Hironori Nagano

Reconstruction of putative DNA virus from endogenous rice tungro bacilliform virus-like sequences in the rice genome: implications for integration and evolution.

BackgroundPlant genomes contain various kinds of repetitive sequences such as transposable elements, microsatellites, tandem repeats and virus-like sequences. Most of them, with the exception of virus-like sequences, do not allow us to trace their origins nor to follow the process of their integration into the host genome. Recent discoveries of virus-like sequences in plant genomes led us to set the objective of elucidating the origin of the repetitive sequences. Endogenous rice tungro bacilliform virus (RTBV)-like sequences (ERTBVs) have been found throughout the rice genome. Here, we reconstructed putative virus structures from RTBV-like sequences in the rice genome and characterized to understand evolutionary implication, integration manner and involvements of endogenous virus segments in the corresponding disease response.ResultsWe have collected ERTBVs from the rice genomes. They contain rearranged structures and no intact ORFs. The identified ERTBV segments were shown to be phylogenetically divided into three clusters. For each phylogenetic cluster, we were able to make a consensus alignment for a circular virus-like structure carrying two complete ORFs. Comparisons of DNA and amino acid sequences suggested the closely relationship between ERTBV and RTBV. The Oryza AA-genome species vary in the ERTBV copy number. The species carrying low-copy-number of ERTBV segments have been reported to be extremely susceptible to RTBV. The DNA methylation state of the ERTBV sequences was correlated with their copy number in the genome.ConclusionsThese ERTBV segments are unlikely to have functional potential as a virus. However, these sequences facilitate to establish putative virus that provided information underlying virus integration and evolutionary relationship with existing virus. Comparison of ERTBV among the Oryza AA-genome species allowed us to speculate a possible role of endogenous virus segments against its related disease.

Diversification in flowering time due to tandem FT-like gene duplication, generating novel Mendelian factors in wild and cultivated rice.

The complex structure of a single Mendelian factor widespread in the Asian cultivated rice (Oryza sativa) and its wild progenitor (Oryza rufipogon) that caused diverse phenotypes in the timing of flowering under natural field conditions was investigated in near isogenic lines. These near isogenic lines showed differences in flowering time despite all eight accessions collected from tropical regions possessing a recessive gene allelic to the se‐pat gene. Fine mapping in two of these near‐isogenic lines revealed that cultivated (Patpaku) and wild (W593) accessions had three and two linked quantitative trait loci (QTL) in the candidate regions, respectively, showing that Patpaku and W593 possessed linked QTLs with different effects in addition to the commonly‐observed recessive gene (se‐pat). Molecular dissection suggested that the tandemly duplicated FT‐like genes (Hd3a and RFT1) could be the candidate genes for these QTLs. Interestingly, the linked QTLs differed in their epistases, degree of dominance, and genotype × environment interactions. The nucleotide sequences showed that RFT1 has diverged more rapidly than Hd3a during rice evolution, suggesting phenotypic diversification of the two genes. Phylogenetic analysis implied that the se‐pat+ alleles might have emerged in different lineages within O. sativa. The present results strongly suggest that nucleotide divergence and shuffling of the linked QTLs by recombination might have created novel Mendelian factors that probably contribute to responding to local environments.

The sugar beet mitochondrial nad4 gene: an intron loss and its phylogenetic implication in the Caryophyllales

Abstract The sugar beet mitochondrial gene for subunit IV of NADH dehydrogenase (nad4) has been characterized. Unlike the corresponding genes in wheat and turnip, sugar beet nad4 lacks the second intron (nad4-i2). Northern-blot analysis demonstrates transcription of the gene. A total of 19 RNA editing sites were identified in the sugar beet nad4 transcripts; interestingly, there is no editing in the region which flanks the lost intron. This observation is in favour of intron loss via homologous recombination of an edited RNA intermediate. We also found that the nad4-i2 intron is absent from the mitochondrial genomes of all examined members of the Caryophyllales, but present in the closely related orders, Polygonales and Plumbaginales, which suggests that the intron was lost in the common ancestor of the Caryophyllales.

Structural differences in the vicinity of the waxy locus among the Oryza species with the AA-genome: identification of variable regions

Abstract We constructed a fine physical map for a 260-kb rice BAC contig surrounding the waxy locus. In order to identify variable regions within this 260-kb as to the restriction fragments length polymorphisms and copy numbers, sixty overlapping fragments derived from the 260-kb contig were used as probes to compare their corresponding structures among the Oryza species with AA-genome. According to the hybridization patterns, each fragment was classified into four types; true single copy (class 1), single copy with a smear background (class 2), multiple copy without a smear background (class 3), and only a smear background (class 4). Out of 16 single copy (class 1 and class 2) regions obtained in this map, the one site corresponding to wx gave rise to remarkable polymorphisms among AA-genome species in Oryza. In most of the fragments observed as repetitive segments (class 4), we could not find obvious differences in the hybridization pattern. However, interestingly, one site sorted into class-3 showed copy numbers varying among the lines. The lines belonging to O. sativaO. rufipogon, O. meridionalis,and O. longistaminata possessed high-copy numbers of this fragment, whereas only a few bands were detected in the lines from O. glaberrima, O. barthii, and O. glumaepatula. The two variable regions found within the AA-genome species represented genomic dynamisms.

Contrasting allelic distribution of CO/Hd1 homologues in Miscanthus sinensis from the East Asian mainland and the Japanese archipelago

Highlight Homologues of CONSTANS/Heading date 1 were cloned from Miscanthus sinensis and named MsiHd1. MsiHd1a in most Japanese accessions contained non-functional alleles, whereas Asian mainland accessions harboured only functional alleles.

Candidate Gene Approach in Miscanthus spp. for Biorefinery

Cost-effective production of bioethanol and chemicals from lignocellulose, has attracted significant interest around the world. Rhizomatous and perennial warm-season C4 grasses such as Miscanthus spp. are potential dedicated feedstock crops, which are efficient at fixing CO2 in temperate regions and require less fertilizer for cultivation. Among Miscanthus spp., Miscanthus sinensis is the most broadly distributed in Asia. The degree of population differentiation using molecular markers, such as restriction site-associated DNA sequencing single nucleotide polymorphism (SNP) markers, Golden Gate SNPs and ten plastid microsatellite markers, has been evaluated for M. sinensis over its native range. Wide range of genetic variability in Asian Miscanthus germplasm resources was observed, and it would be valuable for the breeding programs. Targets for the improvement of grasses as feedstocks for bio-refineries are modifying biomass cell wall composition to reduce lignin concentrations to improve saccharification, regulation of flowering time for extending the vegetative phase to increase biomass potential and abiotic stresses such as cold tolerance. In this chapter, we outlined our recent research activities on molecular breeding such as candidate gene approach in Miscanthus spp.

Enhancement of the Stimulated Brillouin Scattering of Higher-Order Acoustic Modes in Hole-Assisted Fibers

By using an accurate numerical method we show that both the higher-order peaks and main peak of the SBS in hole-assisted-fibers can be enhanced by more than 3-dB, by appropriate selection of the design parameters.