{"id":258,"date":"2019-03-19T23:57:11","date_gmt":"2019-03-19T23:57:11","guid":{"rendered":"http:\/\/uni.hi.is\/einararn\/?p=258"},"modified":"2019-03-20T00:34:40","modified_gmt":"2019-03-20T00:34:40","slug":"extensive-structural-variation-between-ecotypes-of-atlantic-cod-gadus-morhua-revealed-with-linked-read-sequencing-and-optical-mapping","status":"publish","type":"post","link":"https:\/\/uni.hi.is\/einararn\/is\/2019\/03\/19\/extensive-structural-variation-between-ecotypes-of-atlantic-cod-gadus-morhua-revealed-with-linked-read-sequencing-and-optical-mapping\/","title":{"rendered":"Extensive structural variation between ecotypes of Atlantic cod, Gadus morhua, revealed with linked-read sequencing and optical mapping"},"content":{"rendered":"<p><strong>Katr\u00edn Halld\u00f3rsd\u00f3ttir and Einar \u00c1rnason. 2019.\u00a0 Extensive structural variation between ecotypes of Atlantic cod, Gadus morhua, revealed\u00a0<\/strong><strong>with linked-read sequencing and optical mapping.<\/strong><\/p>\n<p>Poster presented at Speciation: Gordon Research Conference, Ventura, California, USA. March 10--15, 2019.<\/p>\n<p>&nbsp;<\/p>\n<p>Several \u201cstocks\u201d are recognized for fisheries management among Atlantic cod. The stocks are populations<br \/>\nthat differ from each other in various biological traits, life history, habitat selection, and productivity, but their<br \/>\nevolutionary status and connectivity are debated. To what extent, if any, are they reproductively isolated?<br \/>\nIn Norway, the migratory Northeast-Arctic cod and the stationary Norway coastal cod, which differ in otolith<br \/>\nshape and some phenotypes were considered cryptic sibling species (M\u00f8ller, 1968) based on hemoglobin<br \/>\nand other protein variation, whereas Williams (1975) argued for panmixia and that strong natural selection in<br \/>\nevery generation recreates the observed differentiation. These two forms are now referred to as the shallow-<br \/>\nwater stationary or coastal and deep-water migratory or frontal behavioral ecotypes among Atlantic cod as<br \/>\ndefined by storage tag data (Pampoulie et al., 2007). Chromosomal rearrangements on linkage group LG01<br \/>\n(Kirubakaran et al., 2016) and on linkage groups LG02, LG07, and LG12 (Berg et al., 2016) promote diver-<br \/>\ngence between the ecotypes. The reference genome sequence of Atlantic cod, Gadmor2 (T\u00f8rresen et al.,<br \/>\n2016), was based on DNA from the migratory frontal behavioral ecotype. Here, we study structural variation<br \/>\nusing single molecule sequencing of DNA from a coastal ecotype specimen from Iceland and compare it to<br \/>\nthe reference genome.<\/p>\n<p>The large chromosomal rearrangements, primarily inversion, on linkage groups LG01, LG02, LG07, and LG12<br \/>\nhave been interpreted as a case of genomic islands of divergence, associated with ecological divergence, un-<br \/>\nder high levels of gene flow between the two ecotypes (Hemmer-Hansen et al., 2013). Here we show, using<br \/>\nwhole genome sequencing of single molecules and optical mapping, that the structural variation is much<br \/>\nmore widespread over the genome than previously described. We found signs of large chromosomal structural\u00a0variation in almost all Linkage groups, to a different extent. The results of the linked-read sequencing showed147 large structural variants calls (that are &gt;= 30kb). These results show the importance of look-<br \/>\ning at phased data when investigating structural variation. The observed chromosomal structural variation<br \/>\nlikely suppresses recombination in heterozygotes thus affecting gene flow and local adaptation and promoting<br \/>\nreproductive isolation and speciation among ecotypes.<\/p>","protected":false},"excerpt":{"rendered":"<p>Katr\u00edn Halld\u00f3rsd\u00f3ttir and Einar \u00c1rnason. 2019.\u00a0 Extensive structural variation between ecotypes of Atlantic cod, Gadus morhua, revealed\u00a0with linked-read sequencing and optical mapping. Poster presented at Speciation: Gordon Research Conference, Ventura, California, USA. March 10--15, 2019. &nbsp; Several \u201cstocks\u201d are recognized for fisheries management among Atlantic cod. The stocks are populations that differ from each other [&hellip;]<\/p>\n","protected":false},"author":997,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[64760],"tags":[],"class_list":["post-258","post","type-post","status-publish","format-standard","hentry","category-education"],"_links":{"self":[{"href":"https:\/\/uni.hi.is\/einararn\/is\/wp-json\/wp\/v2\/posts\/258","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/uni.hi.is\/einararn\/is\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/uni.hi.is\/einararn\/is\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/uni.hi.is\/einararn\/is\/wp-json\/wp\/v2\/users\/997"}],"replies":[{"embeddable":true,"href":"https:\/\/uni.hi.is\/einararn\/is\/wp-json\/wp\/v2\/comments?post=258"}],"version-history":[{"count":8,"href":"https:\/\/uni.hi.is\/einararn\/is\/wp-json\/wp\/v2\/posts\/258\/revisions"}],"predecessor-version":[{"id":267,"href":"https:\/\/uni.hi.is\/einararn\/is\/wp-json\/wp\/v2\/posts\/258\/revisions\/267"}],"wp:attachment":[{"href":"https:\/\/uni.hi.is\/einararn\/is\/wp-json\/wp\/v2\/media?parent=258"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/uni.hi.is\/einararn\/is\/wp-json\/wp\/v2\/categories?post=258"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/uni.hi.is\/einararn\/is\/wp-json\/wp\/v2\/tags?post=258"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}