Article Complete Chloroplast Genome of Japanese Larch (Larix kaempferi): Insights into Intraspecific Variation with an Isolated Northern Limit Population Shufen Chen 1, Wataru Ishizuka 2, Toshihiko Hara 3 and Susumu Goto 1,* 1 Education and Research Center, The University of Tokyo Forests, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan;
[email protected] 2 Forestry Research Institute, Hokkaido Research Organization, Koushunai, Bibai, Hokkaido 079-0166, Japan;
[email protected] 3 Institute of Low Temperature Science, Hokkaido University, Sapporo-city, Hokkaido 060-0819, Japan;
[email protected] * Correspondence:
[email protected]; Tel.: +81-3-5841-5493 Received: 25 July 2020; Accepted: 11 August 2020; Published: 14 August 2020 Abstract: Research Highlights: The complete chloroplast genome for eight individuals of Japanese larch, including from the isolated population at the northern limit of the range (Manokami larch), revealed that Japanese larch forms a monophyletic group, within which Manokami larch can be phylogenetically placed in Japanese larch. We detected intraspecific variation for possible candidate cpDNA markers in Japanese larch. Background and Objectives: The natural distribution of Japanese larch is limited to the mountainous range in the central part of Honshu Island, Japan, with an isolated northern limit population (Manokami larch). In this study, we determined the phylogenetic position of Manokami larch within Japanese larch, characterized the chloroplast genome of Japanese larch, detected intraspecific variation, and determined candidate cpDNA markers. Materials and Methods: The complete genome sequence was determined for eight individuals, including Manokami larch, in this study.