A near-complete genome assembly of the allotetrapolyploid Cenchrus fungigraminus(JUJUNCAO)provides insights into its evolution and C4 photosynthesis

JUJUNCAO(Cenchrus fungigraminus;2n=4x=28)is a Cenchrus grass with the highest biomass production among cultivated plants,and it can be used for mushroom cultivation,animal feed,and biofuel production.Here,we report a nearly complete genome assembly of JUJUNCAO and reveal that JUJUNCAO is an allopolyploid that originated2.7 million years ago(mya).Its genome consists of two subgenomes,and subgenome A shares high collinear synteny with pearl millet.We also investigated the genome evolution of JUJUNCAO and suggest that the ancestral karyotype of Cenchrus split into the A and B ancestral karyotypes of JUJUNCAO.Comparative transcriptome and DNA methylome analyses revealed functional divergence of homeologous gene pairs between the two subgenomes,which was a further indication of asymmetric DNA methylation.The three types of centromeric repeat in the JUJUNCAO genome(CEN137,CEN148,and CEN156)may have evolved independently within each subgenome,with some introgressions of CEN156 from the B to the A subgenome.We investigated the photosynthetic characteristics of JUJUNCAO,revealing its typical C4 Kranz anatomy and high photosynthetic efficiency.NADP-ME and PEPCK appear to cooperate in the major C4 decarboxylation reaction of JUJUNCAO,which is different from other C4 photosynthetic subtypes and may contribute to its high photosynthetic efficiency and biomass yield.Taken together,our results provide insights into the highly efficient photosynthetic mechanism of JUJUNCAO and provide a valuable reference genome for future genetic and evolutionary studies,as well as genetic improvement of Cenchrus grasses.

Involvement of a Putative Bipartite Transit Peptide in Targeting Rice Pheophorbide a Oxygenase into Chloroplasts for Chlorophyll Degradation during Leaf Senescence

Leaf senescence is one of the major factors contributing to the productivity and the grain quality in crops. The regulatory mechanism of leaf senescence remains largely unknown. Here, we report the identification and characterization of a rice e_aarly senescence 1 （easl） mutant, which displayed an early leaf senescence phenotype, accompanying by dwarfism and reduced tiller number, eventually leading to the reduction of grain yield. Map-based cloning revealed that the nuclear gene EAS1 encodes a pheophorbide a oxygenase （PaO）, a key enzyme for chlorophyll breakdown. A highly conserved Thr residue of PaO was mutated into Ile in the easl mutant. Phylogenetic analysis indicates that PaO is an evolutionarily conserved protein, and EAS1 is 68% identical to the Arabidopsis ACCERLERATED CELL DEATH （ACD1） protein. Unlike ACD1 that contains a single transit peptide, EAS1 contains two putative transit peptides at its N-ter- minus, which are essential for its functionality, suggesting that targeting of EAS1 to the chloroplast is likely mediated by a putative bipartite transit peptide. Consistently, only a short version of EAS1 lacking the first putative transit peptide, but not the full-length EAS1, was capable of rescuing the Arabidopsis acdl mutant phenotype. These results suggest that rice EASI represents a functional PaO, which is involved in chlorophyl/degradation and may utilize a unique mechanism for its import into the chloroplast.

LATERAL ROOTLESS2, a Cyclophilin Protein, Regulates Lateral Root Initiation and Auxin Signaling Pathway in Rice

Dear Editor, Cyclophilins （CYP） are a class of highly conserved pepti- dyl-prolyl cis-trans isomerases （PPlases） that play important roles in various biological processes in eukaryotes （reviewed in Romano et al. （2004））. In higher plants, a conserved sin- gle domain cyclophilin has been identified as a novel com- ponent of the auxin signaling pathway by analyzing the tomato diageotropica （dgt） mutant （Ivanchenko et al., 2006; Oh et al., 2006）. The dgt mutant displays a lateral-rootless and auxin-resistant phenotype （Ivanchenko et aL, 2006）. Further studies revealed that mutations in the DGT-like genes of Physcomitrella patens also exhibited an auxin-resistant phenotype, suggesting a conserved role of DGT-like proteins in auxin signaling. Moreover,