Heterogeneity of Three Molecular Data Partition Phylogenies of Mints Related to M. × piperita (Mentha; Lamiaceae)

Abstract

Phylogenetic reconstructions with molecular tools are now widely used, thanks to advances in PCR and sequencing technologies. The choice of the molecular target still remains a problem because too few comparative data are available. This is particularly true for hybrid taxa, where differential introgression of genome parts leads to incongruity between data sets. We have studied the potential of three data partitions to reconstruct the phylogeny of mints related to M. × piperita. These included nuclear DNA (ITS), chloroplast DNA (non-coding regions trnL intron, intergenic spacers trnL-trnF, and psbA-trnH), and AFLP and ISSR, markers. The taxonomic sampling was composed of hybrids, diploid and polyploid genomes. Since the genealogy of cultivated mint hybrids is known, they represent a model group to compare the usefulness of various molecular markers for phylogeny inference. Incongruities between ITS, chloroplast DNA, and AFLP-ISSR phylogenetic trees were recorded, although DNA fingerprinting data were congruent with morphological classification. Evidence of chloroplast capture events was obtained for M. × piperita. Direct sequencing of ITS led to biased results because of the existence of pseudogenes. Sequencing of cloned ITS further failed to provide evidence of the existence of the two parental copy types for M. × piperita, a sterile hybrid that has had no opportunity for concerted evolution of ITS copies. AFLP-ISSR data clustered M. × piperita with the parent that had the largest genome. This study sheds light on differential of introgression of different genome regions in mint hybrids.

Genomic fingerprinting - hybridization - ITS - Lamiaceae - Mentha - non-coding chloroplast DNA - polyploidy.

References

• 1 Alvarez I., Wendel J. F.. Ribosomal ITS sequences and plant phylogenetic inference.  Molecular Phylogenetics and Evolution. (2003);  29 417-434
• 2 Arnheim N., Krystal M., Schmickel R., Wilson G., Ryder O., Zimmer E.. Molecular evidence for genetic exchanges among ribosomal genes on non-homologous chromosomes in man and apes.  Proceedings of the National Academy of Sciences of the USA. (1980);  77 7323-7327
• 3 Bakker F. T., Culham A., Pankhurst C. E., Gibby M.. Mitochondrial and chloroplast DNA-based phylogeny of Pelargonium (Geraniaceae).  American Journal of Botany. (2000);  87 727-734
• 4 Baldwin B. G.. Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: an example from the Compositae.  Molecular Phylogenetics and Evolution. (1992);  1 3-16
• 5 Baldwin B. G., Sanderson M. J., Porter J. M., Wojciechowski M. F., Campbell C. S., Donoghue M. J.. The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny.  Annals of the Missouri Botanical Garden. (1995);  82 247-277
• 6 Barriel V.. Phylogénies moléculaires et insertions-délétions de nucléotides.  Compte Rendus de l'Académie des Sciences, Paris, Sciences de la Vie. (1994);  317 693-701
• 7 Blair R. J., Panaud O., McCouch S. R.. Inter-simple sequence repeat (ISSR) amplification for analysis of microsatellite motif frequency and fingerprinting in rice (Oryza sativa L.).  Theoretical and Applied Genetics. (1999);  98 780-792
• 8 Brouat C., Gielly L., Mckey D.. Phylogenetic relationships in the genus Leonardoxa (Leguminosae: Caesalpinioideae) inferred from chloroplast trnL intron and trnL-trnF intergeneric spacer sequences.  American Journal of Botany. (2001);  88 143-149
• 9 Buckler E. S., Ippolito A., Holtsford T. P.. The evolution of ribosomal DNA: divergent paralogues and phylogenetic implications.  Genetics. (1997);  145 821-832
