619
Views
4
CrossRef citations to date
0
Altmetric
Mitogenome Announcement

The complete chloroplast genomes of two cold hardness coffee trees, Coffea arabica L. (Rubiaceae)

ORCID Icon, ORCID Icon, , ORCID Icon, ORCID Icon, , , & show all
Pages 1619-1621 | Received 03 Jan 2020, Accepted 07 Jan 2020, Published online: 31 Mar 2020

References

  • Bentley JW, Baker PS. 2000. The Colombian Coffee Growers’ Federation: organised, successful smallholder farmers for 70 years. ODI.
  • Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30(15):2114–2120.
  • Cho MS, Kim Y, Kim SC, Park J. 2019. The complete chloroplast genome of Korean Pyrus ussuriensis Maxim. (Rosaceae): providing genetic background of two types of P. ussuriensis. Mitochondrial DNA Part B. 4(2):2424–2425.
  • Choi Y G, Yun N, Park J, Xi H, Min J, Kim Y, Oh S-H. 2020. The second complete chloroplast genome sequence of the Viburnum erosum (Adoxaceae) showed a low level of intra-species variations. Mitochondrial DNA Part B. 5(1):271–272. doi:10.1080/23802359.2019.1698360.
  • Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30(4):772–780.
  • Kim Y, Heo KI, Park J. 2019. The second complete chloroplast genome sequence of Pseudostellaria palibiniana (Takeda) Ohwi (Caryophyllaceae): intraspecies variations based on geographical distribution. Mitochondrial DNA Part B. 4(1):1310–1311.
  • Kim Y, Yi JS, Min J, Xi H, Kim DY, Son J, Park J, Jeon JI. 2019. The complete chloroplast genome of Aconitum coreanum (H. Lév.) Rapaics (Ranunculaceae). Mitochondrial DNA Part B. 4(2):3404–3406.
  • Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Molecular Biology and Evolution. 35(6):1547–1549.
  • Kwon W, Kim Y, Park J. 2019. The complete chloroplast genome of Korean Marchantia polymorpha subsp. ruderalis Bischl. and Boisselier: low genetic diversity between Korea and Japan. Mitochondrial DNA Part B. 4(1):959–960.
  • Lashermes P, Combes M.-C, Robert J, Trouslot P, D’Hont A, Anthony F, Charrier A. 1999. Molecular characterisation and origin of the Coffea arabica L. genome. Mol Gen Genet. 261(2):259–266.
  • Li H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv. preprint arXiv:13033997.
  • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools. Bioinformatics. 25(16):2078–2079.
  • Maughan PJ, Chaney L, Lightfoot DJ, Cox BJ, Tester M, Jellen EN, Jarvis DE. 2019. Mitochondrial and chloroplast genomes provide insights into the evolutionary origins of quinoa (Chenopodium quinoa Willd.). Sci Rep. 9(1):185.
  • Min J, Kim Y, Xi H, Jang T, Kim G, Park J, Park J-H. 2019. The complete chloroplast genome of a new candidate cultivar, Sang Jae, of Abeliophyllum distichum Nakai (Oleaceae): initial step of A. distichum intraspecies variations atlas. Mitochondrial DNA Part B. 4(2):3716–3718. doi:10.1080/23802359.2019.1679678.
  • Min J, Kim Y, Xi H, Heo KI, Park J. 2019. The complete chloroplast genome of coffee tree, Coffea arabica L. ‘Typica’ (Rubiaceae). Mitochondrial DNA Part B. 4(2):2240–2241.
  • Min J, Park J, Kim Y, Kwon W. 2019. The complete chloroplast genome of Artemisia fukudo Makino (Asteraceae): providing insight of intraspecies variations. Mitochondrial DNA Part B. 4(1):1510–1512.
  • O’brien TG, Kinnaird MF. 2003. Caffeine and conservation. Washington, D.C: American Association for the Advancement of Science.
  • Oh SH, Suh HJ, Park J, Kim Y, Kim S. 2019. The complete chloroplast genome sequence of Goodyera schlechtendaliana in Korea (Orchidaceae). Mitochondrial DNA Part B. 4(2):2692–2693.
  • Park J, Min J, Kim Y, Xi H, Kwon W, Jang T, Kim G, Park J-H. 2019. The complete chloroplast genome of a new candidate cultivar, Dae Ryun, of Abeliophyllum distichum Nakai (Oleaceae). Mitochondrial DNA Part B. 4(2):3713–3715. doi:10.1080/23802359.2019.1679676.
