A chromosome-scale genome assembly and evaluation of mtDNA variation in the willow leaf beetle Chrysomela aeneicollis

Abstract The leaf beetle Chrysomela aeneicollis has a broad geographic range across Western North America but is restricted to cool habitats at high elevations along the west coast. Central California populations occur only at high altitudes (2,700–3,500 m) where they are limited by reduced oxygen s...

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Bibliographic Details
Published in:	G3 : genes - genomes - genetics Vol. 13; no. 7
Main Authors:	Bracewell, Ryan R, Stillman, Jonathon H, Dahlhoff, Elizabeth P, Smeds, Elliott, Chatla, Kamalakar, Bachtrog, Doris, Williams, Caroline, Rank, Nathan E
Format:	Journal Article
Language:	English
Published:	US Oxford University Press 05-07-2023
Subjects:	Animals Chromosomes Coleoptera - genetics DNA, Mitochondrial - genetics Female Genome Report Genome, Mitochondrial Male RNA, Ribosomal, 16S Salix - genetics Hi-C mitochondria genome assembly
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Summary:	Abstract The leaf beetle Chrysomela aeneicollis has a broad geographic range across Western North America but is restricted to cool habitats at high elevations along the west coast. Central California populations occur only at high altitudes (2,700–3,500 m) where they are limited by reduced oxygen supply and recent drought conditions that are associated with climate change. Here, we report a chromosome-scale genome assembly alongside a complete mitochondrial genome and characterize differences among mitochondrial genomes along a latitudinal gradient over which beetles show substantial population structure and adaptation to fluctuating temperatures. Our scaffolded genome assembly consists of 21 linkage groups; one of which we identified as the X chromosome based on female/male whole genome sequencing coverage and orthology with Tribolium castaneum. We identified repetitive sequences in the genome and found them to be broadly distributed across all linkage groups. Using a reference transcriptome, we annotated a total of 12,586 protein-coding genes. We also describe differences in putative secondary structures of mitochondrial RNA molecules, which may generate functional differences important in adaptation to harsh abiotic conditions. We document substitutions at mitochondrial tRNA molecules and substitutions and insertions in the 16S rRNA region that could affect intermolecular interactions with products from the nuclear genome. This first chromosome-level reference genome will enable genomic research in this important model organism for understanding the biological impacts of climate change on montane insects.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Conflicts of interest statement The author(s) declare no conflict of interest.
ISSN:	2160-1836 2160-1836
DOI:	10.1093/g3journal/jkad106