BEDTools: a flexible suite of utilities for comparing genomic features

Aaron Quinlan, Ira Hall (2010)

Motivation: Testing for correlations between different sets of genomic features is a fundamental task in genomics research. However, searching for overlaps between features with existing web-based methods is complicated by the massive datasets that are routinely produced with current sequencing technologies. Fast and flexible tools are therefore required to ask complex questions of these data in an efficient manner. Results: This article introduces a new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format. BEDTools also supports the comparison of sequence alignments in BAM format to both BED and GFF features. The tools are extremely efficient and allow the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks. BEDTools can be combined with one another as well as with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that can quickly answer intricate questions of large genomic datasets. Availability and implementation: BEDTools was written in C++. Source code and a comprehensive user manual are freely available at http://code.google.com/p/bedtools Contact: aaronquinlan@gmail.com; imh4y@virginia.edu Supplementary information: Supplementary data are available at Bioinformatics online.

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Author and article information

Contributors

Tobias Baril:

ORCID: http://orcid.org/0000-0002-5936-7531

tb529@exeter.ac.uk

Alexander Hayward:

ORCID: https://orcid.org/0000-0001-7413-718X

alex.hayward@exeter.ac.uk

Journal

Journal ID (nlm-ta): Mob DNA

Journal ID (iso-abbrev): Mob DNA

Title: Mobile DNA

Publisher: BioMed Central (London )

ISSN (Electronic): 1759-8753

Publication date (Electronic): 16 February 2022

Publication date PMC-release: 16 February 2022

Publication date Collection: 2022

Volume: 13

Electronic Location Identifier: 5

Affiliations

GRID grid.8391.3, ISNI 0000 0004 1936 8024, Centre for Ecology and Conservation, , University of Exeter, ; Penryn Campus, Penryn, Cornwall TR10 9FE UK

Author information

Tobias Baril http://orcid.org/0000-0002-5936-7531

Alexander Hayward https://orcid.org/0000-0001-7413-718X

Article

Publisher ID: 263

DOI: 10.1186/s13100-022-00263-5

PMC ID: 8848866

PubMed ID: 35172896

SO-VID: dcdccc39-c594-45ea-b78a-76754d761387

License:

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

History

Date received : 29 September 2021

Date accepted : 6 February 2022

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;

Award ID: BB/M009122/1

Award ID: BB/N020146/1

Custom metadata

ScienceOpen disciplines: Genetics

Keywords: transposon,te annotation,lepidoptera,danaus plexippus,butterfly,genomic deletion,repeat,genome evolution

Data availability:

ScienceOpen disciplines: Genetics

Keywords: transposon, te annotation, lepidoptera, danaus plexippus, butterfly, genomic deletion, repeat, genome evolution

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Migrators within migrators: exploring transposable element dynamics in the monarch butterfly, Danaus plexippus

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Abstract

Background

Results

Conclusions

Supplementary Information

Related collections

Genome Integrity

Most cited references 115

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

BEDTools: a flexible suite of utilities for comparing genomic features

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Cited by 12

Most referenced authors 1,746