Journal
GENOME BIOLOGY
Volume 21, Issue 1, Pages -Publisher
BMC
DOI: 10.1186/s13059-019-1925-7
Keywords
Arthropods; Genome assembly; Genomics; Protein domains; Gene content; Evolution; DNA methylation
Funding
- National Human Genome Research Institute [U54 HG003273]
- NSF [DBI-1564611]
- Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) [281125614/GRK2220]
- Swiss National Science Foundation [PP00P3_170664, 31003A_143936]
- NSF-DEB grant [1355169]
- USDA-APHIS [15-8130-0547-CA]
- German Research foundation [NI 1387/3-1, MI 649/12-1]
- Leibnitz Graduate School on Genomic Biodiversity Research
- Blanton J. Whitmire endowment
- Housing and Urban Development [NCHHU-0007-13]
- National Science Foundation [1557864]
- Alfred P. Sloan Foundation [2013-5-35 MBE]
- Australian Wool Innovation
- Australian Research Council
- YourGene Bioscience
- Melbourne Water Corporation
- Victorian Life Sciences Computation Initiative (VLSCI) [VR0007]
- NSERC
- University of Melbourne
- NHMRC
- Direct For Biological Sciences
- Division Of Environmental Biology [1355169] Funding Source: National Science Foundation
- Division Of Integrative Organismal Systems
- Direct For Biological Sciences [1557864] Funding Source: National Science Foundation
- Swiss National Science Foundation (SNF) [31003A_143936] Funding Source: Swiss National Science Foundation (SNF)
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Background Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods. Results Using 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception. Conclusions These analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity.
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