Deciphering the mitochondrial genome of Juglans mandshurica (Juglandaceae)

References

• Alverson AJ, Wei XX, Rice DW, Stern DB, Barry K, Palmer JD. 2010. Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae). Mol Biol Evol. 27(6):1436–1448.
   PubMed Web of Science ®Google Scholar
• Bi G, Mao Y, Xing Q, Cao M. 2018. HomBlocks: a multiple-alignment construction pipeline for organelle phylogenomics based on locally collinear block searching. Genomics. 110(1):18–22.
   PubMed Web of Science ®Google Scholar
• Chen Y, Ye W, Zhang Y, Xu Y. 2015. High speed BLASTN: an accelerated MegaBLAST search tool. Nucleic Acids Res. 43(16):7762–7768.
   PubMed Web of Science ®Google Scholar
• Chen DP, You JH, Liu DD, Wang XY, Li Y, Xu GZ, Lu JM. 2018. A comparative study on evolutionary structures of the Juglans mandshurica different ecological environment stress. J. Northeast Univ Nat Sci Ed. 50(02):97–102.
   Google Scholar
• De Coster W, D'Hert S, Schultz DT, Cruts M, Van Broeckhoven C. 2018. NanoPack: visualizing and processing long read sequencing data. Bioinformatics. 34(15):2666–2669.
   PubMed Web of Science ®Google Scholar
• Hiesel R, von Haeseler A, Brennicke A. 1994. Plant mitochondrial nucleic acid sequences as a tool for phylogenetic analysis. Proc Natl Acad Sci U S A. 91(2):634–638.
   PubMed Web of Science ®Google Scholar
• Hu YH, Woeste KE, Zhao P. 2016. Completion of the chloroplast genomes of five chinese juglans and their contribution to chloroplast phylogeny. Front Plant Sci. 7:1955.
   PubMed Web of Science ®Google Scholar
• Huang GL, Mao LR, Liu YF, Qin DZ, Sun L, Zhang HJ. 2010. Economic value and cultivation techniques of Juglans mandshurica. Forest Sci Technol.. (3):52–53,56.
   Google Scholar
• Jansen RK, Cai Z, Raubeson LA, Daniell H, Boore JL. 2008. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc Natl Acad Sci U S A. 104(49):19369–19374.
   Web of Science ®Google Scholar
• Kolmogorov M, Yuan J, Lin Y, Pevzner PA. 2019. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 37(5):540–546.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Li H. 2016. Minimap and miniasm: fast mapping and de novo assembly fornoisy long sequences. Bioinformatics. 32(14):2103–2110.
   PubMed Web of Science ®Google Scholar
• Li H. 2018. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 34(18):3094–3100.
   PubMed Web of Science ®Google Scholar
• Li JN, Gao RX. 2020. Research progress on the genetic breeding of Juglans mandshurica in China. J Anhui Agri Sci. 48(17):4–7.
   Google Scholar
• Li J, Li J, Ma Y, Kou L, Wei J, Wang W. 2022. The complete mitochondrial genome of okra (Abelmoschus esculentus): using nanopore long reads to investigate gene transfer from chloroplast genomes and rearrangements of mitochondrial DNA molecules. BMC Genom. 23:481.
   PubMed Web of Science ®Google Scholar
• Liu DN. 2020. Effects of different seedling rearing methods and fertilization on growth and physiology of Juglans mandshurica Maxim. Mudanjiang Normal University. China (master thesis).
   Google Scholar
• Liu D, Guo H, Zhu J, Qu K, Chen Y, Guo Y, Ding P, Yang H, Xu T, Jing Q, et al. 2022. Complex physical structure of complete mitochondrial genome of quercus acutissima (fagaceae): a significant energy plant. Genes. 13(8):1321.
   PubMed Web of Science ®Google Scholar
• Liu H, Song Q, Wang TM, Zhang H, Zhai YJ, Kang YG. 2021. Establishment of content determination of 5 components and their content difference analysis in the branch and root of Juglans mandshurica. China Pharm. 32(08):933–939.
