High-efficiency 18S microalgae barcoding by coalescent,distance and character-based approaches: a test in Chlorella and Scenedesmus
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摘要
The relatively conserved 18S is often used in the phylogenetic analysis of microalgae. However, whether it can really help in barcoding microalgae needs to be evaluated. In this study the multiple approaches of coalescent, distance and character-based barcoding are first employed in C hlorella and Scenedesmus to test the efficiency of 18S sequences for barcoding green microalgae. We show that most Chlorella and Scenedesmus species, including the cryptic species, can be distinguished by 18S sequences with all coalescent General Mixed Yule-coalescent(GMYC), poisson tree process(PTP), and P ID, distance(ABGD) and character-based approaches. Both GMYC and PTP analyses produce more genetic groups. The P ID and ABGD analyses only cluster some species. All species(apart from a few of lineages) can be separated in character-based barcoding analysis with more than three character attributes. In comparison with previous barcoding results with r bcL, tufA, ITS and 16 S, 18S produces good resolution in identifying Chlorella and Scenedesmus. Our results reveal that 18S is highly efficient in identifying taxa of green microalgae at species level, based on a combination of multiple barcoding approaches. Combining 18S with other gene markers may be useful in barcoding microalgae.
The relatively conserved 18S is often used in the phylogenetic analysis of microalgae. However, whether it can really help in barcoding microalgae needs to be evaluated. In this study the multiple approaches of coalescent, distance and character-based barcoding are first employed in C hlorella and Scenedesmus to test the efficiency of 18S sequences for barcoding green microalgae. We show that most Chlorella and Scenedesmus species, including the cryptic species, can be distinguished by 18S sequences with all coalescent General Mixed Yule-coalescent(GMYC), poisson tree process(PTP), and P ID, distance(ABGD) and character-based approaches. Both GMYC and PTP analyses produce more genetic groups. The P ID and ABGD analyses only cluster some species. All species(apart from a few of lineages) can be separated in character-based barcoding analysis with more than three character attributes. In comparison with previous barcoding results with r bcL, tufA, ITS and 16 S, 18S produces good resolution in identifying Chlorella and Scenedesmus. Our results reveal that 18S is highly efficient in identifying taxa of green microalgae at species level, based on a combination of multiple barcoding approaches. Combining 18S with other gene markers may be useful in barcoding microalgae.
The relatively conserved 18S is often used in the phylogenetic analysis of microalgae. However, whether it can really help in barcoding microalgae needs to be evaluated. In this study the multiple approaches of coalescent, distance and character-based barcoding are first employed in C hlorella and Scenedesmus to test the efficiency of 18S sequences for barcoding green microalgae. We show that most Chlorella and Scenedesmus species, including the cryptic species, can be distinguished by 18S sequences with all coalescent General Mixed Yule-coalescent(GMYC), poisson tree process(PTP), and P ID, distance(ABGD) and character-based approaches. Both GMYC and PTP analyses produce more genetic groups. The P ID and ABGD analyses only cluster some species. All species(apart from a few of lineages) can be separated in character-based barcoding analysis with more than three character attributes. In comparison with previous barcoding results with r bcL, tufA, ITS and 16 S, 18S produces good resolution in identifying Chlorella and Scenedesmus. Our results reveal that 18S is highly efficient in identifying taxa of green microalgae at species level, based on a combination of multiple barcoding approaches. Combining 18S with other gene markers may be useful in barcoding microalgae.
引文
Bergmann T,Hadrys H,Breves G,Schierwater B.2009.Character-based DNA barcoding:a superior tool for species classifi cation.Berl.Munch.Tierarztl.Wochenschr.,122(11-12):446-450.
Bock C,Pr?schold T,Krienitz L.2011.Updating the genus Dictyosphaerium and description of Mucidosphaerium gen.Nov.(Trebouxiophyceae)based on morphological and molecular data.J.Phycol.,47(3):638-652.
