An Assessment of Potential Diatom “Barcode” Genes (cox1, rbcL, 18S and ITS rDNA) and their Effectiveness in Determining Relationships in Sellaphora (Bacillariophyta)

Protist - Tập 158 Số 3 - Trang 349-364 - 2007
Katharine Evans1, Alexandra H. Wortley1, David G. Mann1
1Royal Botanic Garden Edinburgh, 20a Inverleith Row, Edinburgh, EH3 5LR, UK

Tóm tắt

Từ khóa


Tài liệu tham khảo

Álvarez, 2003, Ribosomal ITS sequences and plant phylogenetic inference, Mol Phylogenet Evol, 29, 417, 10.1016/S1055-7903(03)00208-2

Alverson, 2005, Intragenomic nucleotide polymorphism among small subunit (18S) rDNA paralogs in the diatom genus Skeletonema (Bacillariophyta), J Phycol, 41, 1248, 10.1111/j.1529-8817.2005.00136.x

Amato, 2007, Reproductive isolation among sympatric cryptic species in marine diatoms, Protist, 158, 193, 10.1016/j.protis.2006.10.001

Aoyama, 2006, Complete elimination of maternal mitochondrial DNA during meiosis resulting in the paternal inheritance of the mitochondrial genome in Chlamydomonas species, Protoplasma, 228, 231, 10.1007/s00709-006-0155-5

Armbrust, 2004, The genome of the diatom Thalassiosira pseudonana: ecology, evolution and metabolism, Science, 306, 79, 10.1126/science.1101156

Beagley, 1996, Two mitochondrial group I introns in a metazoan, the sea anemone Metridium senile: one intron contains genes for subunits 1 and 3 of NADH dehydrogenase, Proc Natl Acad Sci USA, 93, 5619, 10.1073/pnas.93.11.5619

Behnke, 2004, Reproductive compatibility and rDNA sequence analyses in the Sellaphora pupula species complex (Bacillariophyta), J Phycol, 40, 193, 10.1046/j.1529-8817.2004.03037.x

Bergthorsson, 2003, Widespread horizontal transfer of mitochondrial genes in flowering plants, Nature, 424, 197, 10.1038/nature01743

Beszteri, 2005, Ribosomal DNA sequence variation among sympatric strains of the Cyclotella meneghiniana complex (Bacillariophyceae) reveals cryptic diversity, Protist, 156, 317, 10.1016/j.protis.2005.07.002

Blaxter, 2004, DNA taxonomy of a neglected animal phylum: an unexpected diversity of tardigrades, Proc R Soc Lond B, 271, S189, 10.1098/rsbl.2003.0130

Brodie, 1996, Molecular and morphological characters distinguishing two Porphyra species (Rhodophyta: Bangiophycidae), Eur J Phycol, 31, 303, 10.1080/09670269600651521

Chase, 2005, Land plants and DNA barcodes: short-term and long-term goals, Phil Trans R Soc Lond B, 360, 1889, 10.1098/rstb.2005.1720

Chepurnov, 2004, Experimental studies on sexual reproduction in diatoms, Int Rev Cytol, 237, 91, 10.1016/S0074-7696(04)37003-8

Chepurnov, 2002, Sexual reproduction, mating system and protoplast dynamics of Seminavis (Bacillariophyceae), J Phycol, 38, 1004, 10.1046/j.1529-8817.2002.t01-1-01233.x

Cowan, 2006, 300,000 species to identify: problems, progress, and prospects in DNA barcoding of land plants, Taxon, 55, 611, 10.2307/25065638

Coyer, 2002, Inheritance patterns of ITS1, chloroplasts and mitochondria in artificial hybrids of the seaweeds Fucus serratus and F. evanescens (Phaeophyceae), Eur J Phycol, 37, 173, 10.1017/S0967026202003682

Ehara, 2000, Phylogenetic analysis of diatom cox1 genes and implications of a fluctuating GC content on mitochondrial genetic code evolution, Curr Genet, 37, 29, 10.1007/s002940050004

Ehara, 2000, Distribution of cognates of group II introns detected in mitochondrial cox1 genes of a diatom and a haptophyte, Gene, 256, 157, 10.1016/S0378-1119(00)00359-0

Finlay, 2002, Hypothesis: the rate and scale of dispersal of freshwater diatom species is a function of their global abundance, Protist, 153, 261, 10.1078/1434-4610-00103

Fontaine, 1997, The reverse-transcriptase-like proteins encoded by group II introns in the mitochondrial genome of the brown alga Pylaiella littoralis belong to two different lineages which apparently coevolved with the group II ribosyme lineages, J Mol Evol, 44, 33, 10.1007/PL00006119

