Whole chloroplast genome sequences of the Japanese hemlocks, <i>Tsuga diversifolia</i> and <i>T. sieboldii</i>, and development of chloroplast microsatellite markers applicable to East Asian <i>Tsuga</i>

The genus Tsuga is an ecologically important forest tree genus of Japan with two endemic species, the subalpine Tsuga diversifolia and the temperate Tsuga sieboldii. Despite dominating some of the most important remaining natural forests in Japan, the genetic diversity and structure of these species is unknown with genetic studies hindered by a lack of genetic resources. This study reports the complete chloroplast genome sequences of both T. diversifolia and T. sieboldii and the development of polymorphic chloroplast microsatellite markers. The chloroplast genomes of T. diversifolia and T. sieboldii are 120,802 and 120,797 bp in length, respectively and shared an identical repertoire of 35 tRNA genes, 4 rRNA genes and 72 protein-coding genes. Seven polymorphic chloroplast microsatellite loci were developed and showed an average of 2.24 alleles per locus in T. diversifolia and 3.57 in T. sieboldii. These loci were all successfully genotyped in two other East Asian species (Tsuga chinensis and Tsuga ulleungensis) with an average of 2.28 alleles per locus for both species. The high transferability of these loci, and the fact that all species contained loci with non-overlapping allele size ranges, indicates that these markers will be useful for genetic studies of all East Asian Tsuga species for investigating species boundaries, phylogeography and stand-level processes.