1,128
Views
5
CrossRef citations to date
0
Altmetric
Rapid Communication

Complete mitogenome assemblies from a panel of 13 diverse potato taxa

ORCID Icon, , , , & ORCID Icon
Pages 894-897 | Received 26 Nov 2020, Accepted 02 Feb 2021, Published online: 15 Mar 2021

References

  • Achakkagari SR, Kyriakidou M, Tai HH, Anglin NL, Ellis D, Strömvik MV. 2020. Complete plastome assemblies from a panel of 13 diverse potato taxa. PLOS One. 15(10):e0240124.
  • Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30(15):2114–2120.
  • Bonen L, Scotti NS, Cozzolino SC, Cardi TC. 2007. Mitochondrial DNA variation in cultivated and wild potato species (Solanum spp.) Contribution No. 87 from the Institute of Plant Genetics, Research Division of Portici. Genome. 50(8):706–713.
  • Cho K-S, Cho J-H, Im J-S, Choi J-G, Park Y-E, Hong S-Y, Kwon M, Kang J-H, Park T-H. 2017. The complete mitochondrial genome sequences of potato (Solanum tuberosum L., Solanaceae). Mitochondrial DNA Part B. 2(2):781–782.
  • Cho K-S, Cho J-H, Im J-S, Choi J-G, Park Y-E, Hong S-Y, Park T-H. 2018. Mitochondrial genome sequence of tuber-bearing wild potato, Solanum commersonii Dunal. Mitochondrial DNA Part B. 3(1):198–199.
  • CIP. 2021a. CIP 702472. Solanum stenotomum subsp. goniocalyx (GON1).
  • CIP. 2021b. CIP 704393. Solanum stenotomum subsp. goniocalyx (GON2).
  • CIP. 2021c. CIP 703654. Solanum phureja (PHU).
  • CIP. 2021d. CIP 703810. Solanum xajanhuiri (AJH).
  • CIP. 2021e. CIP 705834. S. stenotomum subsp. stenotomum (STN).
  • CIP. 2021f. CIP 761748. Solanum bukasovii (BUK1).
  • CIP. 2021g. CIP 761748. Solanum bukasovii (BUK2).
  • CIP. 2021h. CIP 700921. Solanum tuberosum subsp. andigena (ADG1).
  • CIP. 2021i. CIP 702853. Solanum tuberosum subsp. andigena (ADG2).
  • CIP. 2021j. CIP 702937. Solanum curtilobum (CUR).
  • CIP. 2021k. CIP 706050. Solanum juzepczukii (JUZ).
  • CIP. 2021l. CIP 707129. Solanum chaucha (CHA).
  • CIP. 2021m. CIP 705053. Solanum tuberosum subsp. tuberosum (TBR).
  • Davis U. 2021. Bioinformatics core. https://github.com/ucdavis-bioinformatics/proc10xG.
  • Dierckxsens N, Mardulyn P, Smits G. 2016. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 45(4):e18.
  • Grun P. 1990. The evolution of cultivated potatoes. Econ Bot. 44(S3):39–55.
  • Hawkes JG. 1990. The potato: evolution, biodiversity and genetic resources. London: Belhaven Press; p. 259.
  • Jackman SD, Coombe L, Chu J, Warren RL, Vandervalk BP, Yeo S, Xue Z, Mohamadi H, Bohlmann J, Jones SJM, et al. 2018. Tigmint: correcting assembly errors using linked reads from large molecules. BMC Bioinformatics. 19(1):393.
  • Jin J-J, Yu W-B, Yang J-B, Song Y, dePamphilis CW, Yi T-S, Li D-Z. 2019. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. bioRxiv. 256479.
  • Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL. 2008. NCBI BLAST: a better web interface. Nucleic Acids Res. 36(Web Server issue):W5–W9.
  • Katoh K, Misawa K, Kuma K, Miyata T. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30(14):3059–3066.
  • Khelik K, Sandve GK, Nederbragt AJ, Rognes T. 2020. NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads. BMC Bioinformatics. 21(1):66.
  • Kozik A, Rowan BA, Lavelle D, Berke L, Schranz ME, Michelmore RW, Christensen AC. 2019. The alternative reality of plant mitochondrial DNA: one ring does not rule them all. PLOS Genet. 15(8):e1008373.
  • Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 35(6):1547–1549.
  • Kyriakidou M, Achakkagari SR, Gálvez López JH, Zhu X, Tang CY, Tai HH, Anglin NL, Ellis D, Strömvik MV. 2020. Structural genome analysis in cultivated potato taxa. Theor Appl Genet. 133(3):951–966.
  • Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, Greiner S. 2017. GeSeq- versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 45(W1):W6–W11.
  • Varré J-S, D'Agostino N, Touzet P, Gallina S, Tamburino R, Cantarella C, Ubrig E, Cardi T, Drouard L, Gualberto JM, et al. 2019. Complete sequence, multichromosomal architecture and transcriptome analysis of the Solanum tuberosum mitochondrial genome. Int J Mol Sci. 20(19):4788.
  • Warren RL, Yang C, Vandervalk BP, Behsaz B, Lagman A, Jones SJM, Birol I. 2015. LINKS: scalable, alignment-free scaffolding of draft genomes with long reads. Gigascience. 4(1):35.
  • Weisenfeld NI, Kumar V, Shah P, Church DM, Jaffe DB. 2017. Direct determination of diploid genome sequences. Genome Res. 27(5):757–767.
  • Yeo S, Coombe L, Chu J, Warren RL, Birol I. 2017. ARCS: assembly roundup by chromium scaffolding. bioRxiv. 100750.