Linkage maps of the Japanese eel and integration of the map and the assembled sequences. (A) Female linkage map. Bars on each linkage group represent the loci of mapped SNP and SSR markers. Genetic distances (cM) were calculated using the Kosambi function. (B) Male linkage map. Detailed maps of female and male are shown in Additional file 1: Figure S2 and Figure S3. An asterisk shows that two marker loci are linked with a LOD threshold of 4.0. (C) Integration of the linkage map and the assembled sequences for LG1. Vertical red and blue bars represent female and male linkage group, respectively. SNP markers are black, and SSR markers are red. Boxes sandwiched between the female and male linkage groups represent scaffolds. Scaffolds for which the relative order on each chromosome has been determined are labeled in green. A scaffold that is mapped on other linkage groups is labeled in gray. This inconsistency could be caused by a misassembly in the current assembly. Transverse lines link the location of each marker on the genetic maps with its corresponding anchored scaffolds. Gaps between scaffolds are arbitrary because the actual distance between scaffolds is unknown. Scale bars represent 10 cM and 500 kb. Details of all chromosomes and anchored scaffolds are shown in Additional file 1: Figure S4.