Gompert, 2006, Identifying units for conservation using molecular systematics: the cautionary tale of the Karner blue butterfly, Mol Ecol, 15, 1759, 10.1111/j.1365-294X.2006.02905.x

Gray, 2004, Mitochondria of protists, Annu Rev Genet, 38, 477, 10.1146/annurev.genet.37.110801.142526

Guillard, 1972, Yellow-green algae with chlorophyllide c, J Phycol, 8, 10

Hajibabaei, 2006, DNA barcodes distinguish species of tropical Lepidoptera, Proc Natl Acad Sci USA, 103, 968, 10.1073/pnas.0510466103

Hebert, 2003, Biological identifications through DNA barcodes, Proc R Soc Lond B, 270, 313, 10.1098/rspb.2002.2218

Hebert, 2004, Identification of birds through DNA barcodes, PLoS Biology, 2, 1657, 10.1371/journal.pbio.0020312

Hughes Martiny, 2006, Microbial biogeography: putting microorganisms on the map, Nat Rev Microbiol, 4, 102, 10.1038/nrmicro1341

Hurst, 2005, Problems with mitochondrial DNA as a marker in population, phylogeographic and phylogenetic studies: the effects of inherited symbionts, Proc R Soc Lond B, 272, 1525

Jensen, 2003, Ultrastructure of the male gametes from two centric diatoms, Chaetoceros laciniosus and Coscinodiscus wailesii (Bacillariophyceae), Phycologia, 42, 98, 10.2216/i0031-8884-42-1-98.1

Jones, 2005, Life history and systematics of Petroneis (Bacillariophyta), with special reference to British waters, Eur J Phycol, 40, 61, 10.1080/09670260400024675

Kato, 2006, Inheritance of mitochondrial and chloroplast genomes in the isogamous brown alga Scytosiphon lomentaria (Phaeophyceae), Phycol Res, 54, 65, 10.1111/j.1440-1835.2006.00409.x

Knoop, 2004, The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective, Curr Genet, 46, 123, 10.1007/s00294-004-0522-8

Kress, 2005, Use of DNA barcodes to identify flowering plants, Proc Natl Acad Sci USA, 102, 8369, 10.1073/pnas.0503123102

Lundholm, 2006, Inter- and intraspecific variation of the Pseudo-nitzschia delicatissima complex (Bacillariophyceae) illustrated by rRNA probes, morphological data and phylogenetic analyses, J Phycol, 42, 464, 10.1111/j.1529-8817.2006.00211.x

Mann, 1984, Observations on copulation in Navicula pupula and Amphora ovalis in relation to the nature of diatom species, Ann Bot, 54, 429, 10.1093/oxfordjournals.aob.a086813

Mann, 1989, The species concept in diatoms: evidence for morphologically distinct, sympatric gamodemes in four epipelic species, Plant Syst Evol, 164, 215, 10.1007/BF00940439

Mann, 1996, Chloroplast Morphology, Movements and Inheritance in Diatoms, 249

Mann, 1999, The species concept in diatoms, Phycologia, 38, 437, 10.2216/i0031-8884-38-6-437.1

Mann, 2004, What have the Romans ever done for us? The past and future contribution of culture studies to diatom systematics, Nova Hedwigia, 79, 237, 10.1127/0029-5035/2004/0079-0237

Mann, 2005, Auxosporulation, mating system, and reproductive isolation in Neidium (Bacillariophyta), Phycologia, 44, 335, 10.2216/0031-8884(2005)44[335:AMSARI]2.0.CO;2

Mann, 1996, Biodiversity, biogeography and conservation of diatoms, Hydrobiologia, 336, 19, 10.1007/BF00010816

Mann, 1999, Sexuality, incompatibility, size variation, and preferential polyandry in natural populations and clones of Sellaphora pupula (Bacillariophyceae), J Phycol, 35, 152, 10.1046/j.1529-8817.1999.3510152.x

Mann, 2004, The Sellaphora pupula species complex (Bacillariophyceae): morphometric analysis, ultrastructure and mating data provide evidence for five new species, Phycologia, 43, 459, 10.2216/i0031-8884-43-4-459.1

Mayr, 1942

Medlin, 1991, Morphological and genetic variation within the diatom Skeletonema costatum (Bacillariophyta): evidence for a new species, Skeletonema pseudocostatum, J Phycol, 27, 514, 10.1111/j.0022-3646.1991.00514.x

Meyer, 2005, DNA barcoding: error rates based on comprehensive sampling, PLoS Biology, 3, 2229, 10.1371/journal.pbio.0030422

