Reconstruction of the Brassica rapa ancestral genome.

The Brassicaceae family includes important crop plants as well as the model plant Arabidopsis thaliana. The evolutionary history of this family is characterized by a number of whole genome duplications (WGDs), and the relationships within the family have been a matter of study and debate for decades. Recent multi-gene phylogenetic analyses have revealed that the Brassicaceae family can be divided into three main lineages (reviewed in Franzke et al., 2011). The Brassiceae tribe including Brassica rapa is found in lineage II, whereas A. thaliana is in lineage I of the Brassicaceae family. The ancestral genome of lineage I, referred to as the Ancestral Crucifer Karyotype (ACK), is thought to have contained eight chromosomes, whereas that of lineage II, the ProtoCalepineae Karyotype (PCK), was likely n5 7 (Mandáková and Lysak, 2008). A subsequent translocation event gave rise to the translocation PCK (tPCK) found in some tribes of lineage II. The mesohexaploid B. rapa contains ten chromosomes, which are made up of three subgenomes derived from a hexaploid ancestor. Now, Cheng et al. (pages 1541– 1554) have made use of the availability of the full B. rapa genome (Wang et al., 2011) to reconstruct the ancestral genome of the Brassica genus. Cheng and co-workers compared the arrangement of ancestral genomic blocks in the B. rapa subgenomes (see Figure) to the arrangements in the predicted ancestral karyotypes ACK, PCK and tPCK, finding that the tPCK was most similar in structure to the three B. rapa subgenomes. The authors next looked for paleocentromeres. If the three B. rapa subgenomes were derived from triplication of an n 5 7 tPCK ancestor, there should be 21 paleocentromeric regions in the B. rapa genome. Cheng et al. were able to identify 18 paleocentromeres and found that all 10 modern B. rapa centromeres were derived from those ancestral regions (see Figure). Cheng et al. went on to examine whether similar arrangements of genomic blocks were also present in other lineage II species for which whole-genome sequences or geneticmapsare available. This analysis showed that the tPCKwas likely the ancestral genome not just for Brassica and the Brassiceae tribe, but also for the recently sequenced genomes of Schrenkiella and Thellungiella, which represent other tribes. This work emphasizes the power of complete genome sequence data to elucidate evolutionary history and answer longstanding questions like those surrounding the chromosome number and genome structure of the Brassica ancestors. By establishing the tPCK-like n5 7 genome as the ancestral genome of the Brassiceae tribe, it provides a reference for future analyses of the agronomically and scientifically important Brassicaceae family. Nancy R. Hofmann Science Editor [email protected]