-
钻天柳(Chosenia arbutifolia (Pall.) A. Skv.)是一种主要分布在亚洲东北部的雌雄异株树种,原属杨柳科(Salicaceae)的一个单种属,钻天柳属(Chosenia) [1]。由于其形态特征介于杨属(Populus)植物和柳属(Salix)植物之间,钻天柳分类地位的确定对于研究杨柳科家族的演化有着十分重要的价值。然而,近期的研究对钻天柳在杨柳科中的系统发育位置提出了质疑。例如,Sohma[2]研究了72种柳及杂交种的孢粉形态,其结果认为钻天柳属可合并到柳属中;Azuma等[3]、Chen等[4]基于叶绿体片段分析探讨了一些主要的柳属分类系统,同样支持将钻天柳属归入柳属。然而,这些系统发育研究只是基于个别片段的分析,也并未得到国内分类学家的重视。另外,森林的过度砍伐,使钻天柳生长的林地环境条件发生了变化,供其生长的河流受到污染,极大地影响了钻天柳种子的萌发与幼苗的生长,导致钻天柳的分布区正在日益缩减。钻天柳,因其分布高度受限而濒临灭绝[5],因此,被列为国家Ⅱ级重点保护野生植物。钻天柳系统发育地位的确定,将为钻天柳的保护提供重要的理论基础。
叶绿体起源于与之内共生的蓝藻[6],并且有其自身的遗传物质。叶绿体基因组由120~160 kb的环状双链分子组成,这是一种高度保守的结构[7]。植物叶绿体基因组一般都有其独特的DNA区域,称为长单拷贝区(LSC)和短单拷贝区(SSC),它们由两个反向重复序列(IRS)分隔开[8]。与植物核基因组相比,植物叶绿体基因组的替换率低得多[9],并且由于叶绿体基因组是单亲遗传的,这意味着叶绿体基因组是系统发育分析遗传标记的重要来源[10]。所以,叶绿体基因组可以用来研究植物种群之间的相互关系和生物多样性[11]。
本研究从头测序、组装并注释了钻天柳叶绿体基因组完整的DNA序列并将其与从美国国家生物技术信息中心(NCBI)上得到的所有其他可用的杨属和柳属物种完整的叶绿体基因组DNA序列进行分析比对。这些分析揭示了钻天柳叶绿体基因组的结构和功能信息,并明确了钻天柳在杨柳科的系统发育地位。
叶绿体全基因组序列确定钻天柳在杨柳科中的系统发育位置
Phylogenetic Position of Chosenia arbutifolia in the Salicaceae Inferred from Whole Chloroplast Genome
-
摘要:
目的 为解决濒危物种钻天柳在杨柳科中分类学位置的争议。 方法 本研究通过二代测序技术,从头测序、拼接得到钻天柳叶绿体基因组全序列,并与已发表的9种杨属植物和4种柳属植物的叶绿体基因组全序列进行比较,采用最大似然法、最大简约法和贝叶斯推断法分析了这些物种的系统发育关系。 结果 研究发现:钻天柳总基因组为155 661 bp,由长度为84 536 bp的长单拷贝(LSC)区域和16 215 bp的短单拷贝(SSC)区域,以及一对分隔开它们的27 455 bp的反向重复序列(IRS)组成。钻天柳叶绿体基因组总GC含量为36.68%,共有113个不同的基因,包括79个蛋白质编码基因,30个tRNA基因和4个rRNA基因,其中,有20个基因分布于反向重复区;在所有基因中,有14个基因包含1个内含子,3个基因(rps12、clpP、ycf3)内含有2个内含子;系统发育分析以100%的支持率将钻天柳与柳属黄花柳亚属的2个物种聚为一支,杨属的所有物种聚为另一支。 结论 本研究首次组装并注释了钻天柳叶绿体基因组全序列,并明确支持钻天柳并入柳属,而非单独成属,这将为钻天柳甚至杨柳科的系统进化研究提供重要参考。 Abstract:Objective To resolve the controversy over the phylogenetic position of Chosenia arbutifolia in Salicaceae. Method The whole chloroplast genome sequences of C. arbutifolia was determined by next-generation sequencing, and the phylogenetic position of C. arbutifolia was investigated by comparing its sequences with all available complete chloroplast genome sequences from the genera Populus and Salix. Result The total genome was 155, 661 bp, consisting of two single-copy regions separated by a pair of inverted repeats (IRs) of 27, 455 bp. The large single-copy (LSC) and small single-copy (SSC) regions spanned 84, 536 bp and 16, 215 bp, respectively. The total GC content of the chloroplast genome was 36.68% and 113 unique genes were annotated, including 79 protein coding genes, 30 tRNA genes, and four rRNA genes. Twenty genes were duplicated in the inverted repeat regions, 14 genes contained one intron, and three genes (rps12, clpP, and ycf3) contained two introns. Conclusion A phylogenetic tree constructed from all available complete chloroplast genome sequences from the genera Populus and Salix based on maximum likelihood, maximum parsimony and Bayesian inference strongly supports the merging of C. arbutifolia into the genus Salix. This study would supply an important basis for the genetic study as well as conservation of C. arbutifolia. -
Key words:
- Chosenia arbutifolia
- / chloroplast genome
- / next-generation sequencing
- / Salicaceae
- / Salix
-
-