Newmaster, 2006, DNA barcoding in land plants: evaluation of rbcL in a multigene tiered approach, Can J Bot, 84, 335, 10.1139/b06-047

Nozaki, 2002, Evolution of rbcL group IA introns and intron open reading frames within the colonial Volvocales (Chlorophyceae), Mol Phylogenet Evol, 23, 326, 10.1016/S1055-7903(02)00030-1

Orsini, 2004, Multiple rDNA ITS-types within the diatom Pseudo-nitzschia delicatissima (Bacillariophyceae) and their relative abundances across a spring bloom in the Gulf of Naples, Mar Ecol Progr Ser, 271, 87, 10.3354/meps271087

Oudot-le Secq, 2002, The mitochondrial genome of the brown alga Laminaria digitata: a comparative analysis, Eur J Phycol, 37, 163, 10.1017/S0967026202003542

Oudot-Le Secq, 2006, Complete mitochondrial genomes of the three brown algae (Heterokonta: Phaeophyceae) Dictyota dichotoma, Fucus vesiculosus and Desmarestia viridis, Curr Genet, 49, 47, 10.1007/s00294-005-0031-4

Pace, 1997, A molecular view of microbial diversity and the biosphere, Science, 276, 734, 10.1126/science.276.5313.734

Pedrós-Alió, 2006, Marine microbial diversity: can it be determined?, Trends Microbiol, 14, 257, 10.1016/j.tim.2006.04.007

Pons, 2006, Sequence-based species delimitation for the DNA taxonomy of undescribed insects, Syst Biol, 55, 595, 10.1080/10635150600852011

Posada, 1998, MODELTEST: testing the model of DNA substitution, Bioinformatics, 14, 817, 10.1093/bioinformatics/14.9.817

Robba, 2006, Assessing the use of the mitochondrial cox1 marker for use in DNA barcoding of red algae (Rhodophyta), Am J Bot, 93, 1101, 10.3732/ajb.93.8.1101

Round, 1990

Rozen, 2000, PRIMER3 on the WWW for General Users and for Biologist Programmers, 365

Rubinoff, 2006, Utility of mitochondrial DNA barcodes in species conservation, Conservat Biol, 20, 1026, 10.1111/j.1523-1739.2006.00372.x

Sánchez Puerta, 2004, The complete mitochondrial genome sequence of the haptophyte Emiliania huxleyi and its relation to Heterokonts, DNA Res, 11, 1, 10.1093/dnares/11.1.1

Sarno, 2005, Diversity in the genus Skeletonema (Bacillariophyceae), II. An assessment of the taxonomy of S. costatum-like species with the description of four new species. J Phycol, 41, 151

Saunders, 2005, Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future application, Phil Trans R Soc Lond B, 360, 1879, 10.1098/rstb.2005.1719

Savolainen, 2005, Towards writing the encyclopaedia of life: an introduction to DNA barcoding, Phil Trans R Soc Lond B, 360, 1805, 10.1098/rstb.2005.1730

Seifert, 2007, Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case, Proc Natl Acad Sci USA, 104, 3901, 10.1073/pnas.0611691104

Sims, 2006, Evolution of the diatoms: insights from fossil, biological and molecular data, Phycologia, 45, 361, 10.2216/05-22.1

Šlapeta, 2005, The extent of protist diversity: insights from molecular ecology of freshwater eukaryotes, Proc R Soc Lond B, 272, 2073

Sluiman, 1999, Phylogenetic position of Chaetosphaeridium (Chlorophyta), a basal lineage in the Charophyceae, inferred from 18S rDNA sequences, J Phycol, 35, 395, 10.1046/j.1529-8817.1999.3520395.x

Swofford, 2002

Taylor, 2000, Phylogenetic species recognition and species concepts in fungi, Fungal Genet Biol, 31, 21, 10.1006/fgbi.2000.1228

Taylor NG (1996) Variation Within Sellaphora pupula (Bacillariophyta) in Relation to the Species Concept. MSc Thesis, University of Edinburgh

Vanormelingen, 2007, Congruence of morphological, reproductive and ITS rDNA sequence data in some Australasian Eunotia bilunaris (Bacillariophyta), Eur J Phycol, 42, 61, 10.1080/09670260600942635

Watanabe, 1998, Distinctive origins of group I introns found in the cox1 genes of three green algae, Gene, 213, 1, 10.1016/S0378-1119(98)00235-2

Witt, 2006, DNA barcoding reveals extraordinary cryptic diversity in an amphipod genus: implications for desert spring conservation, Mol Ecol, 15, 3073, 10.1111/j.1365-294X.2006.02999.x