Phylogenetic utility of the nuclear gene arginine decarboxylase: an example from Brassicaceae

Galloway, Gregory L.; Malmberg, Russell L.; Price, Robert A.

doi:10.1093/oxfordjournals.molbev.a025859

Cited by 125 publications

(114 citation statements)

References 42 publications

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“…It is polyphyletic. Some genetic studies as done on the tribes, [27] [69] [71] [72] [73]. In the present study the tribe Lepideae (Coronopus didymus) are placed with some species of tribe Brassiceae, this agree with some traditional studies as [5] which put them in the same tribe but in different sub-tribes, or placed with species of tribe Alysseae (Farsetia burtonae) in the same group.…”

Section: Discussionsupporting

confidence: 88%

Significance of Fruit and Seed Coat Morphology in Taxonomy and Identification for Some Species of Brassicaceae

Gabr¹

2018

AJPS

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Fruit, seed morphology and seed coat sculpturing were recorded for 10 species belongs to 9 genera and five tribes of Brassicaceae in eastern region of Saudi Arabia by using light microscope (LM) and scanning electron microscope (SEM). Four seed patterns were recognized based on surface sculpturing pattern; Reticulate, with four subtypes, undulate, verrucate and ocellate. The results of numerical analysis showed that species were grouped into two major clusters and each cluster divided into two groups. The cluster analysis indicates that the characters of fruit and seed are very important characters for identification and taxonomical classification of the tribes. The results indicate that the most tribes of Brassicaceae are polyphyletic, and some are related to each other's as Lepidieae, Alyssieae and Sisymbrieae.

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Section: Discussionsupporting

confidence: 88%

Significance of Fruit and Seed Coat Morphology in Taxonomy and Identification for Some Species of Brassicaceae

Gabr¹

2018

AJPS

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“…Analyses assumed a general time-reversible model of sequence evolution, with γ-distributed rate heterogeneity; partitions in the combined matrix were allowed to evolve independently. The topology and clade support in the resulting trees are consistent with previously published phylogenetic estimates using ndhF (17) and other plastid (49) and nuclear (3,22,50,51) markers.…”

Section: Methodssupporting

confidence: 87%

Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana

Beilstein

Nagalingum

Clements

et al. 2010

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

412

467

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Dated molecular phylogenies are the basis for understanding species diversity and for linking changes in rates of diversification with historical events such as restructuring in developmental pathways, genome doubling, or dispersal onto a new continent. Valid fossil calibration points are essential to the accurate estimation of divergence dates, but for many groups of flowering plants fossil evidence is unavailable or limited. Arabidopsis thaliana, the primary genetic model in plant biology and the first plant to have its entire genome sequenced, belongs to one such group, the plant family Brassicaceae. Thus, the timing of A. thaliana evolution and the history of its genome have been controversial. We bring previously overlooked fossil evidence to bear on these questions and find the split between A. thaliana and Arabidopsis lyrata occurred about 13 Mya, and that the split between Arabidopsis and the Brassica complex (broccoli, cabbage, canola) occurred about 43 Mya. These estimates, which are two-to threefold older than previous estimates, indicate that gene, genomic, and developmental evolution occurred much more slowly than previously hypothesized and that Arabidopsis evolved during a period of warming rather than of cooling. We detected a 2-to 10-fold shift in species diversification rates on the branch uniting Brassicaceae with its sister families. The timing of this shift suggests a possible impact of the Cretaceous-Paleogene mass extinction on their radiation and that Brassicales codiversified with pierid butterflies that specialize on mustard-oil-producing plants.he most important genetic model in plant biology is Arabidopsis thaliana. It is the first plant to have its entire genome sequenced, and it serves as a key comparison point with other eukaryotic genomes. A. thaliana is diploid and has a small genome distributed on just five chromosomes, considerations in its choice as a model (1). The age of the Arabidopsis crown group (CG), previously estimated at 5.8-3 Mya (2, 3), and of splits within Brassicaceae have been used to understand the pace of evolution in genes affecting self-incompatibility (4, 5), the rate of change in signal transduction and gene expression (6, 7), the persistence of shared chromosomal rearrangements in A. thaliana and Brassica oleracea (8), the tempo of evolution of miRNA sequences (9), the evolution of pierid butterflies specializing in plants that produce mustard oils (10), and the ages of wholegenome duplication (WGD) events giving rise to gene pairs in Arabidopsis (11). As genomes of additional Brassicaceae (e.g., Capsella rubella) and other Brassicales (e.g., Carica papaya) (12) are sequenced, the importance of robust estimates of divergence dates relating these genomes to one another and to the geological record increases substantially.The accuracy of divergence times inferred from sequence data depends on valid, verifiable fossils to calibrate phylogenetic trees. Previous dates for the origin of Arabidopsis relied on the report of fossil pollen assigned to the genus Rori...

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“…However, our estimate is in good agreement with the work of Galloway et al (1998) who studied the phylogeny of 13 Brassicaceae species using arginine decarboxylase (Adc) nuclear genes. Most of the sampled crucifer species have orthologs of both of the two paralogous Arabidopsis Adc genes, which are located in a pair of recently duplicated blocks on chromosomes 2 and 4.…”

Section: Genome Research 141supporting

confidence: 91%

A Recent Polyploidy Superimposed on Older Large-Scale Duplications in the Arabidopsis Genome

Blanc

Hokamp²,

Wolfe³

2003

Genome Res.

657

697

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The Arabidopsis genome contains numerous large duplicated chromosomal segments, but the different approaches used in previous analyses led to different interpretations regarding the number and timing of ancestral large-scale duplication events. Here, using more appropriate methodology and a more recent version of the genome sequence annotation, we investigate the scale and timing of segmental duplications in Arabidopsis. We used protein sequence similarity searches to detect duplicated blocks in the genome, used the level of synonymous substitution between duplicated genes to estimate the relative ages of the blocks containing them, and analyzed the degree of overlap between adjacent duplicated blocks. We conclude that the Arabidopsis lineage underwent at least two distinct episodes of duplication. One was a polyploidy that occurred much more recently than estimated previously, before the Arabidopsis/Brassica rapa split and probably during the early emergence of the crucifer family (24-40 Mya). An older set of duplicated blocks was formed after the monocot/dicot divergence, and the relatively low level of overlap among these blocks indicates that at least some of them are remnants of a larger duplication such as a polyploidy or aneuploidy.

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Phylogenetic utility of the nuclear gene arginine decarboxylase: an example from Brassicaceae

Cited by 125 publications

References 42 publications

Significance of Fruit and Seed Coat Morphology in Taxonomy and Identification for Some Species of Brassicaceae

Significance of Fruit and Seed Coat Morphology in Taxonomy and Identification for Some Species of Brassicaceae

Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana

A Recent Polyploidy Superimposed on Older Large-Scale Duplications in the Arabidopsis Genome

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