An Evolutionary Framework for the Study of Developmental Evolution in a Set of Nematodes Related toCaenorhabditis elegans

Baldwin, J. G.; Frisse, Linda M.; Vida, J. T.; Eddleman, C. D.; Thomas, W. Kelley

doi:10.1006/mpev.1997.0433

Cited by 52 publications

(33 citation statements)

References 30 publications

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“…However, to do this, we also needed a closely related outgroup. Molecular data had placed the strain PS1010 within the genus Caenorhabditis, although its males have very distinctive tails (Baldwin et al 1997). We found that the sequences of FOG-1 and FOG-3 from PS1010 were also dramatically different from those of other Caenorhabditis species ( Fig.…”

Section: Sp Ps1010 Is An Outgroup For the Elegans Subgroup Of Nemmentioning

confidence: 80%

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A Phylogeny of Caenorhabditis Reveals Frequent Loss of Introns During Nematode Evolution

Cho¹,

Jin²,

Cohen³

et al. 2004

Genome Res.

162

141

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Since introns were discovered 26 years ago, people have wondered how changes in intron/exon structure occur, and what role these changes play in evolution. To answer these questions, we have begun studying gene structure in nematodes related to Caenorhabditis elegans. As a first step, we cloned a set of five genes from six different Caenorhabditis species, and used their amino acid sequences to construct the first detailed phylogeny of this genus. Our data indicate that nematode introns are lost at a very high rate during evolution, almost 400-fold higher than in mammals. These losses do not occur randomly, but instead, favor some introns and do not affect others. In contrast, intron gains are far less common than losses in these genes. On the basis of the sequences at each intron site, we suggest that several distinct mechanisms can cause introns to be lost. The small size of C. elegans introns should increase the rate at which each of these types of loss can occur, and might account for the dramatic difference in loss rate between nematodes and mammals.

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Section: Sp Ps1010 Is An Outgroup For the Elegans Subgroup Of Nemmentioning

confidence: 80%

“…CB5161 (Baird et al 1992), PS1010 for C. sp. PS1010 (Baldwin et al 1997), and CEW1 for Oscheius tipulae (Evans et al 1997). …”

Section: Genetic Methods and Nematode Strainsmentioning

confidence: 99%

A Phylogeny of Caenorhabditis Reveals Frequent Loss of Introns During Nematode Evolution

Cho¹,

Jin²,

Cohen³

et al. 2004

Genome Res.

162

141

View full text Add to dashboard Cite

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“…The 18S rDNA was partially amplified using two sets of primers: 1A (forward) and 3B (reverse; Baldwin et al, 1997), and two primers specially designed for this study: MelF (forward) and MelR (reverse) ( Table 2). A 50 µl reaction was used containing 5.0 µl of 10× reaction buffer, 1.5 mM MgCl 2 , 0.2 mM dNTPs, 2 pM of forward and reverse primers of each set, 1.25 U of Taq polymerase (CLP, San Diego, CA, USA) and 2 µl of genomic DNA.…”

Section: Amplification Of 18s Rna Gene By Pcrmentioning

confidence: 99%

Phylogeny of Meloidogyne spp. based on 18S rDNA and the intergenic region of mitochondrial DNA sequences

Tigano¹,

Carneiro²,

Jeyaprakash³

et al. 2005

Nematol

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Summary -The 18S rDNA of 19 populations of Meloidogyne spp. was amplified and directly sequenced. The region of mitochondrial DNA, located in the 3 portion of the gene that codes for cytochrome oxidase subunit II (COII) through a portion of the 16S rRNA (lRNA) gene, from 16 of these populations was cloned and sequenced. Heteroplasmic sequences were identified from both rDNA and mtDNA regions for several taxa. Several sequences sampled from nominal taxa differed from previously published accounts. Phylogenetic trees based on alignments of these sequences were constructed using distance, parsimony and likelihood optimality criteria. For 18S rDNA data, three main clades were identified. One well supported clade (86-91% bootstrap) included the most common and widely disseminated species, e.g., M. arenaria, M. javanica and M. incognita, some recently described or redescribed species (M. floridensis, M. paranaensis, and M. ethiopica) plus numerous unidentified isolates. All mitotic parthenogenetic species, except for M. oryzae, were included in this clade. Other, less well supported clades included the amphimictic and facultative meiotic species M. hapla, M. microtyla, M. maritima and M. duytsi. One such clade comprised three meiotic parthenogens (M. exigua, M. graminicola and M. chitwoodi) and M. oryzae. This clade was moderately supported (77% bootstrap) but the relationships within this clade were poor. For mitochondrial DNA data, only the species in clade I from rDNA analysis, and M. hapla were analysed. These species formed a well supported clade (100% bootstrap) to the exclusion of M. mayaguensis and M. hapla. The addition of taxa and mtDNA data to publicly available records improved the discrimination sensitivity of species and atypical, non-identified, isolates.

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“…Manufacturer-supplied Display-TAQ buffer (PGC Scienti c, Gaithersburg, MD, USA), 250 ¹M dNTPs, 4 mM MgCl 2 , and 600 ¹M of each ribosomal DNA primer, originally designed by W. Kelley Thomas, University of Missouri, Kansas City, MO, USA. Primers D3A (5 0 -GACCCGTCTTGAAACACGGA-3 0 ) and D3B (5 0 -TCGGAAGGAACCAGCTACTA-3 0 ) (Baldwin et al, 1997) were added to the bottom of 0.5 ml thinwall microcentrifuge tubes. A drop (ca 25 ¹l) of parafn wax was overlaid and allowed to cool, forming an even barrier.…”

Section: Amplification and Sequencingmentioning

confidence: 99%

Morphological and molecular characterisation of Pratylenchus arlingtoni n. sp., P.convallariae and P.fallax (Nematoda: Pratylenchidae)

Handoo¹,

Carta²,

Skantar³

2001

Nematol

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Summary -Pratylenchus arlingtoni n. sp. from the rhizosphere of grasses Poa pratensis and Festuca arundinacea at Arlington National Cemetery, VA, USA is characterised by six to eight lines in the lateral eld, and pyriform to slightly overlapping pharyngeal glands. Morphological comparisons are made with lesion nematodes having similar morphometrics, six lateral lines, or crenate tail tips. Molecular sequences of the LS 28S rDNA were generated for the new species as well as P. fallax and P. convallariae. The new species differs by only 1% from identical sequences found in P. fallax and P. convallariae.

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An Evolutionary Framework for the Study of Developmental Evolution in a Set of Nematodes Related toCaenorhabditis elegans

Cited by 52 publications

References 30 publications

A Phylogeny of Caenorhabditis Reveals Frequent Loss of Introns During Nematode Evolution

A Phylogeny of Caenorhabditis Reveals Frequent Loss of Introns During Nematode Evolution

Phylogeny of Meloidogyne spp. based on 18S rDNA and the intergenic region of mitochondrial DNA sequences

Morphological and molecular characterisation of Pratylenchus arlingtoni n. sp., P.convallariae and P.fallax (Nematoda: Pratylenchidae)

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