• 10 Bunsawat J., Elliott N. E., Hertweck K. L., Sproles E., Alice L. A.. Phylogenetics of Mentha (Lamiaceae): evidence from Chloroplast DNA sequences.  Systematic Botany. (2004);  29 959-964
• 11 Charters Y. M., Robertson A., Wilkinson M. J., Ramsay G.. PCR analysis of oilseed rape cultivars (Brassica napus L. ssp. oleifera) using 5′-anchored simple sequence repeat (SSR) primers.  Theoretical and Applied Genetics. (1996);  92 442-447
• 12 De Rijk P., De Wachter R.. RnaViz, a program for the visualisation of RNA secondary structure.  Nucleic Acids Research. (1997);  25 4679-4684
• 13 Després L., Gielly L., Redoutet B., Taberlet P.. Using AFLP to resolve phylogenetic relationships in a morphologically diversified plant species complex when nuclear and chloroplast sequences fail to reveal variability.  Molecular Phylogenetics and Evolution. (2003);  27 185-196
• 14 Doyle J. J., Doyle J. L.. Isolation of plant DNA from fresh tissue.  Focus. (1990);  12 13-15
• 15 Doyle J. J., Gaut B. S.. Evolution of genes and taxa: a primer.  Plant Molecular Biology. (2000);  42 1-23
• 16 Farris J. S., Källersjö M., Kluge A. G., Bult C.. Testing significance of incongruence.  Cladistics. (1995);  10 315-319
• 17 Felsenstein J.. Confidence limits on phylogenies: an approach using the bootstrap.  Evolution. (1985);  39 783-791
• 18 Fenwick A. L., Ward S. M.. Use of random amplified polymorphic DNA markers for cultivar identification in mint.  Hortscience. (2001);  36 761-764
• 19 Gernandt D. S., Liston A., Pinero D.. Variation in the nrDNA ITS of Pinus subsection Cembroides: implications for molecular systematic studies of pine species complexes.  Molecular Phylogenetics and Evolution. (2001);  21 449-467
• 20 Gobert V., Moja S., Colson M., Taberlet P.. Hybridization in the section Mentha (Lamiaceae) inferred from AFLP markers.  American Journal of Botany. (2002);  89 2017-2023
• 21 Hamilton M. B.. Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation.  Molecular Ecology. (1999);  8 521-523
• 22 Harley R. M.. The spicate mints.  Proceedings of the Botanical Society of the British Isles. (1967);  6 369-372
• 23 Harley R. M.. Notes on the genus Mentha (Labiatae).  Botanical Journal of the Linnaean Society. (1972);  65 250-253
• 24 Harley R. M., Brighton C. A.. Chromosomes numbers in the genus Mentha L.  Botanical Journal of the Linnaean Society. (1977);  74 71-96
• 25 Heimans J.. Chromosomes in the genus Mentha.  Chronica Botanica. (1938);  4 389-390
• 26 Hershkovitz M. A., Zimmer E. A.. Conservation patterns in angiosperm rDNA ITS2 sequences.  Nucleic Acids Research. (1996);  24 2857-2876
• 27 Higgins D. G., Fuchs R., Blesby A.. CLUSTAL: a new multiple sequence alignment program.  Comparative Applied Biosciences. (1992);  8 189-191
• 28 Hillis D. M.. Discriminating between phylogenetic signal and random noise in DNA sequences. Miyamoto, M. M. and Cracraft, J., eds. Phylogenetic Analysis of DNA Sequences. New York; Oxford University Press (1991): 278-294
• 29 Johnson L. A., Soltis D. E.. Assessing congruence: empirical examples from molecular data. Soltis, D. E., Soltis, P. S., and Doyle, J. J., eds. Molecular Systematics of Plants. II. DNA Sequencing. Dordrecht; Kluwer Academic Publishers (1998): 297-348
• 30 Kantety R. V., Zeng X. P., Bennetzen J. L., Zehr B. E.. Assessment of genetic diversity in dent and popcorn (Zea mays L.) inbred lines using inter-simple sequence repeat (ISSR) amplification.  Molecular Breeding. (1995);  1 365-373
• 31 Kaufmann M., Wink M.. Molecular systematics of the Nepetoideae (Family Labiatae): phylogenetic implications from rbcL gene sequences.  Zeitschrift für Naturforschung. (1994);  49c 635 -645
