Intraspecies Analysis: Comparison of ITS Sequence Data and Gene Intron Sequence Data with Breeding Data for a Worldwide Collection of Gonium pectorale

Fabry, Stefan; Köhler, Astrid; Coleman, Annette W.

doi:10.1007/pl00006449

Cited by 63 publications

(37 citation statements)

References 18 publications

(33 reference statements)

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“…There has been a series of previous efforts to resolve the phylogeny of the Volvocaceae. These include a cladistic analysis of morphological data by Nozaki (8) and sequence comparisons of variable regions of nuclear ribosomal genes (rSSU and rLSU) (9, 10), of gene introns (1,11), and of the plastid-encoded rbcL and atpB genes (summarized in ref. 12).…”

Section: Discussionmentioning

confidence: 99%

“…I sequenced the internal transcribed spacer (ITS) sequence ITS-1 and ITS-2 regions of the nuclear rRNA cistron because previous results with Volvocales have demonstrated that they are Ͼ10-fold more variable than rRNA genes yet are homogenized by unknown mechanisms with very high frequency, such that they behave essentially as a single locus despite the presence of Ͼ100 tandem copies in a genome (1). Furthermore, knowledge of the ITS RNA transcript secondary structure (2, 3) is valuable in guiding alignment among more distantly related taxa.…”

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confidence: 99%

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Phylogenetic analysis of “Volvocacae” for comparative genetic studies

Coleman

1999

Proc. Natl. Acad. Sci. U.S.A.

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Sequence analysis based on multiple isolates representing essentially all genera and species of the classic family Volvocaeae has clarified their phylogenetic relationships. Cloned internal transcribed spacer sequences (ITS-1 and ITS-2, flanking the 5.8S gene of the nuclear ribosomal gene cistrons) were aligned, guided by ITS transcript secondary structural features, and subjected to parsimony and neighbor joining distance analysis. Results confirm the notion of a single common ancestor, and Chlamydomonas reinharditii alone among all sequenced green unicells is most similar. Interbreeding isolates were nearest neighbors on the evolutionary tree in all cases. Some taxa, at whatever level, prove to be clades by sequence comparisons, but others provide striking exceptions. The morphological species Pandorina morum, known to be widespread and diverse in mating pairs, was found to encompass all of the isolates of the four species of Volvulina. Platydorina appears to have originated early and not to fall within the genus Eudorina, with which it can sometimes be confused by morphology. The four species of Pleodorina appear variously associated with Eudorina examples. Although the species of Volvox are each clades, the genus Volvox is not. The conclusions confirm and extend prior, more limited, studies on nuclear SSU and LSU rDNA genes and plastid-encoded rbcL and atpB. The phylogenetic tree suggests which classical taxonomic characters are most misleading and provides a framework for molecular studies of the cell cycle-related and other alterations that have engendered diversity in both vegetative and sexual colony patterns in this classical family. The Volvocaceae (classically including Astrephomene and all species of Gonium) are a coherent family of 40 species of colonial green algae common in freshwater habitats the world over. The genus Volvox, discovered by van Leeuwenhoek 300 years ago, has particularly intrigued biologists because of its peculiar manner of colony formation, involving an inversion superficially similar to the gastrulation of typical animal embryos. Volvox and the other members of the Volvocaceae also represent a novel origin of multicellularity, complete with specialized cell types in an organized, determinate body plan. The family provides an ideal grouping to test molecular methods of phylogenetic assessment. My purpose here is threefold: (i) to derive the evolutionary history of the family from DNA sequence comparisons, using representatives of all of the taxa available, including multiple isolates; (ii) to compare these results with those of previous DNA sequence studies; and (iii) to assess the position of the major facets of development on the phylogenetic tree derived from sequence comparisons to predict evolutionary parallisms that can now be tested utilizing molecular techniques.I sequenced the internal transcribed spacer (ITS) sequence ITS-1 and ITS-2 regions of the nuclear rRNA cistron because previous results with Volvocales have demonstrated that they are Ͼ10-fold more variable than ...

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

Phylogenetic analysis of “Volvocacae” for comparative genetic studies

Coleman

1999

Proc. Natl. Acad. Sci. U.S.A.