[1] Skvortsov A K. Willows of Russia and Adjacent Countries:Taxonomical and Geographical Revision[M]. Joensuu:University of Joensuu, 1999:1-307. [2] Sohma K. Pollen diversity in Salix (Salicaceae)[J]. Sci Rep Tohoku Univ, Ⅳ, 1993, 40(2):77-178. [3] Azuma T, Kajita T, Yokoyama J, et al. Phylogenetic relationships of Salix (Salicaceae) based on rbcL sequence data[J]. American Journal of Botany, 2000, 87(1):67-75. doi: 10.2307/2656686 [4] Chen J H, Sun H, Wen J, et al. Molecular phylogeny of Salix L.(Salicaceae) inferred from three chloroplast datasets and its systematic implications[J]. Taxon, 2010, 59(1):29-37. doi: 10.1002/tax.2010.59.issue-1 [5] Hoshikawa T, Kikuchi S, Nagamitsu T, et al. Eighteen microsatellite loci in Salix arbutifolia (Salicaceae) and cross-species amplification in Salix and Populus species[J]. Molecular Ecology Resources, 2009, 9(4):1202-1205. doi: 10.1111/men.2009.9.issue-4 [6] McFadden G I, van Dooren G G. Evolution:red algal genome affirms a common origin of all plastids[J]. Current Biology, 2004, 14(13):R514-R516. doi: 10.1016/j.cub.2004.06.041 [7] Odintsova M S, Yurina N P. Chloroplast genomics of land plants and algae[J]. Biotechnological applications of photosynthetic proteins:biochips, biosensors and biodevices, 2006:57-72. [8] Jansen R K, Raubeson L A, Boore J L, et al. Methods for obtaining and analyzing whole chloroplast genome sequences[M]//Methods in enzymology. Academic Press, 2005, 395:348-384. [9] Wolfe K H, Li W H, Sharp P M. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs[J]. Proceedings of the National Academy of Sciences, 1987, 84(24):9054-9058. doi: 10.1073/pnas.84.24.9054 [10] Ravi V, Khurana J P, Tyagi A K, et al. An update on chloroplast genomes[J]. Plant Systematics and Evolution, 2008, 271(1-2):101-122. doi: 10.1007/s00606-007-0608-0 [11] Chen D, Zhang X, Kang H, et al. Phylogeography of Quercus variabilis based on chloroplast DNA sequence in East Asia:multiple glacial refugia and mainland-migrated island populations[J]. PLoS One, 2012, 7(10):e47268. doi: 10.1371/journal.pone.0047268 [12] Li R, Li Y, Kristiansen K, et al. SOAP:short oligonucleotide alignment program[J]. Bioinformatics, 2008, 24(5):713-714. doi: 10.1093/bioinformatics/btn025 [13] Lu G, Moriyama E N. Vector NTI, a balanced all-in-one sequence analysis suite[J]. Briefings in Bioinformatics, 2004, 5(4):378-388. doi: 10.1093/bib/5.4.378 [14] Wyman S K, Jansen R K, Boore J L. Automatic annotation of organellar genomes with DOGMA[J]. Bioinformatics, 2004, 20(17):3252-3255. doi: 10.1093/bioinformatics/bth352 [15] Lohse M, Drechsel O, Kahlau S, et al. OrganellarGenomeDRAW-a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets[J]. Nucleic Acids Research, 2013, 41(W1):W575-W581. doi: 10.1093/nar/gkt289 [16] Frazer K A, Pachter L, Poliakov A, et al. VISTA:computational tools for comparative genomics[J]. Nucleic Acids Research, 2004, 32(suppl_2):W273-W279. [17] Kumar S, Stecher G, Tamura K. MEGA7:molecular evolutionary genetics analysis version 7.0 for bigger datasets[J]. Molecular Biology and Evolution, 2016, 33(7):1870-1874. doi: 10.1093/molbev/msw054 [18] Ronquist F, Huelsenbeck J, Teslenko M. Draft MrBayes version 3.2 manual: tutorials and model summaries[M/OL]. Distributed with the software from http://brahms.biology.rochester.edu/software.html, 2011. [19] Kersten B, Rampant P F, Mader M, et al. Genome sequences of Populus tremula chloroplast and mitochondrion:implications for holistic poplar breeding[J]. PloS One, 2016, 11(1):e0147209. doi: 10.1371/journal.pone.0147209