基于核基因和叶绿体基因序列的杏属系统发育分析——探讨洪平杏的起源和亲缘关系
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摘要
洪平杏(Armeniaca hongpingensis C. L. Li)是杏属的一个狭域分布种,基于形态观察被推测为杏(A.vulgaris Lam.)和梅(A. mume Sieb.)的天然杂交种,但目前尚无该种与杏、梅亲缘关系的分子系统学研究。本文以洪平杏的成株和实生苗以及包括杏、梅在内的6种(含1变种)杏属植物为研究材料,分别采用核基因(ITS和SBEI)和叶绿体基因(mat K和ycf1b)序列构建系统发育树,并采用mat K、ycf1b和SBEI基因序列构建单倍型网络图,探讨该物种与杏、梅及杏梅(A. mume Sieb. var. bungo Makino)之间的亲缘关系。基于核基因和叶绿体基因序列分别构建的系统发育树均显示,洪平杏的成株及其全部实生苗个体单独聚为一支,且具有较高的支持率(分别为99/79、71/81),独立于杏属其他种之外。而基于核基因ITS序列的系统发育分析结果表明,洪平杏除极少数成株与杏、杏梅聚为一支外,其余所有成株与实生苗聚为2大支(支持率分别为0.82和0.97),而没有克隆的与梅聚在一起。单倍型分析结果表明,该物种的成株与实生苗在SBEI和ycf1b基因序列中均未检测到杏或梅的单倍型,仅有少数(2/9)的实生苗个体在叶绿体mat K基因序列中检测到杏的单倍型。研究结果不支持将洪平杏定为杏和梅的天然杂交种的观点,推测洪平杏应为一个独立的物种,与杏之间的亲缘关系更近并且存在可检测到的基因流。
Armeniaca hongpingensis C. L. Li is a narrowly distributed species,which has been hypothesized to be a natural hybrid of A. vulgaris Lam. and A. mume Sieb. based on morphological similarity. However,related molecular phylogenetic research is still lacking. In this study,the phylogenetic relationship between A. hongpingensis and other Armeniaca species was investigated using individuals and seedlings of A. hongpingensis and individuals of five other Armeniaca species( e. g.,A. vulgaris,A. mume,A. mume Sieb. var. bungo Makino). Two nuclear genes( ITS and SBEI) and two chloroplast genes( mat K and ycf1 b)were sequenced to reconstruct molecular phylogenetic trees. mat K,ycf1 b,and SBEI were also used to reconstruct a haplotype network. Phylogenetic analyses of both nuclear and chloroplast genes showed that the individuals and seedlings of A. hongpingensis grouped together with high bootstrap values( 99/79,71/81),independent of other Armeniaca species.The Bayesian phylogram based on ITS sequences showed that most individual and seedling clones of A. hongpingensis were grouped into two single clades with high bootstrap values( 0.82,0.97); the other clones clustered with A. vulgaris and A. mume var. bungo individuals;and no clones clustered with A. mume individuals. On SBEI and ycf1 b loci,haplotypes of A.vulgaris,A. mume,and A. holosericea were not detected in A. hongpingensis; whereas on the mat K locus,only haplotypes of A. vulgaris were detected in a few( 2/9) seedlings of A.hongpingensis. These results suggest that A. hongpingensis is likely an independent species rather than a natural hybrid of A. vulgaris and A. mume,with a closer genetic relationship as well as detectable gene flow with A. vulgaris.
