Abstract
Taiwania cryptomerioides is an endangered relict conifer species native to East Asia with a variety of practical applications. To contribute to its conservation and sustainable utilization, its complete chloroplast genome was assembled from Illumina sequencing reads. The circular genome is 131,427 bp in size with a biased nucleotide composition (33.5% A, 17.5% C, 17.2% G & 31.8% T). It encodes a panel of 114 gene species, including 83 protein-coding genes (PCGs) and 31 tRNAs. Gene duplication was detected for three tRNA gene species (trnI-CAU, trnQ-UUG & trnV-GAC). Besides, 15 gene species (atpF, ndhA, ndhB, petB, petD, rpl16, rpl2, rpoC1, rps16, trnA-UGC, trnG-UCC, trnI-GAU, trnK-UUU, trnL-UAA & trnV-UAC) possess a single intron, and another one (ycf3) has a couple of introns. Phylogenetic analysis suggests that T. cryptomerioides and T. flousiana are closely related to each other within the family Cupressaceae.
This is a preview of subscription content, log in via an institution to check access.
References
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170
Chen Y-R, Lee Y-R, Wang S-Y, Chang S-T, Shaw J-F, Chu F-H (2004) Establishment of expressed sequence tags from Taiwania (Taiwania cryptomerioides Hayata) seedling cDNA. Plant Sci 167:955–957. https://doi.org/10.1016/j.plantsci.2004.05.032
Chen Y-H, Lin C-Y, Yen P-L, Yeh T-F, Cheng S-S, Chang S-T (2017) Antifungal agents from heartwood extract of Taiwania cryptomerioides against brown root rot fungus Phellinus noxius. Wood Sci Technol 51:639–651. https://doi.org/10.1007/s00226-017-0901-1
Chou Y-W, Thomas PI, Ge X-J, LePage BA, Wang C-N (2011) Refugia and phylogeography of Taiwania in East Asia. J Biogeogr 38:1992–2005. https://doi.org/10.1111/j.1365-2699.2011.02537.x
Dierckxsens N, Mardulyn P, Smits G (2017) NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucl Acids Res 45:e18. https://doi.org/10.1093/nar/gkw955
Farjon A (2000) Monograph of Cupressaceae and Sciadopitys. Royal Botanic Garden, Kew (UK)
Fu L, Yu Y, Mill RR (1999) Taxodiaceae. Flora China 4:54–61
Global Witness (2009) A disharmonius trade: China and the continued destruction of Burma’s northern frontier forests. Global Witness Ltd., London (UK)
Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307–321. https://doi.org/10.1093/sysbio/syq010
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:W575-W581. https://doi.org/10.1093/nar/gkt289
Nguyen TH, Phan KL, Nguyen DTL, Thomas PI, Farjon A, Averyanov L, Regalado J Jr (2004) Vietnam conifers: conservation status review 2004. Fauna & Flora International, Hanoi (Vietnam)
State Forestry Administration of P. R. China, Ministry of Agriculture of P. R. China (1999) List of the state-protected key wild plants (batch I). State Forestry Administration website. http://www.forestry.gov.cn/portal/main/s/3094/minglu1.htm. Accessed 14 Feb 2018
Thomas P, Farjon A (2011) Taiwania cryptomerioides. IUCN Red List Threat Species 2011:e.T31255A9620141. https://doi.org/10.2305/IUCN.UK.2011-2.RLTS.T31255A9620141.en
Acknowledgements
This work was supported by the Natural Science Foundation of Shanxi Province (201701D221166), the Funding Project for ‘131’ Pioneering Talents in Yuncheng University (XK-2015034) and the Doctoral Startup Foundation of Yuncheng University (YQ-2014020).
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Wang, LL., Shi, YL., Zhang, QL. et al. The complete chloroplast genome of Taiwania cryptomerioides (Cupressales: Cupressaceae), an endangered relict conifer species endemic to East Asia. Conservation Genet Resour 11, 321–323 (2019). https://doi.org/10.1007/s12686-018-1025-0
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12686-018-1025-0