   Google Scholar
• Logacheva MD, Schelkunov MI, Fesenko AN, Kasianov AS, Penin AA. 2020. Mitochondrial genome of Fagopyrum esculentum and the genetic diversity of extranuclear genomes in buckwheat. Plants. 9(5):618.
   Google Scholar
• Luo M, Qiao Q, Mu YS, Ruan X, Yang X, Xing WM, Duan XH. 2017. Temporal and spatial variations of active ingredients in Juglans mandshurica Maxim and antitumor their anti-tumor activity. Bull Bot Res. 37(6):947–952.
   Google Scholar
• Marechal A, Brisson N. 2010. Recombination and the maintenance of plant organelle genome stability. New Phytol. 186(2):299–317.
   PubMed Web of Science ®Google Scholar
• Morley SA, Nielsen BL. 2017. Plant mitochondrial DNA. Front Biosci. 22(6):1023–1032.
   Google Scholar
• Oldenburg DJ, Bendich AJ. 2015. DNA maintenance in plastids and mitochondria of plants. Front Plant Sci. 6:883.
   PubMed Web of Science ®Google Scholar
• Palmer JD, Herbon LA. 1988. Plant mitochondrial DNA evolves rapidly in atructure, but alowly in Herbon sequence. J Mol Evol. 28(1-2):87–97.
   PubMed Web of Science ®Google Scholar
• Pang Y. 2021. Exploration of the cultivation technology of Juglans mandshurica. Seed Sci Technol. 39(22):113–114.
   Google Scholar
• Parks M, Cronn R, Liston A. 2009. Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biol. 7:84.
   PubMed Web of Science ®Google Scholar
• Patel RK, Jain M. 2012. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS One. 7(2):e30619.
   PubMed Web of Science ®Google Scholar
• She R. 2021. Population genomics and phylogeny of walnut (Juglans). Northwest University. China (master thesis).
   Google Scholar
• Shen GZ, Zou GH, Liang T, Liang QC, Wu YY. 2015. Chemical constituents of Juglans mandshurica. Chin J Exp Trad Med Form. 21(17):219–224.
   Google Scholar
• Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 30(9):1312–1313.
   PubMed Web of Science ®Google Scholar
• Uddin MS, Sun W, He X, Teixeira Da Silva JA, Cheng QX. 2014. An improved method to extract DNA from mango Mangifera indica. Biologia. 69(2):133–138.
   Web of Science ®Google Scholar
• Wang DN, Mu CC, Feng FJ. 2010. Establishment and optimization of ISSR-PCR reaction system for Juglans mandshurica Maxim. Res Exp Lab. 29(11):18–22.
   Google Scholar
• Wang TM, Xu SZ, Yu WJ, Di X, Zhang H, Zhai YJ, Kang YG. 2018. Morphological study of Juglans mandshurica. Chin Arch Trad Chin Me. 36(03):675–677.
   Google Scholar
• Wick RR, Schultz MB, Zobel J, Holt KE. 2015. Bandage: interactive visualization of de novo genome assemblies. Bioinformatics. 31(20):3350–3352.
   PubMedGoogle Scholar
• Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLOS Comput Biol. 13(6):e1005595.
   PubMed Web of Science ®Google Scholar
• Wynn EL, Christensen AC. 2018. Repeats of unusual size in plant mitochondrial genomes: identification, incidence and evolution. G3-Genes Genomes Genet. 9(2):549–559.
   Web of Science ®Google Scholar
• Yang Z, Ni Y, Lin Z, Yang L, Chen G, Nijiati N, Hu Y, Chen X. 2022. De novo assembly of the complete mitochondrial genome of sweet potato (Ipomoea batatas [L.] Lam) revealed the existence of homologous conformations generated by the repeat-mediated recombination. BMC Plant Biol. 22(1):285.
   PubMed Web of Science ®Google Scholar
• Zhang F, Li W, Gao CW, Zhang D, Gao LZ. 2019. Deciphering tea tree chloroplast and mitochondrial genomes of Camellia sinensis var. assamica. Sci Data. 6(1).
   Google Scholar