title: Two plastid DNA lineages--Rapa/Oleracea and Nigra--within the tribe Brassiceae can be best explained by reciprocal crosses at hexaploidy: evidence from divergence times of the plastid genomes and R-block genes of the A and B genomes of Brassica juncea.
abstract: Brassica species (tribe Brassiceae) belonging to U's triangle--B. rapa (AA), B. nigra (BB), B. oleracea (CC), B. juncea (AABB), B. napus (AACC) and B. carinata (BBCC)--originated via two polyploidization rounds: a U event producing the three allopolyploids, and a more ancient b genome-triplication event giving rise to the A-, B-, and C-genome diploid species. Molecular mapping studies, in situ hybridization, and genome sequencing of B. rapa support the genome triplication origin of tribe Brassiceae, and suggest that these three diploid species diversified from a common hexaploid ancestor. Analysis of plastid DNA has revealed two distinct lineages--Rapa/Oleracea and Nigra--that conflict with hexaploidization as a single event defining the tribe Brassiceae. We analysed an R-block region of A. thaliana present in six copies in B. juncea (AABB), three copies each on A- and B-genomes to study gene fractionation pattern and synonymous base substitution rates (Ks values). Divergence time of paralogues within the A and B genomes and homoeologues between the A and B genomes was estimated. Homoeologous R blocks of the A and B genomes exhibited high gene collinearity and a conserved gene fractionation pattern. The three progenitors of diploid Brassicas were estimated to have diverged approximately 12 mya. Divergence of B. rapa and B. nigra, calculated from plastid gene sequences, was estimated to have occurred approximately 12 mya, coinciding with the divergence of the three genomes participating in the b event. Divergence of B. juncea A and B genome homoeologues was estimated to have taken place around 7 mya. Based on divergence time estimates and the presence of distinct plastid lineages in tribe Brassiceae, it is concluded that at least two independent triplication events involving reciprocal crosses at the time of the b event have given rise to Rapa/Oleracea and Nigra lineages.
authors.affiliation: Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India.
authors.forename: Sarita
authors.initials: S
authors.lastname: Sharma
authors.affiliation: Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India.
authors.forename: K Lakshmi
authors.initials: KL
authors.lastname: Padmaja
authors.affiliation: Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India.
authors.forename: Vibha
authors.initials: V
authors.lastname: Gupta
authors.affiliation: Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India.
authors.forename: Kumar
authors.initials: K
authors.lastname: Paritosh
authors.affiliation: Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India; Department of Genetics, University of Delhi South Campus, New Delhi, India.
authors.forename: Akshay K
authors.initials: AK
authors.lastname: Pradhan
authors.affiliation: Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India; Department of Genetics, University of Delhi South Campus, New Delhi, India.
authors.forename: Deepak
authors.initials: D
authors.lastname: Pental
mesh_terms: D019607:Brassicaceae / Q000145:classification / Q000235:genetics*; D002874:Chromosome Mapping; D019295:Computational Biology; D003433:Crosses, Genetic; D019143:Evolution, Molecular; D017343:Genes, Plant; D014644:Genetic Variation; D054627:Genome, Plastid; D008957:Models, Genetic; D010802:Phylogeny; D018087:Plastids / Q000235:genetics*; D011123:Polyploidy; D032107:Populus / Q000235:genetics; D031822:Portulaca / Q000235:genetics; D017422:Sequence Analysis, DNA