Sequence-Level Analysis of the Diploidization Process in the TriplicatedFLOWERING LOCUS CRegion ofBrassica rapa

Abstract

Strong evidence exists for polyploidy having occurred during the evolution of the tribe Brassiceae. We show evidence for the dynamic and ongoing diploidization process by comparative analysis of the sequences of four paralogous Brassica rapa BAC clones and the homologous 124-kb segment of Arabidopsis thaliana chromosome 5. We estimated the times since divergence of the paralogous and homologous lineages. The three paralogous subgenomes of B. rapa triplicated 13 to 17 million years ago (MYA), very soon after the Arabidopsis and Brassica divergence occurred at 17 to 18 MYA. In addition, a pair of BACs represents a more recent segmental duplication, which occurred ;0.8 MYA, and provides an exception to the general expectation of three paralogous segments within the B. rapa genome. The Brassica genome segments show extensive interspersed gene loss relative to the inferred structure of the ancestral genome, whereas the Arabidopsis genome segment appears little changed. Representatives of all 32 genes in the Arabidopsis genome segment are represented in Brassica, but the hexaploid complement of 96 has been reduced to 54 in the three subgenomes, with compression of the genomic region lengths they occupy to between 52 and 110 kb. The gene content of the recently duplicated B. rapa genome segments is identical, but intergenic sequences differ.

Fast Diploidization in Close Mesopolyploid Relatives ofArabidopsis

“…In the nigra (B) and oleracea (C) genomes, only seven (29%) (Panjabi et al, 2008) and eight (33%) (Kaczmarek et al, 2009) GBs were reported as three or more homoeologous copies in B. juncea and B. oleracea, respectively. Comparing these data with 83 to 100% of duplicated GBs retained in the Australian species, triplicated Brassiceae genomes show faster diploidization and/or originated earlier (13 to 17 mya suggested by Yang et al, 2006). A loss of paralogous gene copies was documented herein for all three single-copy nuclear genes and all analyzed species.…”

“…A loss of paralogous gene copies was documented herein for all three single-copy nuclear genes and all analyzed species. Extensive gene loss was also found in the mesopolyploid genomes of B. rapa (Yang et al, 2006) and B. oleracea (Town et al, 2006).…”

Karyotype and Identification of All Homoeologous Chromosomes of AllopolyploidBrassica napusand Its Diploid Progenitors

“…In addition, these karyotypes will aid the ongoing sequencing of Brassica genomes by integrating the genetic, physical, and cytogenetic maps, as we have demonstrated for chromosome A7 . Because the genus Brassica shares a wholegenome triplication event (Lukens 2004;Lysak et al 2005;Parkin et al 2005;Yang et al 2006;Mandakova and Lysak 2008;Cheung et al 2009;Trick et al 2009), repetitive sequence blocks and molecular fingerprinting errors have made it difficult to assemble the physical map and BAC contigs in Brassica (Gregory et al 1997;Mun et al 2008). Using the karyotype approach presented here, individual BAC clones can be accurately localized in detail to chromosomes and linkage groups using FISH.…”

Comparative sequence analysis for Brassica oleracea with similar sequences in B. rapa and Arabidopsis thaliana

“…Comparative mapping between the genomes of crop plants and their respective model species is becoming a common approach for the identification of markers and candidate genes for mapping studies and to expedite positional gene cloning. Genome sequencing projects for B. rapa and B. oleracea are in the process, providing an opportunity to analyze and study the genome changes associated with the origin and evolution of these species in relation to A. thaliana (Ayele et al 2005;Lim et al 2006;Yang et al 2006;Hong et al 2006).…”