CBOL Plant Working Group.2009.A DNA barcode for land plants.Proc.Natl.Acad.Sci.U.S.A.,106(31):12 794-12 797.
China Plant BOL Group,Li D Z,Gao L M,Li H T,Wang H,Ge X J,Liu J Q,Chen Z D,Zhou S L,Chen S L,Yang JB,Fu C X,Zeng C X,Yan H F,Zhu Y J,Sun Y S,Chen SY,Zhao L,Wang K,Yang T,Duan G W.2011.Comparative analysis of a large dataset indicates that internal transcribed spacer(ITS)should be incorporated into the core barcode for seed plants.Proc.Natl.Acad.Sci.U.S.A.,108(49):19 641-19 646.
Damm S,Schierwater B,Hadrys H.2010.An integrative approach to species discovery in odonates:from characterbased DNA barcoding to ecology.Mol.Ecol.,19(18):3 881-3 893.
DeSalle R,Egan M G,Siddall M.2005.The unholy trinity:taxonomy,species delimitation and DNA barcoding.Philos.Trans.Roy.Soc.B:Biol.Sci.,360(1462):1 905-1 916.
Drummond A J,Rambaut A.2007.BEAST:bayesian evolutionary analysis by sampling trees.BMC Evol.Biol.,7:214.
Fujisawa T,Barraclough T G.2013.Delimiting species using single-locus data and the generalized mixed Yule coalescent approach:a revised method and evaluation on simulated data sets.Syst.Biol.,62(5):707-724.
Hebert P D N,Cywinska A C,Ball S L,deWaard J R.2003.Biological identifi cations through DNA barcodes.Philos.Trans.Roy.Soc.B:Biol.Sci.,270(1512):313-321.
Heeg J S,Wolf M.2015.ITS2 and 18S rDNA sequencestructure phylogeny of Chlorella and allies(Chlorophyta,Trebouxiophyceae,Chlorellaceae).Plant Gene,4:20-28.
Kekkonen M,Hebert P D N.2014.DNA barcode-based delineation of putative species:effi cient start for taxonomic workfl ows.Mol.Ecol.Res.,14(4):706-715.
Krawczyk K,Szczecińska M,Sawicki J.2014.Evaluation of11 single-locus and seven multilocus DNA barcodes in Lamium L.(Lamiaceae).Mol.Ecol.Res.,14(2):272-285.
Krienitz L,Hegewald E H,Hepperle D,Huss V A R,Rohrs T,Wolf M.2004.Phylogenetic relationship of Chlorella and Parachlorella gen.nov.(Chlorophyta,Trebouxiophyceae).Phycologia,43:529-542.
Kumar S,Stecher G,Tamura K.2016.MEGA7:Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.Mol.Biol.Evol.,33(7):1870-4.
Luo W,Pfl ugmacher S,Pr?eschold T,Walz N,Krienitz L.2006.Genotype versus phenotype variability in Chlorella and Micractinium(Chlorophyta,Trebouxiophyceae).Protist,157(3):315-333.
Luo W,Pr?eschold T,Bock C,Krienitz L.2010.Generic concept in Chlorella-related coccoid green algae(Chlorophyta,Trebouxiophyceae).Plant Biol.,12(3):545-553.
Maddison D R,Maddison W P.2001.MacClade:Analysis of Phylogeny and Character Evolution,Version 4.03.Sinauer Associates,Sunderland,MA.
Posada D.2008.jModelTest:phylogenetic model averaging.Mol.Biol.Evol.,25(7):1 253-1 256.
R Core Team.2014.R:A language and environment for statistical computing.R Foundation for Statistical Computing,Vienna,Austria.URL http://www.R-project.org/.
Rach J,DeSalle R,Sarkar I N,Schierwater B,Hadrys H.2008.Character-based DNA barcoding allows discrimination of genera,species and populations in Odonata.Philos.Trans.Roy.Soc.B:Biol.Sci.,275(1632):237-247.
