Duplicate Genes and the Root of Angiosperms, with an Example Using Phytochrome Sequences

Donoghue, Michael J.; Mathews, Sarah

doi:10.1006/mpev.1998.0511

Cited by 32 publications

(23 citation statements)

References 88 publications

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“…Although we are confident with our choice of outgroups, an alternative method for rooting the tree would be to use the duplication of the GBSSI gene (Donoghue and Mathews, 1998), as our results fulfill their criteria for using gene duplications to root trees. Their first criterion that all taxa within the ingroup contain duplicate genes, although not fulfilled by the sequences that we have obtained, can be inferred from the Southern hybridization analysis that demonstrates the presence of at least two GBSSI loci in all four subfamilies (Fig.…”

Section: Multiple Gbssi Loci In Rosaceaementioning

confidence: 55%

The Granule-Bound Starch Synthase (GBSSI) Gene in the Rosaceae: Multiple Loci and Phylogenetic Utility

Evans

Alice

Campbell

et al. 2000

Molecular Phylogenetics and Evolution

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Section: Multiple Gbssi Loci In Rosaceaementioning

confidence: 55%

The Granule-Bound Starch Synthase (GBSSI) Gene in the Rosaceae: Multiple Loci and Phylogenetic Utility

Evans

Alice

Campbell

et al. 2000

Molecular Phylogenetics and Evolution

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“…Unfortunately, which repeats from the outgroup sequences aligned with which repeats from the ingroup sequences could not be determined. Therefore, duplicate gene rooting (Gogarten et al, 1989;Iwabe et al, 1989;Donoghue and Mathews, 1998) was used to root the gene tree between the vegetative-and reproductive-expressed paralogs.…”

Section: Sequence Alignment and Phylogenetic Analysismentioning

confidence: 99%

Whole-Genome Comparison of Leucine-Rich Repeat Extensins in Arabidopsis and Rice. A Conserved Family of Cell Wall Proteins Form a Vegetative and a Reproductive Clade,

et al. 2003

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We have searched the Arabidopsis and rice (Oryza sativa) genomes for homologs of LRX1, an Arabidopsis gene encoding a novel type of cell wall protein containing a leucine-rich repeat (LRR) and an extensin domain. Eleven and eight LRX (LRR/EXTENSIN) genes have been identified in these two plant species, respectively. The LRX gene family encodes proteins characterized by a short N-terminal domain, a domain with 10 LRRs, a cysteine-rich motif, and a variable C-terminal extensin-like domain. Phylogenetic analysis performed on the conserved domains indicates the existence of two major clades of LRX proteins that arose before the eudicot/monocot divergence and then diversified independently in each lineage. In Arabidopsis, gene expression studies by northern hybridization and promoter::uidA fusions showed that the two phylogenetic clades represent a specialization into "reproductive" and "vegetative" LRXs. The four Arabidopsis genes of the "reproductive" clade are specifically expressed in pollen, whereas the seven "vegetative" genes are predominantly expressed in various sporophytic tissues. This separation into two expression classes is also supported by previous studies on maize (Zea mays) and tomato (Lycopersicon esculentum) LRX homologs and by information on available rice ESTs. The strong conservation of the amino acids responsible for the putative recognition specificity of the LRR domain throughout the family suggests that the LRX proteins interact with similar ligands.With the completion of the Arabidopsis genome sequence, it became clear that many Arabidopsis genes are members of multigene families. Although this had already been suggested by the analysis of expressed sequence tag (EST) databases and by classical gene searches, the availability of the full gene set of a plant provides the unique opportunity to get a complete inventory of all the members of a gene family. Among the 25,500 genes predicted in the Arabidopsis genome, 65% are members of a multigene family and 37% belong to families of more than five members (Arabidopsis Genome Initiative, 2000). Although the predicted total gene number of Arabidopsis is significantly larger than that of other sequenced multicellular eukaryotes such as Caenorhabditis elegans (19,000; C. elegans Sequencing Consortium, 1998) or Drosophila melanogaster (13,600; Adams et al., 2000), the absolute number of gene families and singletons (11,601 in Arabidopsis) is comparable in all these organisms (Arabidopsis Genome Initiative, 2000). This indicates that frequent gene duplications and consequently large gene families are a distinctive feature of the Arabidopsis genome, and possibly of all plant genomes. With the recent publication of a high-quality draft from two different subspecies, rice (Oryza sativa) is the second plant whose genome can be comprehensively investigated. Depending on the stringency applied in gene prediction, the rice genome contains between 32,277 and 61,668 genes (Goff et al., 2002;Yu et al., 2002). With 77% of the genes distributed in about 15,000 m...

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“…But lately, exciting new methods and data are available that have enormous potential to resolve this set of problems. New kinds of fossils have been discovered from critical times (2-4); new algorithms are available for the rapid comparative analysis of all kinds of data (5), and molecular genetics is providing data on nucleic acid sequences and homeotic genes like the MADS family (6)(7)(8)(9)(10)(11)(12). These allow invaluable insights into homology of floral organs.…”

mentioning

confidence: 99%

“…Actually the article referred to a consensus of independent studies of extant angiosperms. This consensus included four independent analyses that pointed to the same result: Amborella at the base of the flowering plants (7)(8)(9)(10)(11)(12). Although not all scientists were convinced that the matter of the basal angiosperm was settled, the response was dramatic with one morphologist heralding the identification of a basal angiosperm as ''the answer'' (15), even though it conflicted with his own previous analyses (16).…”

mentioning

confidence: 99%

Progress in understanding angiosperm history, success, and relationships: Darwin's abominably “perplexing phenomenon”

Crepet

2000

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

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Duplicate Genes and the Root of Angiosperms, with an Example Using Phytochrome Sequences

Cited by 32 publications

References 88 publications

The Granule-Bound Starch Synthase (GBSSI) Gene in the Rosaceae: Multiple Loci and Phylogenetic Utility

The Granule-Bound Starch Synthase (GBSSI) Gene in the Rosaceae: Multiple Loci and Phylogenetic Utility

Whole-Genome Comparison of Leucine-Rich Repeat Extensins in Arabidopsis and Rice. A Conserved Family of Cell Wall Proteins Form a Vegetative and a Reproductive Clade,

Progress in understanding angiosperm history, success, and relationships: Darwin's abominably “perplexing phenomenon”

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