Reference genome of the bicolored carpenter ant, Camponotus vicinus

Carpenter ants in the genus Camponotus are large, conspicuous ants that are abundant and ecologically influential in many terrestrial ecosystems. The bicolored carpenter ant, C. vicinus Mayr, is distributed across a wide range of elevations and latitudes in western North America, where it is a prominent scavenger and predator. Here, we present a high-quality genome assembly of C. vicinus from a sample collected in Sonoma County, CA, near the type locality of the species. This genome assembly consists of 38 scaffolds spanning 302.74 Mb, with contig N50 of 15.9Mb, scaffold N50 of 19.9 Mb, and BUSCO completeness of 99.2%. This genome sequence will be a valuable resource for exploring the evolutionary ecology of C. vicinus and carpenter ants generally. It also provides an important tool for clarifying cryptic diversity within the C. vicinus species complex, a genetically diverse set of populations, some of which are quite localized and of conservation interest.

[1]  B. Shapiro,et al.  Seizing the moment: The opportunity and relevance of the California Conservation Genomics Project to state and federal conservation policy , 2022, The Journal of heredity.

[2]  H. B. Shaffer,et al.  The phylogeny of California, and how it informs setting multispecies conservation priorities , 2022, The Journal of heredity.

[3]  L. Keller,et al.  Radiation and hybridization underpin the spread of the fire ant social supergene , 2022, Proceedings of the National Academy of Sciences of the United States of America.

[4]  J. Manthey,et al.  Impact of host demography and evolutionary history on endosymbiont molecular evolution: A test in carpenter ants (genus Camponotus) and their Blochmannia endosymbionts , 2022, Ecology and evolution.

[5]  Russell B. Corbett-Detig,et al.  Landscape genomics to enable conservation actions: The California Conservation Genomics Project. , 2022, The Journal of heredity.

[6]  C. Faulk,et al.  De novo sequencing, diploid assembly, and annotation of the black carpenter ant, Camponotus pennsylvanicus, and its symbionts by one person for $1000, using nanopore sequencing , 2022, bioRxiv.

[7]  S. Sim,et al.  HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly , 2022, BMC Genomics.

[8]  S. Aron,et al.  Chromosome-level genome assembly and annotation of two lineages of the ant Cataglyphis hispanica: stepping stones towards genomic studies of hybridogenesis and thermal adaptation in desert ants , 2022, bioRxiv.

[9]  A. Goesmann,et al.  Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification , 2021, Microbial genomics.

[10]  Heng Li,et al.  Robust haplotype-resolved assembly of diploid individuals without parental data , 2021, 2109.04785.

[11]  Heng Li,et al.  New strategies to improve minimap2 alignment accuracy , 2021, Bioinform..

[12]  Felipe A. Simão,et al.  BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes , 2021, Molecular biology and evolution.

[13]  Thomas M. Keane,et al.  Twelve years of SAMtools and BCFtools , 2020, GigaScience.

[14]  Guojie Zhang,et al.  High-quality chromosome-level genome assembly and full-length transcriptome analysis of the pharaoh ant Monomorium pharaonis , 2020, GigaScience.

[15]  Sergey Koren,et al.  Towards complete and error-free genome assemblies of all vertebrate species , 2020, Nature.

[16]  M. Schatz,et al.  GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes , 2020, Nature Communications.

[17]  S. Koren,et al.  Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies , 2020, Genome Biology.

[18]  Chris Burge.  Broad Institute , 2020, Definitions.

[19]  Mark Blaxter,et al.  BlobToolKit – Interactive Quality Assessment of Genome Assemblies , 2019, G3: Genes, Genomes, Genetics.

[20]  James M. Pflug,et al.  Measuring Genome Sizes Using Read-Depth, k-mers, and Flow Cytometry: Methodological Comparisons in Beetles (Coleoptera) , 2019, bioRxiv.

[21]  F. Delsuc,et al.  MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics , 2019, bioRxiv.

[22]  Nezar Abdennur,et al.  Cooler: scalable storage for Hi-C data and other genomically-labeled arrays , 2019, bioRxiv.

[23]  D. Kronauer,et al.  The genomic architecture and molecular evolution of ant odorant receptors , 2018, Genome research.

[24]  Amber K Weiner,et al.  High-Quality Genome Assemblies Reveal Long Non-coding RNAs Expressed in Ant Brains , 2018, Cell reports.

[25]  Sergey Koren,et al.  Integrating Hi-C links with assembly graphs for chromosome-scale assembly , 2018, bioRxiv.

[26]  Adam M. Phillippy,et al.  MUMmer4: A fast and versatile genome alignment system , 2018, PLoS Comput. Biol..

[27]  Jonas Korlach,et al.  De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads , 2017, GigaScience.

[28]  Heng Li,et al.  Minimap2: pairwise alignment for nucleotide sequences , 2017, Bioinform..

[29]  Hadley Wickham,et al.  ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .

[30]  Jacob M. Luber,et al.  HiGlass: web-based visual exploration and analysis of genome interaction maps , 2017, Genome Biology.

[31]  Kin Chung Lam,et al.  High-resolution TADs reveal DNA sequences underlying genome organization in flies , 2017, Nature Communications.

[32]  S. Koren,et al.  Scaffolding of long read assemblies using long range contact information , 2016, BMC Genomics.

[33]  Laura E. Williams,et al.  Genome evolution in an ancient bacteria-ant symbiosis: parallel gene loss among Blochmannia spanning the origin of the ant tribe Camponotini , 2015, PeerJ.

[34]  Brian Bushnell,et al.  BBMap: A Fast, Accurate, Splice-Aware Aligner , 2014 .

[35]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[36]  Heng Li.  Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.

[37]  Zhaozhi Zhang,et al.  displayHTS: a R package for displaying data and results from high-throughput screening experiments , 2013, Bioinform..

[38]  Heng Li,et al.  A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data , 2011, Bioinform..

[39]  Jun Wang,et al.  Genomic Comparison of the Ants Camponotus floridanus and Harpegnathos saltator , 2010, Science.

[40]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[41]  Martin J. Mueller,et al.  Nutritional upgrading for omnivorous carpenter ants by the endosymbiont Blochmannia , 2007, BMC Biology.

[42]  P. Degnan,et al.  Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects. , 2005, Genome research.

[43]  O. Gascuel,et al.  A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.

[44]  Jürgen Gadau,et al.  The genome sequence of Blochmannia floridanus: Comparative analysis of reduced genomes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[45]  Sequence analysis Advance Access publication June 7, 2011 The variant call format and VCFtools , 2010 .

[46]  J. Silverman.  Carpenter Ants of the United States and Canada , 2007 .

[47]  Robert S. Harris,et al.  Improved pairwise alignment of genomic dna , 2007 .

[48]  Heng Li,et al.  BIOINFORMATICS ORIGINAL PAPER , 2022 .