The Genome Architecture of the Copepod Eurytemora carolleeae-the Highly Invasive Atlantic Clade of the Eurytemoraaffinis Species Complex  

作　　者：Zhenyong Du Gregory Gelembiuk Wynne Moss Andrew Tritt Carol Eunmi Lee 

机构地区：[1]Department of Integrative Biology,University of Wisconsin,Madison,WI 53706,USA [2]U.S.Geological Survey,Northern Rocky Mountain Science Center,Bozeman,MT 59715,USA [3]Applied Mathematics and Computational Research Division,Lawrence Berkeley National Laboratory,Berkeley,CA 94720,USA

出　　处：《Genomics, Proteomics & Bioinformatics》2024年第5期121-136,共16页基因组蛋白质组与生物信息学报(英文版)

基　　金：funded by the National Science Foundation(Grant Nos.OCE-1658517 and NSF DEB-2055356);the French National Research Agency(Grant No.ANR-19-MPGA-0004)(Macron's"Make Our Planet Great Again"award)to Carol E.Lee.Karyotype visualization was performed by David Stern,Jesse Hunter,and Kim Oxendine at the Wisconsin State Laboratory of Hygiene,Department of Pediatrics,University of Wisconsin School of Medicine and Public Health.

摘　　要：Copepods are among the most abundant organisms on the planet and play critical functions in aquatic ecosystems.Among copepods,populations of the Eurytemora affinis species complex are numerically dominant in many coastal habitats and serve as food sources for major fisheries.Intriguingly,certain populations possess the unusual capacity to invade novel salinities on rapid time scales.Despite their ecological importance,high-quality genomic resources have been absent for calanoid copepods,limiting our ability to comprehensively dissect the genome architecture underlying the highly invasive and adaptive capacity of certain populations.Here,we present the first chromosome-level genome of a calanoid copepod,from the Atlantic clade(Eurytemora carolleeae)of the E.affinis species complex.This genome was assembled using high-coverage PacBio long-read and Hi-C sequences of an inbred line,generated through 30 generations of full-sib mating.This genome,consisting of 529.3 Mb(contig N50=4.2 Mb,scaffold N50=140.6 Mb),was anchored onto four chromosomes.Genome annotation predicted 20,262 protein-coding genes,of which ion transport-related gene families were substantially expanded based on comparative analyses of 12 additional arthropod genomes.Also,we found genome-wide signatures of historical gene body methylation of the ion transport-related genes and the significant clustering of these genes on each chromosome.This genome represents one of the most contiguous copepod genomes to date and is among the highest quality marine invertebrate genomes.As such,this genome provides an invaluable resource to help yield fundamental insights into the ability of this copepod to adapt to rapidly changing environments.

关 键 词：ARTHROPOD CRUSTACEA Genome architecture Invasion OSMOREGULATION 

分 类 号：F42[经济管理—产业经济]