Armeniaca hongpingensis C. L. Li is a narrowly distributed species,which has been hypothesized to be a natural hybrid of A. vulgaris Lam. and A. mume Sieb. based on morphological similarity. However,related molecular phylogenetic research is still lacking. In this study,the phylogenetic relationship between A. hongpingensis and other Armeniaca species was investigated using individuals and seedlings of A. hongpingensis and individuals of five other Armeniaca species( e. g.,A. vulgaris,A. mume,A. mume Sieb. var. bungo Makino). Two nuclear genes( ITS and SBEI) and two chloroplast genes( mat K and ycf1 b)were sequenced to reconstruct molecular phylogenetic trees. mat K,ycf1 b,and SBEI were also used to reconstruct a haplotype network. Phylogenetic analyses of both nuclear and chloroplast genes showed that the individuals and seedlings of A. hongpingensis grouped together with high bootstrap values( 99/79,71/81),independent of other Armeniaca species.The Bayesian phylogram based on ITS sequences showed that most individual and seedling clones of A. hongpingensis were grouped into two single clades with high bootstrap values( 0.82,0.97); the other clones clustered with A. vulgaris and A. mume var. bungo individuals;and no clones clustered with A. mume individuals. On SBEI and ycf1 b loci,haplotypes of A.vulgaris,A. mume,and A. holosericea were not detected in A. hongpingensis; whereas on the mat K locus,only haplotypes of A. vulgaris were detected in a few( 2/9) seedlings of A.hongpingensis. These results suggest that A. hongpingensis is likely an independent species rather than a natural hybrid of A. vulgaris and A. mume,with a closer genetic relationship as well as detectable gene flow with A. vulgaris.
引文
[1] Wu ZY,Raven PH,Hong DY. Flora of China:Vol. 9[M].Beijing:Science Press,2003.
[2]王利兵.我国3种杏的地理分布及其植物学性状[J].林业科学研究,2010,23(3):435-439.Wang LB. Geographic distribution and botanical characters of 3 Armeniaca plant in China[J]. Forest Research,2010,23(3):435-439.
[3]王家琼,吴保欢,崔大方,羊海军,黄峥,齐安民.基于30个形态性状的中国杏属(Armeniaca Scop.)植物分类学研究[J].植物资源与环境学报,2016,25(3):103-111.Wang JQ,Wu BH,Cui DF,Yang HJ,Huang Z,Qi AM.Taxonomic study on Armeniaca Scop. species in China based on thirty morphological characters[J]. Journal of Plant Resources and Environment,2016,25(3):103-111.
[4] Layne REC,Bailey CH,Hough LF. Apricots[M]//Janick J,Moore JN, eds. Fruit Breeding:Tree and Tropical Fruits,Vol.Ⅱ. New York:John Wiley and Sons,1996.
[5] Shimada T,Haji T,Yamaguchi M,Takeda T,Nomura K,Yoshida M. Classification of mume(Prunus mume Sieb. et Zucc.)by RAPD assay[J]. J Jpn Soc Hortic Sci,1994,63(3):543-551.
[6] Byrne DH. Isozyme phenotypes support the interspecific hybrid origin of Prunus xdasycarpa Ehrh[J]. Fruit Varieties J,1993,47(3):143-145.
[7] Li M,Zhao Z,Miao XJ. Genetic diversity and relationships of apricot cultivars in north China revealed by ISSR and SRAP markers[J]. Sci Hortic,2014,173(3):20-28.
[8]张加延,吕亩南,王志明.杏属二新种[J].植物分类学报,1999,37(1):105-109.Zhang JT,LüMN,Wang ZM. Two new species of the genus Armeniaca(Rosaceae)[J]. Acta Phytotaxonomica Sinica,1999,37(1):105-109.
[9]杨红花,陈学森,冯宝春,吴燕.李梅杏类种质资源的RAPD分析[J].果树学报,2007,24(3):303-307.Yang HH,Chen XS,Feng BC,Wu Y. Assessment of Prunus armeniaca limeixing germplasm by RAPD[J].Journal of Fruit Science,2007,24(3):303-307.
[10]杨红花.李梅杏种质资源的系统起源研究进展[J].泰山学院学报,2010,32(3):106-109.Yang HH. Advances in system origin of Prunus armeniaca limeixing J. Y. Zhang et Z. M. Wang germplasm[J]. Journal of Taishan University,2010,32(3):106-109.
[11]俞德浚,陆玲娣,谷粹芝.中国植物志:第38卷[M].北京:科学出版社,1986.
[12]包满珠.我国川、滇、藏部分地区野梅种质资源及梅的系统学研究[D].北京:北京林业大学,1991.
[13]陈俊愉,包满珠.中国梅的植物学分类与园艺学分类[J].浙江农林大学学报,1992(2):119-132.Chen JY,Bao MZ. Botanical classification and horticultural classification of Chinese Mei(Prunus mume)resources[J]. Journal of Zhejiang Forestry College,1992(2):119-132.
