Characteristics and phylogenetic analysis of the complete chloroplast genome of Cornus hongkongensis Hemsl. 1888 (Cornaceae)

References

• Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30(15):2114–2120. doi:10.1093/bioinformatics/btu170.
   PubMed Web of Science ®Google Scholar
• Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, et al. 2021. Twelve years of SAMtools and BCFtools. GigaScience. 10(2):giab008. doi:10.1093/gigascience/giab008.
   PubMed Web of Science ®Google Scholar
• Dan-Qi X, Cheng-Xiang LU. 2008. Germplasm resource distribution and recent research advance in Dendrobenthamia. J Gansu Forest Sci Technol. 33:24–26, 68.
   Google Scholar
• Fu CN, Li HT, Milne R, Zhang T, Ma PF, Yang J, Li DZ, Gao LM. 2017. Comparative analyses of plastid genomes from fourteen Cornales species: inferences for phylogenetic relationships and genome evolution. BMC Genomics. 18(1):956. doi:10.1186/s12864-017-4319-9.
   PubMedGoogle Scholar
• Fu CN, Mo ZQ, Yang JB, Ge XJ, Li DZ, Xiang QJ, Gao LM. 2019. Plastid phylogenomics and biogeographic analysis support a trans-Tethyan origin and rapid early radiation of Cornales in the Mid-Cretaceous. Mol Phylogenet Evol. 140:106601. doi:10.1016/j.ympev.2019.106601.
   PubMed Web of Science ®Google Scholar
• Jijun X, Biting HE, Zhaoyou XU, Huanwei C, Jun LI. 2017. A study on container seedling quality grading of Cornus hongkongensis Hemsl. ssp. elegans. J Fujian Forest Sci Technol. 44(4):102-106. doi:10.13428/j.cnki.fjlk.2017.04.022.
   Google Scholar
• Jin J-J, Yu W-B, Yang J-B, Song Y, Depamphilis CW, Yi T-S, Li D-Z. 2020. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 21(1):241. doi:10.1186/s13059-020-02154-5.
   PubMed Web of Science ®Google Scholar
• Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30(4):772–780. doi:10.1093/molbev/mst010.
   PubMed Web of Science ®Google Scholar
• Kaveriappa KM, Phillips LM, Trigiano RN. 1997. Micropropagation of flowering dogwood (Cornus florida) from seedlings. Plant Cell Rep. 16(7):485–489. doi:10.1007/bf01092771.
   PubMed Web of Science ®Google Scholar
• Li H. 2018. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 34(18):3094–3100. doi:10.1093/bioinformatics/bty191.
   PubMed Web of Science ®Google Scholar
• Li X, Ma Q, Zhou H, Yang Y, Li H, Wang J. 2020. Characterization of the complete chloroplast genome of Cornus bretschneideri (Cornaceae). Mitochondrial DNA B Resour. 5(1):543–544. doi:10.1080/23802359.2019.1710281.
   PubMed Web of Science ®Google Scholar
• Liu S, Ni Y, Li J, Zhang X, Yang H, Chen H, Liu C. 2023. CPGView: a package for visualizing detailed chloroplast genome structures. Mol Ecol Resour. 23(3):694–704. doi:10.1111/1755-0998.13729.
   PubMed Web of Science ®Google Scholar
• Lu H, Tang J, Li D. 2021. The complete chloroplast genome sequences of Cornus elliptica (Cornaceae). Mitochondrial DNA B Resour. 6(3):931–932. doi:10.1080/23802359.2021.1888333.
   PubMed Web of Science ®Google Scholar
• Lv ZY, Huang XH, Luo J, Zhang X, Deng T, Li ZM. 2019. The complete chloroplast genome sequence of Cornus sunhangii (Cornaceae). Mitochondrial DNA B Resour. 4(2):3242–3243. doi:10.1080/23802359.2019.1669090.
   PubMed Web of Science ®Google Scholar
• Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R. 2020. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 37(5):1530–1534. doi:10.1093/molbev/msaa015.
   PubMed Web of Science ®Google Scholar
• Misra S, Harris N. 2005. Using Apollo to browse and edit genome annotations. Curr Protoc Bioinform. 9(1):9.5.1–9.5.28. doi:10.1002/0471250953.bi0905s12.
   Google Scholar
• Rice P, Longden I, Bleasby A. 2000. EMBOSS: the European molecular biology open software suite. Trends Genet. 16(6):276–277. doi:10.1016/s0168-9525(00)02024-2.
   PubMed Web of Science ®Google Scholar
• Shi L, Chen H, Jiang M, Wang L, Wu X, Huang L, Liu C. 2019. CPGAVAS2, an integrated plastome sequence annotator and analyzer. Nucleic Acids Res. 47(W1):W65–W73. doi:10.1093/nar/gkz345.
   PubMed Web of Science ®Google Scholar
• Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 56(4):564–577. doi:10.1080/10635150701472164.
   PubMed Web of Science ®Google Scholar
• Xiang Q-Y, Thomas DT, Zhang W, Manchester SR, Murrell Z. 2006. Species level phylogeny of the genus Cornus (Cornaceae) based on molecular and morphological evidence – implications for taxonomy and tertiary intercontinental migration. TAXON. 55(1):9–30. doi:10.2307/25065525.
   Web of Science ®Google Scholar
• Xiang Q-Y. 1987. System and synopsis of Cornus subgen. Syncarpea (Nakai) Q. Y. Xiang (Cornaceae). Bull Bot Res. 7(2):33–52.
   Google Scholar
• Yang X, Liu C, Zeng X, Liu X, Zhao H, Feng T, Zhou Y. 2022. Sequence structure and phylogenetic analysis of the chloroplast genomes of Alangium chinense (Lour.) Harms and its different subspecies. Yaoxue Xuebao. 57:3229–3239.
   Google Scholar
• Yuan W, He S, Zhang S, Chang D, He Y. 2021. The complete chloroplast genome sequence of Cornus alba L. (Cornaceae). Mitochondrial DNA B Resour. 6(7):1997–1998. doi:10.1080/23802359.2021.1938727.
   PubMed Web of Science ®Google Scholar
• Yu-Hong Z, Guo-Zheng T, Ming-Shu XU, Yong-Mei YI. 2003. Determination of main nutritious ingredients in the fruit of Dendrobenthamia angustata. J Hubei Inst Natl. (4):21–22.
   Google Scholar