Analyzing and Characterizing the Chloroplast Genome of Salix wilsonii

被引:33
作者
Chen, Yingnan [1 ]
Hu, Nan [1 ]
Wu, Huaitong [1 ]
机构
[1] Nanjing Forestry Univ, Coll Forestry, Key Lab Forest Genet & Biotechnol, Educ Dept China & Jiangsu Prov, Nanjing 210037, Jiangsu, Peoples R China
基金
中国国家自然科学基金;
关键词
PLASTID GENOME; PHYLOGENETIC-RELATIONSHIPS; INVERTED REPEAT; SEQUENCE; DNA; LOSSES; SALICACEAE; EVOLUTION; GENES; CONTRACTION;
D O I
10.1155/2019/5190425
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Salix wilsonii is an important ornamental willow tree widely distributed in China. In this study, an integrated circular chloroplast genome was reconstructed for S. wilsonii based on the chloroplast reads screened from the whole-genome sequencing data generated with the PacBio RSII platform. The obtained pseudomolecule was 155,750 bp long and had a typical quadripartite structure, comprising a large single copy region (LSC, 84,638 bp) and a small single copy region (SSC, 16,282 bp) separated by two inverted repeat regions (IR, 27,415 bp). The S. wilsonii chloroplast genome encoded 115 unique genes, including four rRNA genes, 30 tRNA genes, 78 protein-coding genes, and three pseudogenes. Repetitive sequence analysis identified 32 tandem repeats, 22 forward repeats, two reverse repeats, and five palindromic repeats. Additionally, a total of 118 perfect microsatellites were detected, with mononucleotide repeats being the most common (89.83%). By comparing the S. wilsonii chloroplast genome with those of other rosid plant species, significant contractions or expansions were identified at the IR-LSC/SSC borders. Phylogenetic analysis of 17 willow species confirmed that S. wilsonii was most closely related to S. chaenomeloides and revealed the monophyly of the genus Salix. The complete S. wilsonii chloroplast genome provides an additional sequence-based resource for studying the evolution of organelle genomes in woody plants.
引用
收藏
页数:14
相关论文
共 57 条
  • [1] [Anonymous], 2014, PROC CHECKL 20 KB TE
  • [2] Phylogenetic relationships of Salix (Salicaceae) based on rbcL sequence data
    Azuma, T
    Kajita, T
    Yokoyama, J
    Ohashi, H
    [J]. AMERICAN JOURNAL OF BOTANY, 2000, 87 (01) : 67 - 75
  • [3] Phylogenetic relationships of Salix L. subg. Salix species (Salicaceae) according to sequencing data of intergenic spacers of the chloroplast genome and ITS rDNA
    Barkalov, V. Yu.
    Kozyrenko, M. M.
    [J]. RUSSIAN JOURNAL OF GENETICS, 2014, 50 (08) : 828 - 837
  • [4] Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes
    Chaw, SM
    Chang, CC
    Chen, HL
    Li, WH
    [J]. JOURNAL OF MOLECULAR EVOLUTION, 2004, 58 (04) : 424 - 441
  • [5] Molecular phylogeny of Salix L. (Salicaceae) inferred from three chloroplast datasets and its systematic implications
    Chen, Jia-Hui
    Sun, Hang
    Wen, Jun
    Yang, Yong-Ping
    [J]. TAXON, 2010, 59 (01) : 29 - 37
  • [6] Chloroplast genome of Aconitum barbatum var. puberulum (Ranunculaceae) derived from CCS reads using the PacBio RS platform
    Chen, Xiaochen
    Li, Qiushi
    Li, Ying
    Qian, Jun
    Han, Jianping
    [J]. FRONTIERS IN PLANT SCIENCE, 2015, 6
  • [7] The complete nucleotide sequence of the cassava (Manihot esculenta) chloroplast genome and the evolution of atpF in Malpighiales:: RNA editing and multiple losses of a group II intron
    Daniell, Henry
    Wurdack, Kenneth J.
    Kanagaraj, Anderson
    Lee, Seung-Bum
    Saski, Christopher
    Jansen, Robert K.
    [J]. THEORETICAL AND APPLIED GENETICS, 2008, 116 (05) : 723 - 737
  • [8] Chloroplast genomes: diversity, evolution, and applications in genetic engineering
    Daniell, Henry
    Lin, Choun-Sea
    Yu, Ming
    Chang, Wan-Jung
    [J]. GENOME BIOLOGY, 2016, 17
  • [9] DOWNIE SR, 1991, EVOLUTION, V45, P1245, DOI 10.1111/j.1558-5646.1991.tb04390.x
  • [10] A Comparative Analysis of Whole Plastid Genomes from the Apiales: Expansion and Contraction of the Inverted Repeat, Mitochondrial to Plastid Transfer of DNA, and Identification of Highly Divergent Noncoding Regions
    Downie, Stephen R.
    Jansen, Robert K.
    [J]. SYSTEMATIC BOTANY, 2015, 40 (01) : 336 - 351