The newly developed single nucleotide polymorphism (SNP) markers for a potentially medicinal plant, Crepidiastrum denticulatum (Asteraceae), inferred from complete chloroplast genome data
Tóm tắt
Medicinal effects of Crepidiastrum denticulatum have been previously reported. However, the genomic resources of this species and its applications have not been studied. In this study, based on the next generation sequencing method (Miseq sequencing system), we characterize the chloroplast genome of C. denticulatum which contains a large single copy (84,112 bp) and a small single copy (18,519 bp), separated by two inverted repeat regions (25,074 bp). This genome consists of 80 protein-coding gene, 30 tRNAs, and four rRNAs. Notably, the trnT_GGU is pseudogenized because of a small insertion within the coding region. Comparative genomic analysis reveals a high similarity among Asteraceae taxa. However, the junctions between LSC, SSC, and IRs locate in different positions within rps19 and ycf1 among examined species. Also, we describe a newly developed single nucleotide polymorphism (SNP) marker for C. denticulatum based on amplification‐refractory mutation system (ARMS) technique. The markers, inferred from SNP in rbcL and matK genes, show effectiveness to recognize C. denticulatum from other related taxa through simple PCR protocol. The chloroplast genome-based molecular markers are effective to distinguish a potentially medicinal species, C. denticulatum, from other related taxa. Additionally, the complete chloroplast genome of C. denticulatum provides initial genomic data for further studies on phylogenomics, population genetics, and evolutionary history of Crepidiastrum as well as other taxa in Asteraceae.
Tài liệu tham khảo
Sugiura M (1992) The chloroplast genome. Plant Mol Biol 19:149–168. https://doi.org/10.1007/978-94-011-2656-4_10
Han EH, Cho K, Goo Y, Kim MB, Shin Y-W, Kim Y-H, Lee SW (2016) Development of molecular markers, based on chloroplast and ribosomal DNA regions, to discriminate three popular medicinal plant species, Cynanchum wilfordii, Cynanchum auriculatum, and Polygonum multiflorum. Mol Biol Rep 43:323. https://doi.org/10.1007/s11033-016-3959-1
Ismail NA, Rafii MY, Mahmud TMM, Hanafi MM, Miah G (2016) Molecular markers: a potential resource for ginger genetic diversity studies. Mol Biol Rep 43:1347. https://doi.org/10.1007/s11033-016-4070-3
Bishoyi AK, Kavane A, Sharma A, Geetha KA (2017) A report on identification of sequence polymorphism in barcode region of six commercially important Cymbopogon species. Mol Biol Rep 44:19. https://doi.org/10.1007/s11033-017-4097-0
Salomo K, Smith JF, Field TS, Samain MS, Bond L, Davidson C, Zimmers J, Neinhuis C, Wanke S (2017) The emergence of earliest angiosperms may be earlier than fossil evidence indicates. Syst Bot 42(4):607–619. https://doi.org/10.1600/036364417X696438
Farruggia FT, Lavin M, Wojciechowsk MF (2018) Phylogenetic systematics and biogeography of the pantropical genus Sesbania (Leguminosae). Syst Bot 43(2):414–429. https://doi.org/10.1600/036364418X697175
Kim JS, Kim J-H (2018) Updated molecular phylogenetic analysis, dating and biogeographical history of the lily family (Liliaceae: Liliales). Bot J Linn Soc 187(4):579–593. https://doi.org/10.1093/botlinnean/boy031
Do HDK, Kim JS, Kim JH (2014) A trnI_CAU triplication event in the complete chloroplast genome of Paris verticillataM.Bieb. (Melanthiaceae, Liliales). Genome Biol Evol 6(7):1699–1706. https://doi.org/10.1093/gbe/evu138
Kim JK, Park JY, Lee YS, Lee HO, Park HS, Lee SC, Kang JH, Lee TJ, Sung SH, Yang TJ (2016) The complete chloroplast genome sequence of the Taraxacum officinale F.H.Wigg (Asteraceae). Mitochondr DNA Part B 1(1):228–229. https://doi.org/10.1080/23802359.2016.1155425
