Phylogenetic analysis of Brassiceae based on the nucleotide sequences of the S-locus related gene, SLR1

Abstract

Nucleotide sequences of orthologs of the S-locus related gene, SLR1, in 20 species of Brassicaceae were determined and compared with the previously reported SLR1 sequences of six species. Identities of deduced amino-acid sequences with Brassica oleracea SLR1 ranged from 66.0% to 97.6%, and those with B. oleracea SRK and SLR2 were less than 62% and 55%, respectively. In multiple alignment of deduced amino-acid sequences, the 180-190th amino-acid residues from the initial methionine were highly variable, this variable region corresponding to hypervariable region I of SLG and SRK. A phylogenetic tree based on the deduced amino-acid sequences showed a close relationship of SLR1 orthologs of species in the Brassicinae and Raphaninae. Brassica nigra SLR1 was found to belong to the same clade as Sinapis arvensis and Diplotaxis siifolia, while the sequences of the other Brassica species belonged to another clade together with B. oleracea and Brassica rapa. The phylogenetic tree was similar to previously reported trees constructed using the data of electrophoretic band patterns of chloroplast DNA, though minor differences were found. Based on synonymous substitution rates in SLR1, the diversification time of SLR1 orthologs between species in the Brassicinae was estimated. The evolution and function of SLR1 and the phylogenetic relationship of Brassiceae plants are discussed.

Homeologous Recombination Plays a Major Role in Chromosome Rearrangements That Occur During Meiosis of Brassica napus Haploids

“…This confirms that the A and C homeologous regions of B. napus, which diverged $4 MYA (Inaba and Nishio 2002), remain very closely related. This assertion is in agreement with the fact that very few gene rearrangements differentiate the homeologous regions of B. napus (Rana et al 2004).…”

“…However, paralogous regions seem to recombine less than homeologous regions; this is in agreement with the fact that paralogous regions within B. oleracea and B. rapa genomes diverged four to five times earlier than homeologous regions. Then, more gene rearrangements differentiated paralogous from homeologous regions (Inaba and Nishio 2002;Rana et al 2004;Town et al 2006;Yang et al 2006).…”

A and C Genome Distinction and Chromosome Identification inBrassica napusby Sequential Fluorescencein SituHybridization and Genomicin SituHybridization

“…Molecular phylogenetic analyses of the tribe Brassiceae within the family Brassicaceae place B. nigra in a different lineage to B. oleracea and B. rapa (Warwick and Black 1991). These lineages split 7.9 million years ago (MYA) (Lysak et al 2005) whereas B. oleracea and B. rapa diverged more recently, 3.75 MYA (Inaba and Nishio 2002). This close relationship is also indicated from FISH experiments because only a few probes appear to be species specific.…”

Genetic Differentiation, Molecular Phylogenetic Analysis, and Ethnobotanical Study of <i>Eutrema japonicum</i> and <i>E. tenue</i> in Japan and <i>E. yunnanense</i> in China

“…et Coss., and white mustard, Sinapis alba. The comprehensive interspecific phylogeny of the Brassicaceae has been analyzed using molecular approaches (Inaba and Nishio, 2002;Pradhan et al, 1992;Warwick and Black, 1991;Yang et al, 1999). However, only two phylogenetic studies have included Eutrema species (E. halophilum C. A. Mey.…”