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

Author:

Bracewell Ryan R1,Stillman Jonathon H12,Dahlhoff Elizabeth P3,Smeds Elliott4,Chatla Kamalakar1,Bachtrog Doris1,Williams Caroline1,Rank Nathan E4

Affiliation:

1. Department of Integrative Biology, University of California, Berkeley , Berkeley, CA 94720 , USA

2. Department of Biology, San Francisco State University , San Francisco, CA 94132 , USA

3. Department of Biology, Santa Clara University , Santa Clara, CA 95053 , USA

4. Department of Biology, Sonoma State University , Rohnert Park, CA 94928 , USA

Abstract

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.

Funder

National Science Foundation

California Conservation Genomics

XSEDE Allocation

Publisher

Oxford University Press (OUP)

Subject

Genetics (clinical),Genetics,Molecular Biology

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