Do HDK, Kim J-H (2017) A dynamic tandem repeat in monocotyledons inferred from a comparative analysis of chloroplast genomes in Melanthiaceae. Front Plant Sci 8:693. https://doi.org/10.3389/fpls.2017.00693
Choi IS, Choi BH (2017) The distinct plastid genome structure of Maackia fauriei (Fabaceae: Papilionoideae) and its systematic implications for genistoids and tribe Sophoreae. PLoS ONE 12(4):e0173766. https://doi.org/10.1371/journal.pone.0173766
Kim SC, Kim JS, Kim JH (2016) Insight into infrageneric circumscription through complete chloroplast genome sequences of two Trillium species. AoB PLANTS 8:plw015. https://doi.org/10.1093/aobpla/plw015
Leaché AD, Oaks JR (2017) The utility of single nucleotide polymorphism (SNP) data in phylogenetics. Annu Rev Ecol Evol S 48(1):69–84. https://doi.org/10.1146/annurev-ecolsys-110316-022645
Little S (1995) Amplification-refractory mutation system (ARMS) analysis of point mutations. Curr Protoc Hum Genet 7(1):9.8.1–9.8.12. https://doi.org/10.1002/0471142905.hg0908s07
Kim JS, Jang HW, Kim JS, Kim HJ, Kim JH (2012) Molecular identification of Schisandra chinensis and its allied species using multiplex PCR based on SNPs. Genes Genom 34:283. https://doi.org/10.1007/s13258-011-0201-3
Tharachand C, Immanuel Selvaraj C, Mythili MN (2012) Molecular markers in characterization of medicinal plants: an overview. Res Plant Biol 2(2):01–12
Koc S, Isgor BS, Isgor YG, Shomali Moghaddam N, Yildirim O (2015) The potential medicinal value of plants from Asteraceae family with antioxidant defense enzymes as biological targets. Pharm Biol 53(5):746–751. https://doi.org/10.3109/13880209.2014.942788
Son J-C, Kim S-H, Lee S-I, Lee Y-K, Kim S-D (2012) Effect of ethanol extracts of Youngia denticulata and Youngia sonchifolia on the serum and hepatic lipids and activities of ethanol metabolizing enzymes in acute ethanol-treated rats. J Korean Soc Food Sci Nutr 41(2):197–204. https://doi.org/10.3746/jkfn.2012.41.2.197
Ahn HR, Lee HJ, Kim KA, Kim CY, Nho CW, Jang H, Pan CH, Lee CY, Jung SH (2014) Hydroxycinnamic acids in Crepidiastrum denticulatum protect oxidative stress-induced retinal damage. J Agr Food Chem 62(6):1310–1323. https://doi.org/10.1021/jf4046232
Yoo J-H, Kang K, Yun JH, Kim MA, Nho CW (2014) Crepidiastrum denticulatum extract protects the liver against chronic alcohol-induced damage and fat accumulation in rats. J Med Food 17(4):432–438. https://doi.org/10.1089/jmf.2013.2799
Kim M, Park YG, Lee H-J, Lim SJ, Ahn HR, Jung SH, Nho CW (2015) Youngia denticulata attenuates diet-induced obesity-related metabolic dysfunctions by activating AMP-activated protein kinase and regulating lipid metabolism. J Funct Food 18(A):714–726. https://doi.org/10.1016/j.jff.2015.09.002
Kim M, Yoo G, Randy A, Kim HS, Nho CW (2017) Chicoric acid attenuate a nonalcoholic steatohepatitis by inhibiting key regulators of lipid metabolism, fibrosis, oxidation, and inflammation in mice with methionine and choline deficiency. Mol Nutr Food Res 61(5):1613–4125. https://doi.org/10.1002/mnfr.201600632
Timme RE, Kuehl JV, Boore JL, Jansen RK (2007) A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: identification of divergent regions and categorization of shared repeats. Am J Bot 94:302–312. https://doi.org/10.3732/ajb.94.3.302
Curci PL, De Paola D, Danzi D, Vendramin GG, Sonnante G (2015) Complete chloroplast genome of the multifunctional crop globe artichoke and comparison with other asteraceae. PLoS ONE 10(3):e0120589. https://doi.org/10.1371/journal.pone.0120589
Shen X, Guo S, Yin Y, Zhang J, Yin X, Liang C, Wang Z, Huang B, Liu Y, Xiao ZhuG (2018) Complete chloroplast genome sequence and phylogenetic analysis of Aster tataricus. Molecules 23(10):E2426. https://doi.org/10.3390/molecules23102426
