227
Views
1
CrossRef citations to date
0
Altmetric
Silviculture and Plant Sciences

Characterization of the complete chloroplast genome of Abies sachalinensis and its intraspecific variation hotspots

ORCID Icon, ORCID Icon, & ORCID Icon
Pages 476-482 | Received 21 Aug 2021, Accepted 11 May 2022, Published online: 15 Jun 2022

References

  • Bondar EI, Putintseva YA, Oreshkova NV, Krutovsky KV. 2019. Siberian larch (Larix sibirica Ledeb.) chloroplast genome and development of polymorphic chloroplast markers. BMC Bioinfomatics. 20(1):47–52.
  • Chen S, Ishizuka W, Hara T, Goto S. 2020. Complete chloroplast genome of Japanese larch (Larix kaempferi): insights into intraspecific variation with an isolated northern limit population. Forests. 11(8):884. doi:10.3390/f11080884.
  • Cui Y, Nie L, Sun W, Xu Z, Wang Y, Yu J, Song J, Yao H. 2019. Comparative and phylogenetic analyses of ginger (Zingiber officinale) in the family Zingiberaceae based on the complete chloroplast genome. Plants. 8(8):283. doi:10.3390/plants8080283.
  • Dong W, Xu C, Li C, Sun J, Zuo Y, Shi S, Cheng T, Guo J, Zhou S. 2015. ycf1, the most promising plastid DNA barcode of land plants. Sci. Rep. 5(1):8348. doi:10.1038/srep08348.
  • Farjon A, Filer D. 2013. An atlas of the world’s conifers, an analysis of their distribution, biogeography, diversity and conservation status. Leiden (The Netherlands): Brill.
  • Guo W, Grewe F, Cobo-Clark A, Fan W, Duan Z, Adams RP, Schwarzbach AE, Mower JP. 2014. Predominant and substoichiometric isomers of the plastid genome coexist within Juniperus plants and have shifted multiple times during Cupressophyte evolution. Genome Biol Evol. 6(3):580–590. doi:10.1093/gbe/evu046.
  • Haga N, Kobayashi M, Michiki N, Takano T, Baba F, Kobayashi K, Ohyanagi H, Ohgane J, Yano K, Yamane K. 2019. Complete chloroplast genome sequence and phylogenetic analysis of wasabi (Eutrema japonicum) and its relatives. Sci Rep. 9(1):14377. doi:10.1038/s41598-019-49667-z.
  • Hayashi Y. 1954. The natural distribution of important trees, indigenous to Japan. Conifer report 3. Bull Gov For Exp Sta. 75: 1–173. in Japanese.
  • Hirao T, Watanabe A, Kuria M, Kondo T, Takata K. 2009. A frameshift mutation of the chloroplast matK coding region is associated with chlorophyll deficiency in the Cryptomeria japonica virescent mutant Wogon-Sugi. Curr Genet. 55(3):311–321. doi:10.1007/s00294-009-0247-9.
  • Igarashi Y. 2010. Vegetation and climate history in Sakhalin and Hokkaido: migration, rise and fall of plants inferred from pollen records. Quaternary Res. 49(5):241–253. doi:10.4116/jaqua.49.241.
  • Ishizuka W, Goto S. 2012. Modeling intraspecific adaptation of Abies sachalinensis to local altitude and responses to global warming, based on a 36-year reciprocal transplant experiment. Evol Appl. 5(3):229–244. doi:10.1111/j.1752-4571.2011.00216.x.
  • Ishizuka W, Tabata A, Ono K, Fukuda Y, Hara T. 2017. Draft chloroplast genome of Larix gmelinii var. japonica: insight into intraspecific divergence. J For Res. 22(6):393–399. doi:10.1080/13416979.2017.1386019.
  • Ishizuka W, Kon H, Kita K, Kuromaru M, Goto S. 2021. Local adaptation to contrasting climatic conditions in Sakhalin fir (Abies sachalinensis) revealed by long-term provenance trials. Ecol Res. 36(4):720–732. doi:10.1111/1440-1703.12232.
  • Katoh K, Rozewicki J, Yamada KD. 2019. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics. 20(4):1160–1166. doi:10.1093/bib/bbx108.
  • Kitamura K, Uchiyama K, Ueno S, Ishizuka W, Tsuyama I, Goto S. 2020. Geographical gradients of genetic diversity and differentiation among the southernmost marginal populations of Abies sachalinensis revealed by EST-SSR polymorphism. Forests. 11(2):233. doi:10.3390/f11020233.