[14] China Plant BOL Group,Li DZ,Gao LM,Li HT,Wang H,et al. Comparative analysis of a large dataset indicates that internal transcribed spacer(ITS)should be incorporated into the core barcode for seed plants[J]. Proc Natl Acad Sci,2011,108(49):19641-19646.
[15] Shi S,Li JL,Sun JH,Yu J,Zhou SL. Phylogeny and classification of Prunus sensu lato(Rosaceae)[J]. J Integr Plant Biol,2013,55(11):1069-1079.
[16] Yu J,Xue JH,Zhou SL. New universal mat K primers for DNA barcoding angiosperms[J]. J Syst Evol, 2011,49(3):176-181.
[17] Dong W,Xu C,Li C,Sun J,Zuo Y,et al. ycf1,the most promising plastid DNA barcode of land plants[J]. Sci Rep,2015,5:8348.
[18] Chenna R,Sugawara H,Koike T,Lopez R,Gibson TJ,et al. Multiple sequence alignment with the Clustal series of programs[J]. Nucleic Acids Res,2003,31(13):3497-3500.
[19] Ronquist F,Huelsenbeck JP. Mr Bayes 3:Bayesian phylogenetic inference under mixed models[J]. Bioinformatics,2003,19(12):1572-1574.
[20] Posada D,Crandall KA. Modeltest:testing the model of DNA substitution[J]. Bioinformatics,1998,14(9):817-818.
[21] Nguyen LT,Schmidt HA,von Haeseler A,Minh BQ.IQ-TREE:a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies[J]. Mol Biol Evol,2014,32(1):268-274.
[22] Kalyaanamoorthy S,Minh BQ,Wong TKF,von Haeseler A, Jermiin LS. ModelFinder:fast model selection for accurate phylogenetic estimates[J]. Nat Methods,2017,14(6):587.
[23] Librado P,Rozas J. Dna SP v5:a software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,2009,25(11):1451-1452.
[24] Bandelt HJ,Forster P,R9hl A. Median-joining networks for inferring intraspecific phylogenies[J]. Mol Biol Evol,1999,16(1):37-48.
[25] Wendel JF,Doyle JJ. Phylogenetic incongruence:window into genome history and molecular evolution[M]//Soltis DE,Soltis PS,Doyle JJ,eds. Molecular Systematics of PlantsⅡ:DNA Sequencing. New York:Kluwer Academic Publisher,1998.
[26] Rieseberg LH,Whitton J,Linder CR. Molecular marker incongruence in plant hybrid zones and phylogenetic trees[J]. Plant Biol,1996,45(3):243-262.
[27] Kumar LS. DNA markers in plant improvement:An overview[J]. Biotechnol Adv,1999,17(2-3):143-182.
[2]王利兵.我国3种杏的地理分布及其植物学性状[J].林业科学研究,2010,23(3):435-439.Wang LB. Geographic distribution and botanical characters of 3 Armeniaca plant in China[J]. Forest Research,2010,23(3):435-439.
[3]王家琼,吴保欢,崔大方,羊海军,黄峥,齐安民.基于30个形态性状的中国杏属(Armeniaca Scop.)植物分类学研究[J].植物资源与环境学报,2016,25(3):103-111.Wang JQ,Wu BH,Cui DF,Yang HJ,Huang Z,Qi AM.Taxonomic study on Armeniaca Scop. species in China based on thirty morphological characters[J]. Journal of Plant Resources and Environment,2016,25(3):103-111.
[4] Layne REC,Bailey CH,Hough LF. Apricots[M]//Janick J,Moore JN, eds. Fruit Breeding:Tree and Tropical Fruits,Vol.Ⅱ. New York:John Wiley and Sons,1996.
[5] Shimada T,Haji T,Yamaguchi M,Takeda T,Nomura K,Yoshida M. Classification of mume(Prunus mume Sieb. et Zucc.)by RAPD assay[J]. J Jpn Soc Hortic Sci,1994,63(3):543-551.
[6] Byrne DH. Isozyme phenotypes support the interspecific hybrid origin of Prunus xdasycarpa Ehrh[J]. Fruit Varieties J,1993,47(3):143-145.
[7] Li M,Zhao Z,Miao XJ. Genetic diversity and relationships of apricot cultivars in north China revealed by ISSR and SRAP markers[J]. Sci Hortic,2014,173(3):20-28.