Torres-Martínez L, Emery NC (2016) Genome-wide SNP discovery in the annual herb, Lasthenia fremontii (Asteraceae): genetic resources for the conservation and restoration of a California vernal pool endemic. Conserv Genet Resour 8:145–158. https://doi.org/10.1007/s12686-016-0524-0
Luo Z, Iaffaldano BJ, Zhuang X, Fresnedo-Ramírez J, Cornish K (2017) Analysis of the first Taraxacum kok-saghyz transcriptome reveals potential rubber yield related SNPs. Sci Rep 7:9939. https://doi.org/10.1038/s41598-017-09034-2
Blanc-Jolivet C, Kersten B, Bourland N, Guichoux E, Delcamp A, Doucet J-L, Degen B (2018) Development of nuclear SNP markers for the timber tracking of the African tree species Sapelli, Entandrophragma cylindricum. Conserv Genet Resour 10:539. https://doi.org/10.1007/s12686-017-0872-4
Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Drummond A (2012) Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28(12):1647–1649. https://doi.org/10.1093/bioinformatics/bts199
Lowe TM, Chan PP (2016) tRNAscan-SE On-line: search and contextual analysis of transfer RNA genes. Nucleic Acids Res 44:W54–W57. https://doi.org/10.1093/nar/gkw413
Mayor C, Brudno M, Schwartz JR, Poliakov A, Rubin EM, Frazer KA, Pachter LS, Dubchak I (2000) VISTA: visualizing global dna sequence alignments of arbitrary length. Bioinformatics 16:1046. https://doi.org/10.1093/bioinformatics/16.11.1046
Christoph M (2006) Phobos 3.3.11. <http://www.rub.de/ecoevo/cm/cm_phobos.htm>
Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG (2012) Primer3 - new capabilities and interfaces. Nucleic Acids Res 40(15):e115. https://doi.org/10.1093/nar/gks596
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792–1797. https://doi.org/10.1093/nar/gkh340
Lo YM (1998) The amplification refractory mutation system. Methods Mol Med 16:61–69. https://doi.org/10.1385/0-89603-499-2:61
Haberle RC, Fourcade HM, Boore JL, Jansen RK (2008) Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genes. J Mol Evol 66(4):350–361. https://doi.org/10.1007/s00239-008-9086-4
Lin C-P, Wu C-S, Huang Y-Y, Chaw S-M (2012) The Complete Chloroplast Genome of Ginkgo biloba Reveals the Mechanism of Inverted Repeat Contraction. Genome Biol Evol 4(3):374–381. https://doi.org/10.1093/gbe/evs021
Lee DH, Cho WB, Choi BH, Lee JH (2017) Characterization of two complete chloroplast genomes in the tribe Gnaphalieae (Asteraceae): gene loss or pseudogenization of trnT-GGU and implications for phylogenetic relationships. Hortic Sci Technol 35(6):769–783. https://doi.org/10.12972/kjhst.20170081
Wang RJ, Cheng CL, Chang CC, Wu CL, Su TM, Chaw SM (2008) Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots. BMC Evol Biol 8:36. https://doi.org/10.1186/1471-2148-8-36
Huang YY, Matzke AJM, Matzke M (2013) Complete sequence and comparative analysis of the chloroplast genome of coconut palm (Cocos nucifera). PLoS ONE 8(8):e74736. https://doi.org/10.1371/journal.pone.0074736
Luo J, Hou BW, Niu ZT, Liu W, Xue QY, Ding XY (2014) Comparative chloroplast genomes of photosynthetic orchids: insights into evolution of the orchidaceae and development of molecular markers for phylogenetic applications. PLoS ONE 9(6):e99016. https://doi.org/10.1371/journal.pone.0099016
Ma J, Yang B, Zhu W, Sun L, Tian J, Wan X (2013) The complete chloroplast genome sequence of Mahonia bealei (Berberidaceae) reveals a significant expansion of the inverted repeat and phylogenetic relationship with other angiosperms. Gene 528(2):120–131. https://doi.org/10.1016/j.gene.2013.07.037
de Santa Lopes A, Pacheco GT, Nimz T, do Nascimento Vieira L, Guerra MP, Nodari RO, de Souza ME, de Oliveira Pedrosa F, Rogalski M (2018) The complete plastome of macaw extensive molecular analyses of the evolution of plastid genes in Arecaceae. Planta 247:1011. https://doi.org/10.1007/s00425-018-2841-x