  • Kurtz S. 2001. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucl Acids Res. 29(22):4633–4642. doi:10.1093/nar/29.22.4633.
  • Lohse M, Drechsel O, Kahlau S, Bock R. 2013. OrganellarGenomeDRAW: a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucl Acids Res. 41(W1):W575–581. doi:10.1093/nar/gkt289.
  • Nagasaka K, Wang ZM, Tanaka K. 1997. Genetic variation among natural Abies sachalinensis population in relation to environmental gradients in Hokkaido, Japan. For Genet. 4:43–50.
  • Rozas J, Ferrermata A, Sánchezdelbarrio JC, Guiraorico S, Librado P, Ramosonsins SE, Sánchezgracia A. 2017. Evolution. DnaSP 6: DNA sequence polymorphism analysis of large datasets. Mol Biol. 34(12):3299–3302. doi:10.1093/molbev/msx248.
  • Sakaguchi S, Ueno S, Tsumura Y, Setoguchi H, Ito M, Hattori C, Nozoe S, Takahashi D, Nakamasu R, Sakagami T, et al. 2017. Application of a simplified method of chloroplast enrichment to small amounts of tissue for chloroplast genome sequencing. Appl Plant Sci. 5(5):1700002. doi:10.3732/apps.1700002.
  • Schattner P, Brooks AN, Lowe TM. 2005. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucl Acids Res. 33():686–689. doi:10.1093/nar/gki366.
  • Tsumura Y, Suyama Y. 1998. DIFFERENTIATION OF MITOCHONDRIAL DNA POLYMORPHISMS IN POPULATIONS OF FIVE JAPANESE Abies SPECIES. Evolution. 52(4):1031–1042. doi:10.1111/j.1558-5646.1998.tb01831.x.
  • Tsumura Y, Suyama Y, Yoshimura K. 2000. Chloroplast DNA inversion polymorphism in populations of Abies and Tsuga. Mol Biol Evol. 17(9):1302–1312. doi:10.1093/oxfordjournals.molbev.a026414.
  • Tsuyama I, Ishizuka W, Kitamura K, Taneda H, Goto S. 2020. Ten years of provenance trials and application of multivariate random forests predicted the most preferable seed source for silviculture of Abies sachalinensis in Hokkaido, Japan. Forests. 11(10):1058. doi:10.3390/f11101058.
  • Ueno S, Nakamura Y, Kobayashi M, Terashima S, Ishizuka W, Uchiyama K, Tsumura Y, Yano K, Goto S. 2018. TodoFirGene: developing transcriptome resources for genetic analysis of Abies sachalinensis. Plant Cell Physiol. 59(6):1276–1284. doi:10.1093/pcp/pcy058.
  • Wakasugi T, Tsudzuki J, Ito S, Nakashima K, Tsudzuki T, Sugiura M. 1994. Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii. Proc Natl Acad Sci USA. 91(21):9794–9798. doi:10.1073/pnas.91.21.9794.
  • Wu CS, Lai YT, Lin CP, Wang YN, Chaw SM. 2009. Evolution of reduced and compact chloroplast genomes (cpDNAs) in gnetophytes: selection toward a lower-cost strategy. Mol Phylogenet Evol. 52(1):115–124. doi:10.1016/j.ympev.2008.12.026.
  • Wu CS, Lin CP, Hsu CY, Wang RJ, Chaw SM. 2011. Comparative chloroplast genomes of Pinaceae: insights into the mechanism of diversified genomic organizations. Genome Biol Evol. 3:309–319. doi:10.1093/gbe/evr026.
  • Wyman SK, Jansen RK, Boore JL. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics. 20(17):3252–3255. doi:10.1093/bioinformatics/bth352.
  • Yamazaki T. 1995. Pinaceae. In: In: Iwatsuki K, Yamazaki T, Boufford DE, Ohba H, editors. Pteridophyta and Gymnospermae. Tokyo (Japan): Kodansha; p. 266–277.
  • Yi DK, Choi K, Joo M, Yang C, Mustafina FU, Han JS, Son DC, Chang KS, Shin CH, Lee YM. 2016a. The complete chloroplast genome sequence of Abies nephrolepis (Pinaceae: abietoideae). J Asia-Pacific Biodiv. 9(2):245–249. doi:10.1016/j.japb.2016.03.014.
  • Yi DK, Yang JC, So S, Joo M, Kim DK, Shin CH, Lee YM, Choi K. 2016b. The complete plastid genome sequence of Abies koreana (Pinaceae: abietoideae). Mitochondrial DNA Part A. 27(4):2351–2353. doi:10.3109/19401736.2015.1025260.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.