The Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution.

Patterns of genomic architecture across insects remain largely undocumented or decoupled from a broader phylogenetic context. For instance, it is unknown whether translocation rates differ between insect orders. We address broad scale patterns of genome architecture across Insecta by examining synte...

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Autores principales:	Matthew H Van Dam, Analyn Anzano Cabras, James B Henderson, Andrew J Rominger, Cynthia Pérez Estrada, Arina D Omer, Olga Dudchenko, Erez Lieberman Aiden, Athena W Lam
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Genetics QH426-470
Acceso en línea:	https://doaj.org/article/45b4e7980ea741cc9037bca5ac6b5e28
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spelling	oai:doaj.org-article:45b4e7980ea741cc9037bca5ac6b5e282021-12-02T20:02:50ZThe Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution.1553-73901553-740410.1371/journal.pgen.1009745https://doaj.org/article/45b4e7980ea741cc9037bca5ac6b5e282021-08-01T00:00:00Zhttps://doi.org/10.1371/journal.pgen.1009745https://doaj.org/toc/1553-7390https://doaj.org/toc/1553-7404Patterns of genomic architecture across insects remain largely undocumented or decoupled from a broader phylogenetic context. For instance, it is unknown whether translocation rates differ between insect orders. We address broad scale patterns of genome architecture across Insecta by examining synteny in a phylogenetic framework from open-source insect genomes. To accomplish this, we add a chromosome level genome to a crucial lineage, Coleoptera. Our assembly of the Pachyrhynchus sulphureomaculatus genome is the first chromosome scale genome for the hyperdiverse Phytophaga lineage and currently the largest insect genome assembled to this scale. The genome is significantly larger than those of other weevils, and this increase in size is caused by repetitive elements. Our results also indicate that, among beetles, there are instances of long-lasting (>200 Ma) localization of genes to a particular chromosome with few translocation events. While some chromosomes have a paucity of translocations, intra-chromosomal synteny was almost absent, with gene order thoroughly shuffled along a chromosome. This large amount of reshuffling within chromosomes with few inter-chromosomal events contrasts with patterns seen in mammals in which the chromosomes tend to exchange larger blocks of material more readily. To place our findings in an evolutionary context, we compared syntenic patterns across Insecta in a phylogenetic framework. For the first time, we find that synteny decays at an exponential rate relative to phylogenetic distance. Additionally, there are significant differences in decay rates between insect orders, this pattern was not driven by Lepidoptera alone which has a substantially different rate.Matthew H Van DamAnalyn Anzano CabrasJames B HendersonAndrew J RomingerCynthia Pérez EstradaArina D OmerOlga DudchenkoErez Lieberman AidenAthena W LamPublic Library of Science (PLoS)articleGeneticsQH426-470ENPLoS Genetics, Vol 17, Iss 8, p e1009745 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Genetics QH426-470
spellingShingle	Genetics QH426-470 Matthew H Van Dam Analyn Anzano Cabras James B Henderson Andrew J Rominger Cynthia Pérez Estrada Arina D Omer Olga Dudchenko Erez Lieberman Aiden Athena W Lam The Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution.
description	Patterns of genomic architecture across insects remain largely undocumented or decoupled from a broader phylogenetic context. For instance, it is unknown whether translocation rates differ between insect orders. We address broad scale patterns of genome architecture across Insecta by examining synteny in a phylogenetic framework from open-source insect genomes. To accomplish this, we add a chromosome level genome to a crucial lineage, Coleoptera. Our assembly of the Pachyrhynchus sulphureomaculatus genome is the first chromosome scale genome for the hyperdiverse Phytophaga lineage and currently the largest insect genome assembled to this scale. The genome is significantly larger than those of other weevils, and this increase in size is caused by repetitive elements. Our results also indicate that, among beetles, there are instances of long-lasting (>200 Ma) localization of genes to a particular chromosome with few translocation events. While some chromosomes have a paucity of translocations, intra-chromosomal synteny was almost absent, with gene order thoroughly shuffled along a chromosome. This large amount of reshuffling within chromosomes with few inter-chromosomal events contrasts with patterns seen in mammals in which the chromosomes tend to exchange larger blocks of material more readily. To place our findings in an evolutionary context, we compared syntenic patterns across Insecta in a phylogenetic framework. For the first time, we find that synteny decays at an exponential rate relative to phylogenetic distance. Additionally, there are significant differences in decay rates between insect orders, this pattern was not driven by Lepidoptera alone which has a substantially different rate.
format	article
author	Matthew H Van Dam Analyn Anzano Cabras James B Henderson Andrew J Rominger Cynthia Pérez Estrada Arina D Omer Olga Dudchenko Erez Lieberman Aiden Athena W Lam
author_facet	Matthew H Van Dam Analyn Anzano Cabras James B Henderson Andrew J Rominger Cynthia Pérez Estrada Arina D Omer Olga Dudchenko Erez Lieberman Aiden Athena W Lam
author_sort	Matthew H Van Dam
title	The Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution.
title_short	The Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution.
title_full	The Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution.
title_fullStr	The Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution.
title_full_unstemmed	The Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution.
title_sort	easter egg weevil (pachyrhynchus) genome reveals syntenic patterns in coleoptera across 200 million years of evolution.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/45b4e7980ea741cc9037bca5ac6b5e28
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The Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution.

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