• 32 Kumar L. S., Sawant A. S., Gupta V. S., Ranjekar P. K.. Comparative analysis of genetic diversity among Indian populations of Scirpophaga incertulas by ISSR‐PCR and RAPD‐PCR.  Biochemical Genetics. (2001);  39 297-309
• 33 Lebeau J.. Nouvelles mises au point dans le genre Mentha.  Natura Mosana. (1974);  27 109-141
• 34 Leroy X. J., Leon K., Branchard M.. Plant genomic instability detected by microsatellite primers.  Electronic Journal of Biotechnology. (2000);  3 (2) http://www.ejbiotechnology.info/content/vol3/issue2/full/2/index.html
• 36 Liu J.-S., Schardl C. L.. A conserved sequence in internal transcribed spacer 1 of plant nuclear rRNA.  Plant Molecular Biology. (1994);  26 775-778
• 37 Madisson D. R.. The discovery and importance of multiple islands of most parsimonious trees.  Systematic Zoology. (1991);  40 315-328
• 38 Mai J. C., Coleman A. W.. The internal transcribed spacer 2 exhibits a common secondary structure in green algae and flowering plants.  Journal of Molecular Evolution. (1997);  44 258-271
• 39 Mattioni C., Casasoli M., Gonzalez M., Ipinza R., Villani F.. Comparison of ISSR and RAPD markers to characterize three Chilean Nothofagus species.  Theoretical and Applied Genetics. (2002);  104 1064-1070
• 40 Mayol M., Rossello J. A.. Why nuclear ribosomal DNA spacers (ITS) tell different stories in Quercus.  Molecular Phylogenetics and Evolution. (2001);  19 167-176
• 41 Morton J. K.. The chromosome numbers of the British Menthae.  Watsonia. (1956);  3 244-252
• 42 Murray M. J., Lincoln D. E., Marble P. M.. Oil composition of Mentha aquatica × Mentha spicata F1 hybrids in relation to the origin of × M. piperita. .  Canadian Journal of Genetics and Cytology. (1972);  14 13-29
• 43 Nei M., Li W. H.. Mathematical model for studying genetic variation in terms of restriction endonucleases.  Proceedings of the National Academy of Sciences of the USA. (1979);  76 5269-5273
• 44 Ratnaparkhe M. B., Tekeoglu M., Muehlbauer F. J.. Intersimple sequence repeat (ISSR) polymorphisms are useful for finding markers associated with disease resistance gene clusters.  Theoretical and Applied Genetics. (1998);  97 515-519
• 45 Rieseberg L. H., Brunsfeld S. J.. Molecular evidence and plant introgression. Soltis, P. S., Soltis, D. E., and Doyle, J. J., eds. Molecular Systematics of Plants. New York; Chapmann and Hall (1992): 151-176
• 46 Rieseberg L. H., Baird S. J. E., Gardner K. A.. Hybridization, introgression, and linkage evolution.  Plant Molecular Biology. (2000);  42 205-224
• 47 Russell J. R., Fuller J. D., Macaulay M., Hatz B. G., Jahoor A., Powell W., Waugh R.. Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs.  Theoretical and Applied Genetics. (1997);  95 714-722
• 48 Ruttle M. L.. Cytological and embryological studies of the genus Mentha.  Gartenbauwissenschaft. (1931);  44 428-468
• 49 Sambrook J., Fritsch E. F., Maniatis T.. Molecular Cloning: A Laboratory Manual. New York, Cold Spring Harbor; Laboratory Press (1989)
• 50 Sang T., Crawford D. J., Stuessy F.. Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae).  American Journal of Botany. (1997);  84 1120-1136
• 51 Seehausen O.. Hybridization and adaptative radiation.  Trends in Ecology and Evolution. (2004);  19 198-207
• 52 Sharma A. K., Bhattacharyya N. K.. Cytological studies on different species of Mentha with special reference to the occurrence of chromosomal biotypes.  Cytologia. (1959);  24 198-212
• 53 Singh T. P., Sharma A. K.. Mentha - taxonomic status as interpreted through cytology, genetics and phytochemistry.  Indian Journal of Genetics. (1986);  46 198-208
