Journal of Species Research

  • 제10권2호
  • /
  • Pages.154-158
  • /
  • 2021
  • /
  • 2234-7909(pISSN)
  • /
  • 2713-8615(eISSN)
국립생물자원관 (The National Institute of Biological Resources)
권호 표지
DOI QR코드

DOI QR Code

Chloroplast genome of the conserved Aster altaicus var. uchiyamae B2015-0044 as genetic barcode

  • 투고 : 2021.01.03
  • 심사 : 2021.02.03
  • 발행 : 2021.05.31
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

An endemic endangered species, Aster altaicus var. uchiyamae (Danyang aster) B2015-0044, is cultivated at the Shingu Botanical Garden, which serves as the ex situ conservation institution for this species. In this work, we sequenced the chloroplast genome of A. altaicus var. uchiyamae B2015-0044. We found that the chloroplast (cp) genome of B2015-0044 was 152,457 base pairs(bps) in size: 84,247 bps of large single copy regions(LSC), 25,007 bps of inverted repeats(IRs), and 18,196 bps of small single copy regions. The B2015-0044 cp genome contains 79 protein-coding genes (PCGs), 4 RNA genes, 29 tRNA genes, and 3 pseudogenes. These results were identical to a previously reported cp genome (Park et al., 2017), except for two sites in introns and three in intergenic spacer (IGS) regions. For the intronic differences, we found that clpP.i1 had a 1-bp small simple repeat (SSR) (T) and petD.i had a 3-bp SSR (ATT). We found 1-bp SSRs in the IGSs of trnT_ggu~psbD and psbZ~trnG_gcc, C and A, respectively. The IGS of(ndhF)~rpl32 had a SNP. Based on our results, the cp genome of the A. altaicus var. uchiyamae can be classified into two genotypes, [C]1-[A]12-[T]12-[ATT]4-C and [C]2-[A]11-[T]11-[ATT]2-A.

키워드

과제정보

This research was funded by the National Research Foundation of Korea (NRF), grant number NRF-2019R1F1 A1062617, and was also supported by a grant from the National Institute of Biological Resources under the Ministry of Environment(NIBR201703201), Republic of Korea.

참고문헌

  1. Choi, K.S. and S. Park. 2015. The complete chloroplast genome sequence of Aster spathulifolius(Asteraceae); genomic features and relationship with Asteraceae. Gene 572: 214-221 https://doi.org/10.1016/j.gene.2015.07.020
  2. Conant, G.C. and K.H. Wolfe. 2008. GenomeVx: simple webbased creation of editable circular chromosome maps. Bioinformatics 24:861-862. https://doi.org/10.1093/bioinformatics/btm598
  3. Jeong, H., J.M. Lim, J. Park, Y.M. Sim, H.G. Choi, J. Lee and W.J. Jeong. 2014. Plastid and mitochondrion genomic sequences from Arctic Chlorella sp. ArM0029B. BMC Genomics 15:286. https://doi.org/10.1186/1471-2164-15-286
  4. Kitamura, S. 1937. Aster altaicus Willd., var. Uchiyamae Kitamura var. nov. Memoirs of the College of Science, Kyoto Imperial University, Series B. pp. 367-368.
  5. Laslett, D. and B. Canback. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res. 32:11-16. https://doi.org/10.1093/nar/gkh152
  6. Li, X., Y. Yang, R.J. Henry, M. Rosseto, Y. Wang and S. Chen. 2015. Plant DNA barcoding: from gene to genome. Biol. Rev. 90:157-166. https://doi.org/10.1111/brv.12104
  7. Liu, X., B. Zhou, H. Yang, Y. Li, Q. Yang, Y. Lu and Y. Gao. 2018. Sequencing and Analysis of Chrysanthemum carinatum Schousb and Kalimeris indica. The Complete Chloroplast Genomes Reveal Two Inversions and rbcL as Barcoding of the Vegetable. Molecules 23:1358-1379. https://doi.org/10.3390/molecules23061358
  8. Lowe, T.M. and S.R. Eddy. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955-964. https://doi.org/10.1093/nar/25.5.955
  9. Nock, C.J., D.L.E. Waters, M.A. Edwards, S.G. Bowen, N. Rice, G.M. Cordriro and R.J. Henry. 2011. Chloroplast genome sequences from total DNA for plant identification. Plant. Biotechnology Journal 9:328-333. https://doi.org/10.1111/j.1467-7652.2010.00558.x
  10. Park, J., J. Shim, H. Won and J. Lee. 2017. Plastid genome of Aster altaicus var. uchiyamae Kitam., an endanger species of Korean asterids. Journal of Species Research 6(1):76-90. https://doi.org/10.12651/JSR.2017.6.1.076
  11. Park, S.K., S.-J. Kwon, J. Park, M. Lee, S.Y. Won, Y.C. Kim, Y.-J. Hwang, S.-H. Sohn and J. Lee. 2015. Chloroplast genome of white wild chrysanthemum, Dendranthema sp. K247003, as genetic barcode. Journal of Species Research 4(2):152-158. https://doi.org/10.12651/JSR.2015.4.2.152
  12. Suh, Y.B. and Y.J. Kim. 2014. Korean Red List of Threatened Species. 2nd ed. National Institute of Biological Resources, Korea.
  13. Wyman, S.K., R.K. Jansen and J.L. Boore. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252-3255. https://doi.org/10.1093/bioinformatics/bth352