Draft chloroplast genome of Larix gmelinii var. japonica: insight into intraspecific divergence

ABSTRACT

Larix gmelinii var. japonica is one of the major introduced coniferous species in Hokkaido, Japan, although the genetic origin of this species remains unknown. This is the first report that determined the draft chloroplast genome of L. gmelinii var. japonica and detected the genomic variations within species. Two geographically isolated lineages were assumed. Thus, DNA was isolated from purified intact chloroplasts of three representative strains, their origins covered the two assumed lineages, and their whole chloroplast genomes were analyzed by high-throughput sequencing techniques and compared. It was found that the circular complete chloroplast genomes were 122,553–122,598 bp in length. Among the 3 strains, 19 types of genomic variations were detected, which are: 11 single nucleotide variants, 1 multiple nucleotide variant, 2 insertions or deletions, and 5 simple sequence repeats. The genomic differentiation among two assumed lineages was larger than intra-lineage differentiation. These genome-wide variations would be informative for a phylogenic study of L. gmelinii.

KEYWORDS:

• Chloroplast genome
• Larix gmelinii var. japonica
• complete genome sequence
• genomic variation
• genetic lineage

Acknowledgments

We are grateful to Dr. Makoto Kuromaru for helpful comments during the study and reviewers for critical comments to the manuscript.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This study was supported by the Japan Society for the Promotion of Science [15K18715] and partly by the Grant for Joint Research Program of the Institute of Low Temperature Science, Hokkaido University.