Pangenome Analysis Reveals Gene Content Variation and Evolutionary Dynamics Across the Culex pipiens Species Complex

Abstract

The Culex pipiens L. (Diptera: Culicidae) complex includes the main vectors of West Nile virus in temperate regions, yet few studies have compared the genomes of its members. We compared chromosome-scale assemblies of Cx. pipiens form pipiens, Cx. pipiens form molestus Forskal, Cx. pipiens pallens Coquillett and Culex quinquefasciatus Say, using gene models transferred from the Cx. quinquefasciatus annotation and rooting the tree with Culex perexiguus Theobald, a species outside the complex. The rooted tree paired molestus with pipiens and pallens with quinquefasciatus. Only 59% of the four taxon gene trees agreed; of those that disagreed, 1,746 paired molestus with quinquefasciatus and pallens with pipiens, against 1,384 for the other arrangement. Among the best-supported trees, the count was 349 to 184, and loci with intact gene models leaned the same way. In ABBA-BABA tests, molestus shared more derived alleles with quinquefasciatus than pipiens did, and pallens shared more with both forms of Cx. pipiens than quinquefasciatus did, consistent with gene flow between the lineages and Cx. pipiens ancestry in pallens. Transferred models that shared an error produced false shared derived alleles, which moved the root and inflated two tests until we set such loci aside. Most apparent gene absences were the same gene clustered elsewhere, and gene family changes tracked copy loss during transfer. Median protein identity between forms was near 99%, and synteny was conserved. Comparing genomes in this complex will require independent annotation of each genome, plus checks for errors the annotations share.