Analysis of 142 genes resolves the rapid diversification of the rice genus.
BACKGROUND
The completion of rice genome sequencing has made rice and its wild relatives an attractive system for biological studies. Despite great efforts, phylogenetic relationships among genome types and species in the rice genus have not been fully resolved. To take full advantage of rice genome resources for biological research and rice breeding, we will benefit from the availability of a robust phylogeny of the rice genus.


RESULTS
Through screening rice genome sequences, we sampled and sequenced 142 single-copy genes to clarify the relationships among all diploid genome types of the rice genus. The analysis identified two short internal branches around which most previous phylogenetic inconsistency emerged. These represent two episodes of rapid speciation that occurred approximately 5 and 10 million years ago (Mya) and gave rise to almost the entire diversity of the genus. The known chromosomal distribution of the sampled genes allowed the documentation of whole-genome sorting of ancestral alleles during the rapid speciation, which was responsible primarily for extensive incongruence between gene phylogenies and persisting phylogenetic ambiguity in the genus. Random sample analysis showed that 120 genes with an average length of 874 bp were needed to resolve both short branches with 95% confidence.


CONCLUSIONS
Our phylogenomic analysis successfully resolved the phylogeny of rice genome types, which lays a solid foundation for comparative and functional genomic studies of rice and its relatives. This study also highlights that organismal genomes might be mosaics of conflicting genealogies because of rapid speciation and demonstrates the power of phylogenomics in the reconstruction of rapid diversification.
Zou
Xin-Hui
XH
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China. zouxh@ibcas.ac.cn
Zhang
Fu-Min
FM
Zhang
Jian-Guo
JG
Zang
Li-Li
LL
Tang
Liang
L
Wang
Jun
J
Sang
Tao
T
Ge
Song
S
D001483:Base Sequence; D001947:Breeding; D017343:Genes, Plant; D014644:Genetic Variation; D008969:Molecular Sequence Data; D012275:Oryza / Q000145:classification* / Q000235:genetics*; D010802:Phylogeny