• 54 Soltis P. S., Doyle J. J., Soltis D. E.. Molecular data and polyploid evolution in plants. Soltis, P. S., Soltis, D. E., and Doyle, J. J., eds. Molecular Systematics of Plants. London, UK; Chapman and Hall (1992): 177-201
• 55 Soltis D. E., Soltis P. S.. The dynamic nature of polyploid genomes.  Proceedings of the National Academy of Sciences of the USA. (1995);  92 8089-8091
• 56 Soltis D. E., Soltis P. S.. Polyploidy: recurrent formation and genome evolution.  Trends in Ecology and Evolution. (1999);  14 348-352
• 58 Swofford D. L.. PAUP*: Phylogenetic Analysis Using Parsimony (*and other methods), version 4b8. Massachusetts, USA; Sinauer, Sunderland (1999)
• 59 Taberlet P., Gielly L., Pautou G., Bouvet J.. Universal primers for amplification of three non-coding regions of chloroplast DNA.  Plant Molecular Biology. (1991);  17 1105-1109
• 60 Thioulouse J., Chessel D., Dolédec S., Olivier J. M.. ADE‐4: a multivariate analysis and graphical display software.  Statistics and Computing. (1997);  7 75-83
• 61 Tucker A. O., Chambers H. L.. Mentha canadensis L. (Lamiaceae): a relict amphidiploid from the Lower Tertiary.  Taxon. (2002);  51 703-718
• 62 Van de Peer Y., De Wachter R.. TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment.  Computer Application in the Biosciences. (1994);  10 569-570
• 63 Vos P., Hogers R., Bleeker M., Reijans M., Van de Lee T., Hornes M., Frijters A., Pot J., Peleman J., Kuiper M.. AFLP: a new technique for DNA fingerprinting.  Nucleic Acids Research. (1995);  23 4407-4414 http://jb.asm.org/cgi/ijlink?linkType=ABST&resid=23/21/4407
• 65 Wendel J. F., Schnabel A., Seelanan T.. Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). .  Proceedings of the National Academy of Sciences of the USA. (1995);  92 280-284
• 66 Wendel J. F., Doyle J. J.. Phylogenetic incongruence: window into genome history and molecular evolution. Soltis, D. S., Soltis, P. S., and Doyle, J. J., eds. Molecular Systematics of Plants. II. DNA Sequencing. Boston, MA; Kluwer Academic Publishers (1998): 265-296
• 67 Wendel J. F.. Genome evolution in polyploids.  Plant Molecular Biology. (2000);  42 225-249
• 68 Wink M., Sauer-Gürth H., Martinez F., Doval G., Blanco G., Hatzofe O.. Use of GACA‐PCR for molecular sexing of Old World vultures (Aves: Accipitridae).  Molecular Ecology. (1998);  7 779-782
• 69 Wink M., Guicking D., Fritz U.. Molecular evidence for hybrid origin of Mauremys iversoni Pritchard et McCord, 1991 and Mauremys pritchardi McCord, 1997 (Reptilia: Testudines: Bataguridae).  Zoologische Abhandlungen Staatliches Museum für Tierkunde Dresden. (2000);  51 41-49
• 70 Wolff K., Morgan-Richards M.. PCR markers distinguish Plantago major subspecies.  Theoretical and Applied Genetics. (1998);  96 282-286
• 71 Xu F., Sun M.. Comparative analysis of phylogenetic relationships of Grain Amaranths and their wild relatives (Amaranthus; Amaranthaceae) using internal transcribed spacer, amplified fragment length polymorphism, and double-primer fluorescent intersimple sequence repeat markers.  Molecular Phylogenetics and Evolution. (2001);  21 372-387
• 72 Zeven A. C., Zhukovsky P. M.. Dictionary of Cultivated Plants and their Centres of Diversity. Wageningen, The Netherlands; Centre for Agricultural Publishing and Documentation (1975): 219
• 73 Zietkiewicz E., Raflaski A., Labuda D.. Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification.  Genomics. (1994);  20 176-183
• 74 Zuker M., Mathews D. H., Turner D. H.. Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. Barciszewski, J. and Clark, B. F. C., eds. RNA Biochemistry and Biotechnology. NATO ASI Series, Dordrecht; Kluwer Academic Publishers (1999)

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