Saunders G W,Kucera H.2010.An evaluation of rbcL,tufA,UPA,LSU and ITS as DNA barcode markers for the marine green macroalgae.Cryptogamie Algol.,31(4):487-528.
?kaloud P,NěmcováY,Pytela J,Bogdanov N I,Bock C,Pickinpaugh S H.2014.Planktochlorella nurekis gen.et sp.nov.(Trebouxiophyceae,Chlorophyta),a novel coccoid green alga carrying signifi cant biotechnological potential.Fottea,14(1):53-62.
Talavera G,Dinc?V,Vila R.2013.Factors aff ecting species delimitations with the GMYC model:insights from a butterfl y survey.Methods Ecol.Evol.,4(12):1 101-1 110.
Yassin A,Markow T A,Narechania A,O’Grady P M,DeSalle R.2010.The genus Drosophila as a model for testing tree-and character-based methods of species identifi cation using DNA barcoding.Mol.Phylogenet.Evol.,57(2):509-517.
Zou S M,Fei C,Song J M,Bao Y C,He M L,Wang C H.2016a.Combining and comparing coalescent,distance and character-based approaches for barcoding microalgaes:a test with Chlorella-like species(Chlorophyta).PLoS One,11(4):e015383.
Zou S M,Fei C,Wang C,Gao Z,Bao Y C,He M L,Wang CH.2016b.How DNA barcoding can be more eff ective in microalgae identifi cation:a case of cryptic diversity revelation in Scenedesmus(Chlorophyceae).Sci.Rep.,6:36 822.
Zou S M,Li Q,Kong L F,Yu H,Zheng X D.2011.Comparing the usefulness of distance,monophyly and characterbased DNA barcoding methods in species identifi cation:a case study of Neogastropoda.PLoS One,6(10):e26619.
Bock C,Pr?schold T,Krienitz L.2011.Updating the genus Dictyosphaerium and description of Mucidosphaerium gen.Nov.(Trebouxiophyceae)based on morphological and molecular data.J.Phycol.,47(3):638-652.
CBOL Plant Working Group.2009.A DNA barcode for land plants.Proc.Natl.Acad.Sci.U.S.A.,106(31):12 794-12 797.
China Plant BOL Group,Li D Z,Gao L M,Li H T,Wang H,Ge X J,Liu J Q,Chen Z D,Zhou S L,Chen S L,Yang JB,Fu C X,Zeng C X,Yan H F,Zhu Y J,Sun Y S,Chen SY,Zhao L,Wang K,Yang T,Duan G W.2011.Comparative analysis of a large dataset indicates that internal transcribed spacer(ITS)should be incorporated into the core barcode for seed plants.Proc.Natl.Acad.Sci.U.S.A.,108(49):19 641-19 646.
Damm S,Schierwater B,Hadrys H.2010.An integrative approach to species discovery in odonates:from characterbased DNA barcoding to ecology.Mol.Ecol.,19(18):3 881-3 893.
DeSalle R,Egan M G,Siddall M.2005.The unholy trinity:taxonomy,species delimitation and DNA barcoding.Philos.Trans.Roy.Soc.B:Biol.Sci.,360(1462):1 905-1 916.
Drummond A J,Rambaut A.2007.BEAST:bayesian evolutionary analysis by sampling trees.BMC Evol.Biol.,7:214.
Fujisawa T,Barraclough T G.2013.Delimiting species using single-locus data and the generalized mixed Yule coalescent approach:a revised method and evaluation on simulated data sets.Syst.Biol.,62(5):707-724.
Hebert P D N,Cywinska A C,Ball S L,deWaard J R.2003.Biological identifi cations through DNA barcodes.Philos.Trans.Roy.Soc.B:Biol.Sci.,270(1512):313-321.
