Migrators within migrators: exploring transposable element dynamics in the monarch butterfly, Danaus plexippus.
Migrators within migrators: exploring transposable element dynamics in the monarch butterfly, Danaus plexippus.
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DOI：
10.1186/s13100-022-00263-5
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发表时间：
2022-02-16
期刊：
影响因子：
4.9
通讯作者：
Hayward A
中科院分区：
文献类型：
--
作者：
Baril T;Hayward A
鳞翅目（蝴蝶和飞蛾）是生态学和进化中重要的模式系统。高质量的黑脉金斑蝶（Danaus plexippus）染色体基因组组装是可用的，但它缺乏深入的转座元件（TE）注释，这为探索黑脉金斑蝶TE动力学和TE对形成黑脉金斑蝶基因组的影响提供了机会。我们发现6.21%的黑脉金斑蝶基因组由TE组成，与在基因组组装草图上进行的原始TE注释相比，减少了6.85%。黑脉金斑蝶（Danaus chrysippus）和黑脉金斑蝶（Danaus melanippus）的TE含量分别为33.97%和11.87%。TE对黑脉王基因组大小贡献最大的是LINEs和Penelope-like元件，其中新发现的r2-hero_dPle （LINE）、penelope-1_dPle （Penelope-like）和hase2-1_dPle （SINE）三个家族共贡献了34.92%的TE总含量。我们发现了最近TE活动的证据，两个新的Tc1家族在最近的时间尺度上迅速扩张（Tc1 - 1_dple, Tc1 - 2_dple）。LINE片段显示基因组缺失的特征，表明TE的高周转率。我们研究了TE与翅膀颜色和免疫基因之间的关系，并发现与其他宿主基因相比，免疫基因周围TE含量增加了三倍。我们对黑脉金斑蝶基因组进行了详细的TE注释和分析，发现与两种具有可用基因组片段的密切相关的Danaus物种相比，黑脉金斑蝶对基因组内容的贡献要小得多。我们发现了在最近的时间尺度上迅速扩展的非常成功的新DNA TE家族，并且TE扩展和去除的持续特征突出了帝王蝶基因组中重复内容的动态性质。我们的研究结果还表明，昆虫免疫基因是未来te介导的宿主适应研究的有希望的候选者。在线版本包含补充材料，可在10.1186/s13100-022-00263-5获得。
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. 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. 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. The online version contains supplementary material available at 10.1186/s13100-022-00263-5.
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影响因子：
64.8
作者：
Dasmahapatra, Kanchon K.;Walters, James R.;Briscoe, Adriana D.;Davey, John W.;Whibley, Annabel;Nadeau, Nicola J.;Zimin, Aleksey V.;Hughes, Daniel S. T.;Ferguson, Laura C.;Martin, Simon H.;Salazar, Camilo;Lewis, James J.;Adler, Sebastian;Ahn, Seung-Joon;Baker, Dean A.;Baxter, Simon W.;Chamberlain, Nicola L.;Chauhan, Ritika;Counterman, Brian A.;Dalmay, Tamas;Gilbert, Lawrence E.;Gordon, Karl;Heckel, David G.;Hines, Heather M.;Hoff, Katharina J.;Holland, Peter W. H.;Jacquin-Joly, Emmanuelle;Jiggins, Francis M.;Jones, Robert T.;Kapan, Durrell D.;Kersey, Paul;Lamas, Gerardo;Lawson, Daniel;Mapleson, Daniel;Maroja, Luana S.;Martin, Arnaud;Moxon, Simon;Palmer, William J.;Papa, Riccardo;Papanicolaou, Alexie;Pauchet, Yannick;Ray, David A.;Rosser, Neil;Salzberg, Steven L.;Supple, Megan A.;Surridge, Alison;Tenger-Trolander, Ayse;Vogel, Heiko;Wilkinson, Paul A.;Wilson, Derek;Yorke, James A.;Yuan, Furong;Balmuth, Alexi L.;Eland, Cathlene;Gharbi, Karim;Thomson, Marian;Gibbs, Richard A.;Han, Yi;Jayaseelan, Joy C.;Kovar, Christie;Mathew, Tittu;Muzny, Donna M.;Ongeri, Fiona;Pu, Ling-Ling;Qu, Jiaxin;Thornton, Rebecca L.;Worley, Kim C.;Wu, Yuan-Qing;Linares, Mauricio;Blaxter, Mark L.;Ffrench-Constant, Richard H.;Joron, Mathieu;Kronforst, Marcus R.;Mullen, Sean P.;Reed, Robert D.;Scherer, Steven E.;Richards, Stephen;Mallet, James;McMillan, W. Owen;Jiggins, Chris D.
通讯作者：
Jiggins, Chris D.
影响因子：
4.4
作者：
Chaturvedi, P;Hengeveld, R;Singh, B
通讯作者：
Singh, B
影响因子：
10.5
作者：
Bessa, J;Gebelein, B;Mann, RS
通讯作者：
Mann, RS
影响因子：
10.7
作者：
Casals, F;C치ceres, M;Ruiz, A
通讯作者：
Ruiz, A
DOI：
10.1093/bioinformatics/btp348
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Capella-Gutiérrez S;Silla-Martínez JM;Gabaldón T
通讯作者：
Gabaldón T