Complete Chloroplast Genome of Japanese Larch (Larix kaempferi): Insights into Intraspecific Variation with an Isolated Northern Limit Population

被引:11
|
作者
Chen, Shufen [1 ]
Ishizuka, Wataru [2 ]
Hara, Toshihiko [3 ]
Goto, Susumu [1 ]
机构
[1] Univ Tokyo, Univ Tokyo Forests, Educ & Res Ctr, Grad Sch Agr & Life Sci,Bunkyo Ku, 1-1-1 Yayoi, Tokyo 1138657, Japan
[2] Hokkaido Res Org, Forestry Res Inst, Bibai, Hokkaido 0790166, Japan
[3] Hokkaido Univ, Inst Low Temp Sci, Sapporo, Hokkaido 0600819, Japan
来源
FORESTS | 2020年 / 11卷 / 08期
基金
日本学术振兴会;
关键词
cpDNA; next generation sequencing; northern limit; nucleotide diversity; phylogeny; In; Del; SNP; SSR; Pinaceae; COMPLETE SEQUENCE; DNA; MITOCHONDRIAL; REPEATS; REARRANGEMENTS; RECOMBINATION; GENES;
D O I
10.3390/f11080884
中图分类号
S7 [林业];
学科分类号
0829 ; 0907 ;
摘要
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. The genetic position of the northern limit population was evaluated using phylogenetic analysis. The chloroplast genome of Japanese larch was characterized by comparison with eight individuals. Furthermore, intraspecific variations were extracted to find candidate cpDNA markers.Results:The phylogenetic tree showed that Japanese larch forms a monophyletic group, within which Manokami larch can be phylogenetically placed, based on the complete chloroplast genome, with a bootstrap value of 100%. The value of nucleotide diversity (pi) was calculated at 0.00004, based on SNP sites for Japanese larch, suggesting that sequences had low variation. However, we found three hyper-polymorphic regions within the cpDNA. Finally, we detected 31 intraspecific variations, including 19 single nucleotide polymorphisms, 8 simple sequence repeats, and 4 insertions or deletions.Conclusions:Using a distant genotype in a northern limit population (Manokami larch), we detected sufficient intraspecific variation for the possible candidates of cpDNA markers in Japanese larch.
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页数:10
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