Heeg J S,Wolf M.2015.ITS2 and 18S rDNA sequencestructure phylogeny of Chlorella and allies(Chlorophyta,Trebouxiophyceae,Chlorellaceae).Plant Gene,4:20-28.
Kekkonen M,Hebert P D N.2014.DNA barcode-based delineation of putative species:effi cient start for taxonomic workfl ows.Mol.Ecol.Res.,14(4):706-715.
Krawczyk K,Szczecińska M,Sawicki J.2014.Evaluation of11 single-locus and seven multilocus DNA barcodes in Lamium L.(Lamiaceae).Mol.Ecol.Res.,14(2):272-285.
Krienitz L,Hegewald E H,Hepperle D,Huss V A R,Rohrs T,Wolf M.2004.Phylogenetic relationship of Chlorella and Parachlorella gen.nov.(Chlorophyta,Trebouxiophyceae).Phycologia,43:529-542.
Kumar S,Stecher G,Tamura K.2016.MEGA7:Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.Mol.Biol.Evol.,33(7):1870-4.
Luo W,Pfl ugmacher S,Pr?eschold T,Walz N,Krienitz L.2006.Genotype versus phenotype variability in Chlorella and Micractinium(Chlorophyta,Trebouxiophyceae).Protist,157(3):315-333.
Luo W,Pr?eschold T,Bock C,Krienitz L.2010.Generic concept in Chlorella-related coccoid green algae(Chlorophyta,Trebouxiophyceae).Plant Biol.,12(3):545-553.
Maddison D R,Maddison W P.2001.MacClade:Analysis of Phylogeny and Character Evolution,Version 4.03.Sinauer Associates,Sunderland,MA.
Posada D.2008.jModelTest:phylogenetic model averaging.Mol.Biol.Evol.,25(7):1 253-1 256.
R Core Team.2014.R:A language and environment for statistical computing.R Foundation for Statistical Computing,Vienna,Austria.URL http://www.R-project.org/.
Rach J,DeSalle R,Sarkar I N,Schierwater B,Hadrys H.2008.Character-based DNA barcoding allows discrimination of genera,species and populations in Odonata.Philos.Trans.Roy.Soc.B:Biol.Sci.,275(1632):237-247.
Saunders G W,Kucera H.2010.An evaluation of rbcL,tufA,UPA,LSU and ITS as DNA barcode markers for the marine green macroalgae.Cryptogamie Algol.,31(4):487-528.
?kaloud P,NěmcováY,Pytela J,Bogdanov N I,Bock C,Pickinpaugh S H.2014.Planktochlorella nurekis gen.et sp.nov.(Trebouxiophyceae,Chlorophyta),a novel coccoid green alga carrying signifi cant biotechnological potential.Fottea,14(1):53-62.
Talavera G,Dinc?V,Vila R.2013.Factors aff ecting species delimitations with the GMYC model:insights from a butterfl y survey.Methods Ecol.Evol.,4(12):1 101-1 110.
Yassin A,Markow T A,Narechania A,O’Grady P M,DeSalle R.2010.The genus Drosophila as a model for testing tree-and character-based methods of species identifi cation using DNA barcoding.Mol.Phylogenet.Evol.,57(2):509-517.
Zou S M,Fei C,Song J M,Bao Y C,He M L,Wang C H.2016a.Combining and comparing coalescent,distance and character-based approaches for barcoding microalgaes:a test with Chlorella-like species(Chlorophyta).PLoS One,11(4):e015383.
Zou S M,Fei C,Wang C,Gao Z,Bao Y C,He M L,Wang CH.2016b.How DNA barcoding can be more eff ective in microalgae identifi cation:a case of cryptic diversity revelation in Scenedesmus(Chlorophyceae).Sci.Rep.,6:36 822.
Zou S M,Li Q,Kong L F,Yu H,Zheng X D.2011.Comparing the usefulness of distance,monophyly and characterbased DNA barcoding methods in species identifi cation:a case study of Neogastropoda.PLoS One,6(10):e26619.