Pacheco GT, de Lopes SA, Viana MGD, da Silva NO, da Silva MG, do Nascimento Vieira L, Guerra MP, Nodari OR, de Souza ME, de Oliveira Pedrosa F, Otoni WC, Rogalski M (2018) Genetic, evolutionary and phylogenetic aspects of the plastome of annatto (Bixa orellana L.), the Amazonian commercial species of natural dyes. Planta. https://doi.org/10.1007/s00425-018-3023-6
Peng Y, Zhang Y, Gao X, Tong L, Lisss L, Lisss RY, Zhu ZM, Xian J (2014) A phylogenetic analysis and new delimitation of Crepidiastrum (Asteraceae, tribe Cichorieae). Phytoyaxa 159(4):241–255. https://doi.org/10.11646/phytotaxa.159.4.1
Fu Z, Jiao B, Nie B, Zhang G, Gao T, China Phylogeny Consortium (2016) A comprehensive generic level phylogeny of the sunflower family: Implications for the systematics of Chinese Asteraceae. J Syst Evol 54:416–437. https://doi.org/10.1111/jse.12216
Ohashi H, Ohashi K (2007) Hybrids in Crepidiastrum (Asteraceae). J Jpn Bot 82:337–347
Yamamotoa N, Okihito OY, Ikedab H (2009) A new hybrid, Crepidiastrum × semiauriculatum (Asteraceae: Lactuceae), from Okayama Prefecture, Western Japan. J Jpn Bot 84:224–228
Qin Z, Wang Y, Wang Q, Li A, Hou F, Zhang L (2015) Evolution analysis of simple sequence repeats in plant genome. PLoS ONE 10(12):e0144108. https://doi.org/10.1371/journal.pone.0144108
Fontúrbel FE, Murúa MM, Vega-Retter C (2016) Development of ten microsatellite markers from the keystone mistletoe Tristerix corymbosus (Loranthaceae) using 454 next generation sequencing and their applicability to population genetic structure studies. Mol Biol Rep 43:339. https://doi.org/10.1007/s11033-016-3970-6
Ossa CG, Larridon I, Peralta G, Asselman P, Pérez F (2016) Development of microsatellite markers using next-generation sequencing for the columnar cactus Echinopsis chiloensis (Cactaceae). Mol Biol Rep 43:1315. https://doi.org/10.1007/s11033-016-4069-9
Vieira ML, Santini L, Diniz AL, Munhoz Cde F (2016) Microsatellite markers: what they mean and why they are so useful. Genet Mol Biol 39(3):312–328. https://doi.org/10.1590/1678-4685-GMB-2016-0027
Zhu S, Ding Y, Yap Z, Qiu Y (2016) De novo assembly and characterization of the floral transcriptome of an economically important tree species, Lindera glauca (Lauraceae), including the development of EST-SSR markers for population genetics. Mol Biol Rep 43:1243. https://doi.org/10.1007/s11033-016-4056-1
Oh A, Oh BU (2017) Development and characterization of 24 chloroplast microsatellite markers for two species of Eranthis (Ranunculaceae). Mol Biol Rep 44:359. https://doi.org/10.1007/s11033-017-4117-0
Aranguren-Díaz YC, Varani AM, Michael TP, Miranda VFO (2018) Development of microsatellite markers for the carnivorous plant Genlisea aurea (Lentibulariaceae) using genomics data of NGS. Mol Biol Rep 45:57. https://doi.org/10.1007/s11033-017-4140-1
Gong W, Ma L, Gong P, Liu X, Wang Z, Zhao G (2018) Development and application of EST–SSRs markers for analysis of genetic diversity in erect milkvetch (Astragalus adsurgens Pall.). Mol Biol Rep. https://doi.org/10.1007/s11033-018-4484-1
Klichowska E, Ślipiko M, Nobis M, Szczecińska M (2018) Development and characterization of microsatellite markers for endangered species Stipa pennata (Poaceae) and their usefulness in intraspecific delimitation. Mol Biol Rep 45:639. https://doi.org/10.1007/s11033-018-4192-x
Waikham P, Thongkumkoon P, Chomdej S, Liu A, Wangpakapattanawong P (2018) Development of 13 microsatellite markers for Castanopsis tribuloides (Fagaceae) using next-generation sequencing. Mol Biol Rep 45:27. https://doi.org/10.1007/s11033-017-4137-9