  • Park J, Kim Y. 2019. The second complete chloroplast genome of Dysphania pumilio (R. Br.) mosyakin and clemants (Amranthaceae): intraspecies variation of invasive weeds. Mitochondrial DNA Part B. 4(1):1428–1429.
  • Park J, Kim Y, Kwon W, Nam S, Song M. 2019. The second complete chloroplast genome sequence of Nymphaea alba L. (Nymphaeaceae) to investigate inner-species variations. Mitochondrial DNA Part B. 4(1):1014–1015.
  • Park J, Kim Y, Kwon W, Xi H, Kwon M. 2019. The complete chloroplast genome of tulip tree, Liriodendron tulifipera L.(Magnoliaceae): investigation of intra-species chloroplast variations. Mitochondrial DNA Part B. 4(2):2523–2524.
  • Park J, Kim Y, Lee K. 2019. The complete chloroplast genome of Korean mock strawberry, Duchesnea chrysantha (Zoll. and Moritzi) Miq.(Rosoideae). Mitochondrial DNA Part B. 4(1):864–865.
  • Park J, Kim Y, Xi H. 2019a. The complete chloroplast genome of aniseed tree, Illicium anisatum L. (Schisandraceae). Mitochondrial DNA Part B. 4(1):1023–1024.
  • Park J, Kim Y, Xi H. 2019b. The complete chloroplast genome sequence of male individual of Korean endemic willow, Salix koriyanagi Kimura (Salicaceae). Mitochondrial DNA Part B. 4(1):1619–1621.
  • Park J, Kim Y, Xi H, Heo KI. 2019a. The complete chloroplast genome of coffee tree, Coffea arabica L. ‘Blue Mountain’ (Rubiaceae). Mitochondrial DNA Part B. 4(2):2436–2437.
  • Park J, Kim Y, Xi H, Heo KI. 2019b. The complete chloroplast genome of ornamental coffee tree. Coffea arabica L. (Rubiaceae). Mitochondrial DNA Part B. 4(1):1059–1060.
  • Park J, Kim Y, Xi H, Jang T, Park JH. 2019. The complete chloroplast genome of Abeliophyllum distichum Nakai (Oleaceae), cultivar Ok Hwang 1ho: insights of cultivar specific variations of A. distichum. Mitochondrial DNA Part B. 4(1):1640–1642.
  • Park J, Kim Y, Xi H, Kwon W, Kwon M. 2019. The complete chloroplast and mitochondrial genomes of Hyunsasi tree, Populus alba x Populus glandulosa (Salicaceae). Mitochondrial DNA Part B. 4(2):2521–2522.
  • Park J, Kim Y, Xi H, Nho M, Woo J, Seo Y. 2019. The complete chloroplast genome of high production individual tree of Coffea arabica L. (Rubiaceae). Mitochondrial DNA Part B. 4(1):1541–1542.
  • Park J, Kim Y, Xi H, Oh YJ, Hahm KM, Ko J. 2019a. The complete chloroplast genome of common camellia tree in Jeju island, Korea, Camellia japonica L. (Theaceae): intraspecies variations on common camellia chloroplast genomes. Mitochondrial DNA Part B. 4(1):1292–1293.
  • Park J, Kim Y, Xi H, Oh YJ, Hahm KM, Ko J. 2019b. The complete chloroplast genome of common camellia tree, Camellia japonica L. (Theaceae), adapted to cold environment in Korea. Mitochondrial DNA Part B. 4(1):1038–1040.
  • Park J, Xi H, Kim Y, Heo KI, Nho M, Woo J, Seo Y, Yang JH. 2019. The complete chloroplast genome of cold hardiness individual of Coffea arabica L. (Rubiaceae). Mitochondrial DNA Part B. 4(1):1083–1084.
  • Samson N, Bausher MG, Lee SB, Jansen RK, Daniell H. 2007. The complete nucleotide sequence of the coffee (Coffea arabica L.) chloroplast genome: organization and implications for biotechnology and phylogenetic relationships amongst angiosperms. Plant Biotechnology J. 5(2):339–353.
  • Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18(5):821–829.
  • Zhao QY, Wang Y, Kong YM, Luo D, Li X, Hao P. 2011. Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinformatics. 12(Suppl 14):S2.
  • Zhu Q, Gao P, Liu S, Amanullah S, Luan F. 2016. Comparative analysis of single nucleotide polymorphisms in the nuclear, chloroplast, and mitochondrial genomes in identification of phylogenetic association among seven melon (Cucumis melo L.) cultivars. Breed Sci. 66(5):711–719.