New linkage maps for the Cupressaceae species <i>Chamaecyparis obtusa</i> and <i>Thujopsis dolabrata</i> var. <i>hondae</i> and comparison with the linkage map of <i>Cryptomeria japonica</i>

Comparative mapping studies, which can determine whether the genome structure differs among genera, have yet to be conducted in Cupressaceae. This study analyzed three important forestry species in Japan: <i>Cryptomeria japonica</i>, <i>Chamaecyparis obtusa</i>, and <i>Thujopsis dolabrata</i> var. <i>hondae</i>. To date, linkage maps have only been constructed for <i>C. japonica</i>. We constructed the first linkage maps for <i>C. obtusa</i> and <i>T. dolabrata</i> var. <i>hondae</i> using double digest restriction-site associated DNA sequencing (ddRAD-Seq) data, expressed sequence tag-derived simple sequence repeat (EST-SSR) markers, and single-nucleotide polymorphism (SNP) markers designed from homologous unigenes obtained from RNA-seq data. The lengths of the linkage maps were 1,835 cM (1,981 markers) for <i>C. obtusa</i> and 1,833 cM (1,295 markers) for <i>T. dolabrata</i> var. <i>hondae</i>. A total of 11 distinct linkage groups were identified in these maps, corresponding to the haploid number of Cupressaceae. Using four published linkage maps for <i>C. japonica</i>, we then constructed a composite linkage map with 7,784 markers. Finally, the three linkage maps were compared using 207 SNP markers designed from homologous unigenes. Although most markers were mapped to the same LG despite representing different species, indicating strong synteny. The high level of interspecific and intergeneric synteny and macro-collinearity detected in Cupressaceae were similar to those of other trees. We also detected three major chromosomal rearrangements between but not within subfamilies, which may have been caused by the taxonomic distance. This is the first example of comparative mapping for Cupressaceae species.