Zhang X, Zhou Y, Li YL, Liu J-X (2018) Development of microsatellite markers for the seagrass Zostera japonica using next-generation sequencing. Mol Biol Rep. https://doi.org/10.1007/s11033-018-4491-2
Ishikawa N, Sakaguchi S, Ito M (2016) Development and characterization of SSR markers for Aster savatieri (Asteraceae). Appl Plant Sci 4(6):1500143. https://doi.org/10.3732/apps.1500143
Gutiérrez-Larruscain D, Malvar Ferreras T, Martínez-Ortega MM, Rico E, Andrés-Sánchez S (2018) SSR markers for Filago subg. Filago (Gnaphalieae: Asteraceae) and cross-amplification in three other subgenera. Appl Plant Sci 6(8):e01171. https://doi.org/10.1002/aps3.1171
Han Z, Ma X, Wei Min, Zhao T, Zhan R, Chen W (2018) SSR marker development and intraspecific genetic divergence exploration of Chrysanthemum indicum based on transcriptome analysis. BMC Genom 19:291. https://doi.org/10.1186/s12864-018-4702-1
Iqbal A, Sadaqat HA, Khan AS, Amjad M (2010) Identification of sunflower (Helianthus annuus, Asteraceae) hybrids using simple-sequence repeat markers. Genet Mol Res 10(1):102–106. https://doi.org/10.4238/vol10-1gmr918
Turchetto C, Segatto ACA, Beduschi J, Bonatto SL, Freitas LB (2015) Genetic differentiation and hybrid identification using microsatellite markers in closely related wild species. AoB Plants 7(1):plv084. https://doi.org/10.1093/aobpla/plv084
Zhao X, Zhang J, Zhang Z, Wang Y, Xie W (2017) Hybrid identification and genetic variation of Elymus sibiricus hybrid populations using EST-SSR markers. Hereditas 154:15. https://doi.org/10.1186/s41065-017-0053-1
Han Z, Geng X, Du K, Xu C, Yao P, Bai F, Kang X (2018) Analysis of genetic composition and transmitted parental heterozygosity of natural 2n gametes in Populus tomentosa based on SSR markers. Planta 247:1407. https://doi.org/10.1007/s00425-018-2871-4
Lv T, Teng R, Shao Q, Wang H, Zhang W, Li M, Zhang L (2015) Planta 242:1167. https://doi.org/10.1007/s00425-015-2353-x
Olejniczak SA, Łojewska E, Kowalczyk T, Sakowicz T (2016) Chloroplasts: state of research and practical applications of plastome sequencing. Planta 244:517. https://doi.org/10.1007/s00425-016-2551-1
Yu M, Jiao L, Guo J, Wiedenhoeft AC, He T, Jiang X, Yin Y (2017) DNA barcoding of vouchered xylarium wood specimens of nine endangered Dalbergia species. Planta 246:1165. https://doi.org/10.1007/s00425-017-2758-9
Garrido-Cardenas JA, Mesa-Valle C, Manzano-Agugliaro F (2018) Trends in plant research using molecular markers. Planta 247(3):543–557. https://doi.org/10.1007/s00425-017-2829-y
Emanuelli F, Lorenzi S, Grzeskowiak L, Catalano V, Stefanini M, Troggio M, Grando MS (2013) Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape. BMC Plant Biol 13:39. https://doi.org/10.1186/1471-2229-13-39
Park H, Yoon CY, Kim JS, Kim JH (2015) Molecular identification of Reynoutria japonica Houtt. and R. sachalinensis (F. Schmidt) Nakai using SNP sites. Korean J Plant Resour 28(6):743–751. https://doi.org/10.7732/kjpr.2015.28.6.743
Bieniek W (2015) Mizianty M (2015) Sequence variation at the three chloroplast loci (matK, rbcL, trnH-psbA) in the Triticeae tribe (Poaceae): comments on the relationships and utility in DNA barcoding of selected species. Plant Syst Evol 301:1275–1286. https://doi.org/10.1007/s00606-014-1138-1
Ohsako T, Ohnishi O (2001) Nucleotide sequence variation of the chloroplast trnK/matK region in two wild Fagopyrum (Polygonaceae) species, F. leptopodum and F. statice. Genes Genet Syst 76:39–46. https://doi.org/10.1266/ggs.76.39
Kim WJ, Ji Y, Choi G, Kang YM, Yang S, Moon BC (2016) Molecular identification and phylogenetic analysis of important medicinal plant species in genus Paeonia based on rDNA-ITS, matK, and rbcL DNA barcode sequences. Genet Mol Res. https://doi.org/10.4238/gmr.15038472