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“…The mud came from two small pools of freshwater adjacent to a large hypersaline lake (Cha-gan-nur, Hao-tong-yin) in Inner Mongolia. Mating types of Mongolia 4 and 1 were determined by crossing with Alaska 1 and 2 strains (Fabry et al 1998), whereas those of Kaneko3 and -4 were tested against Mongolia 4 and 1.…”

Section: Experimental Organisms and Culture And Mating Methodsmentioning

confidence: 99%

Identification of the Minus-Dominance Gene Ortholog in the Mating-Type Locus of Gonium pectorale

et al. 2008

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The evolution of anisogamy/oogamy in the colonial Volvocales might have occurred in an ancestral isogamous colonial organism like Gonium pectorale. The unicellular, close relative Chlamydomonas reinhardtii has a mating-type (MT) locus harboring several mating-type-specific genes, including one involved in mating-type determination and another involved in the function of the tubular mating structure in only one of the two isogametes. In this study, as the first step in identifying the G. pectorale MT locus, we isolated from G. pectorale the ortholog of the C. reinhardtii mating-type-determining minus-dominance (CrMID) gene, which is localized only in the MT À locus. 39-and 59-RACE RT-PCR using degenerate primers identified a CrMID-orthologous 164-amino-acid coding gene (GpMID) containing a leucine-zipper RWP-RK domain near the C-terminal, as is the case with CrMID. Genomic Southern blot analysis showed that GpMID was coded only in the minus strain of G. pectorale. RT-PCR revealed that GpMID expression increased during nitrogen starvation. Analysis of F 1 progeny suggested that GpMID and isopropylmalate dehydratase LEU1S are tightly linked, suggesting that they are harbored in a chromosomal region under recombinational suppression that is comparable to the C. reinhardtii MT locus. However, two other genes present in the C. reinhardtii MT locus are not linked to the G. pectorale LEU1S/MID, suggesting that the gene content of the volvocalean MT loci is not static over time. Inheritance of chloroplast and mitochondria genomes in G. pectorale is uniparental from the plus and minus parents, respectively, as is also the case in C. reinhardtii.

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“…Of these, the first internal transcribed spacer (ITS1) diverges rapidly between closely related species, which has enabled it to be utilized for phylogenetic studies at or below the species level (e.g., Fabry et al 1999;Rodriguez-Perez et al 2006). Despite some success at investigating population relationships, intraindividual variation is common for this spacer, and unless a high level of sequence homogeneity has been maintained within species, it can obscure the resolution of phylogenetic trees (Miller et al 1996;Famà et al 2000).…”

Section: Introductionmentioning

confidence: 99%

Internal Repetition and Intraindividual Variation in the rDNA ITS1 of the Anopheles punctulatus Group (Diptera: Culicidae): Multiple Units and Rates of Turnover

Bower

Cooper²,

Beebe

2009

J Mol Evol

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The rapid divergence of repetitive sequences makes them desirable markers for phylogenetic studies of closely related groups, provided that a high level of sequence homogeneity has been maintained within species. Intraspecific polymorphisms are found in an increasing number of studies now, and this highlights the need to determine why these occur. In this study we examined intraindividual variation present in the first ribosomal internal transcribed spacer (ITS1) from a group of cryptic mosquito species. Individuals of the Anopheles punctulatus group contained multiple ITS1 length variants that ranged from 1.2 to 8.0 kb. Nucleotide and copy number variation for several homologous internal repeats is common, yet the intraspecific sequence divergence of cloned PCR isolates is comparable to that of other mosquito species (*0.2-1.5%). Most of the length variation is comprised of a 5 0 -ITS1 repeat that was identified as a duplication of a conserved ITS2 region. Secondary structure conservation for this repeat is pronounced and several repeat types that are highly homogenized have formed. Significant interspecific divergence indicates a high rate of evolutionary change for this spacer. A maximum likelihood tree constructed here was congruent with previous phylogenetic hypotheses and suggests that concerted evolution is also accompanied by interpopulation divergence. The lack of interindividual differences and the presence of homogenized internal repeats suggest that a high rate of turnover has reduced the overall level of variation. However, the intraindividual variation also appears to be maintained by the absence of a single turnover rate and the complex dynamics of ongoing recombination within the spacer.

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Intraspecies Analysis: Comparison of ITS Sequence Data and Gene Intron Sequence Data with Breeding Data for a Worldwide Collection of Gonium pectorale

Cited by 63 publications

References 18 publications

Phylogenetic analysis of “Volvocacae” for comparative genetic studies

Phylogenetic analysis of “Volvocacae” for comparative genetic studies

Identification of the Minus-Dominance Gene Ortholog in the Mating-Type Locus of Gonium pectorale

Internal Repetition and Intraindividual Variation in the rDNA ITS1 of the Anopheles punctulatus Group (Diptera: Culicidae): Multiple Units and Rates of Turnover

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