[8]张加延,吕亩南,王志明.杏属二新种[J].植物分类学报,1999,37(1):105-109.Zhang JT,LüMN,Wang ZM. Two new species of the genus Armeniaca(Rosaceae)[J]. Acta Phytotaxonomica Sinica,1999,37(1):105-109.
[9]杨红花,陈学森,冯宝春,吴燕.李梅杏类种质资源的RAPD分析[J].果树学报,2007,24(3):303-307.Yang HH,Chen XS,Feng BC,Wu Y. Assessment of Prunus armeniaca limeixing germplasm by RAPD[J].Journal of Fruit Science,2007,24(3):303-307.
[10]杨红花.李梅杏种质资源的系统起源研究进展[J].泰山学院学报,2010,32(3):106-109.Yang HH. Advances in system origin of Prunus armeniaca limeixing J. Y. Zhang et Z. M. Wang germplasm[J]. Journal of Taishan University,2010,32(3):106-109.
[11]俞德浚,陆玲娣,谷粹芝.中国植物志:第38卷[M].北京:科学出版社,1986.
[12]包满珠.我国川、滇、藏部分地区野梅种质资源及梅的系统学研究[D].北京:北京林业大学,1991.
[13]陈俊愉,包满珠.中国梅的植物学分类与园艺学分类[J].浙江农林大学学报,1992(2):119-132.Chen JY,Bao MZ. Botanical classification and horticultural classification of Chinese Mei(Prunus mume)resources[J]. Journal of Zhejiang Forestry College,1992(2):119-132.
[14] China Plant BOL Group,Li DZ,Gao LM,Li HT,Wang H,et al. Comparative analysis of a large dataset indicates that internal transcribed spacer(ITS)should be incorporated into the core barcode for seed plants[J]. Proc Natl Acad Sci,2011,108(49):19641-19646.
[15] Shi S,Li JL,Sun JH,Yu J,Zhou SL. Phylogeny and classification of Prunus sensu lato(Rosaceae)[J]. J Integr Plant Biol,2013,55(11):1069-1079.
[16] Yu J,Xue JH,Zhou SL. New universal mat K primers for DNA barcoding angiosperms[J]. J Syst Evol, 2011,49(3):176-181.
[17] Dong W,Xu C,Li C,Sun J,Zuo Y,et al. ycf1,the most promising plastid DNA barcode of land plants[J]. Sci Rep,2015,5:8348.
[18] Chenna R,Sugawara H,Koike T,Lopez R,Gibson TJ,et al. Multiple sequence alignment with the Clustal series of programs[J]. Nucleic Acids Res,2003,31(13):3497-3500.
[19] Ronquist F,Huelsenbeck JP. Mr Bayes 3:Bayesian phylogenetic inference under mixed models[J]. Bioinformatics,2003,19(12):1572-1574.
[20] Posada D,Crandall KA. Modeltest:testing the model of DNA substitution[J]. Bioinformatics,1998,14(9):817-818.
[21] Nguyen LT,Schmidt HA,von Haeseler A,Minh BQ.IQ-TREE:a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies[J]. Mol Biol Evol,2014,32(1):268-274.
[22] Kalyaanamoorthy S,Minh BQ,Wong TKF,von Haeseler A, Jermiin LS. ModelFinder:fast model selection for accurate phylogenetic estimates[J]. Nat Methods,2017,14(6):587.
[23] Librado P,Rozas J. Dna SP v5:a software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,2009,25(11):1451-1452.
[24] Bandelt HJ,Forster P,R9hl A. Median-joining networks for inferring intraspecific phylogenies[J]. Mol Biol Evol,1999,16(1):37-48.
[25] Wendel JF,Doyle JJ. Phylogenetic incongruence:window into genome history and molecular evolution[M]//Soltis DE,Soltis PS,Doyle JJ,eds. Molecular Systematics of PlantsⅡ:DNA Sequencing. New York:Kluwer Academic Publisher,1998.
[26] Rieseberg LH,Whitton J,Linder CR. Molecular marker incongruence in plant hybrid zones and phylogenetic trees[J]. Plant Biol,1996,45(3):243-262.
[27] Kumar LS. DNA markers in plant improvement:An overview[J]. Biotechnol Adv,1999,17(2-3):143-182.