| Transposable elements (TE or transposons) are mobile repetitive DNA sequences widely present in the eukaryotic and prokaryotic genomes. They have a significant effect on genome structure, function, evolution. Although TE are originally thought to be rare,genome-sequencing analyese have indicated that TE effect the genome evolution and amplification, gene structure, new gene creation, and transcriptional regulation, etc.The genus Oryza consists of 24 species. Three of them are cultivated species,including O. sativa ssp. Indica, O. sativa ssp. Japonica, and O. glaberrima, which are distributed in Asia, Africa, Australia, and South America. Ten genomes (AA, BB, CC,BBCC, CCDD, EE, FF, GG, HHJJ and HHKK) have been identified in the Oryza species.The two cultivated rice subspecies under O. sativa (O. sativa ssp. Indica and O. sativa ssp.Japonica), the African cultivated rice species O. glaberrima, and other six species (O.nivara, O. rufipogon, O. barthii, O. glumaepatula, O. longistaminata, and O. meridionalis)contain A genome. The Oryza species supply a powerful system for studying comparative genomics and evolutionary biology. In addition, these rice species represent an invaluable gene pool for rice improvement, which is of crucial significance in worldwide food production and security. Many genes involved in rice improvement are derived from wild species. This has broadened the gene pool of cultivated rice through gene introgression from wild rice species. These rice species containing A genome diverged less than 4.8 Mya from a common ancestor. They have been extensively improved in multiple adaptive and agronomic traits through the evolutionary and domestication processes.As the A genome in these rice species have been completely sequenced, they are becoming a model system for plant comparative, functional and evolutionary genomics studies. The major results were as follows:1. This study performed phylogenomic analyses of 1,937 orthologous and single-copy genes of at least 300 aa from the eight completely sequenced Oryza genomes using O. meridionalis as out-group. Gene-based phylogenetic analysis clearly supported global genome divergences of the species. The general nucleotide substitution rate has been estimated to 6.5×10-9 substitutions per site per year, which was used to date the speciation events in this work. This work has thus found out the major extant AA lineages to be within 4.8 million years, in agreement with other analyses of sequence divergence times for rice.2. Three cultivated rice species and their closest five wild relatives were analyzed for distribution and content of TE in their genomes. We found that 37.5 %, 30.5 %, 35.5 %,25.7 %, 28.9 %, 27.1 %, 21.9 % and 18.4 % of the A genome were TE in O. sativa Japonica, O. rufipogon, O. sativa Indica, O. nivara, O. glaberrima, O. barthii, O.glumaepatula, and O. meridionalis, respectively. These results indicate that the A genome in the three cultivated rice species contain more TE than their close wild relatives. The majority of the TE were LTR elements, followed by DNA transposons and LINEs. The LTR elements contributed 55 to 104 Mbp (or 17 to 25 %) of the cultivated rice genomes,while only 38 to 58 Mbp (or 11 to 17 %) of the wild rice genomes.3. A gene has been defined as a continuous exon and intron sequence, including the the untranslated regions. This study mapped TE onto the rice genomes and observed that at least 10% of TE occurred in gene regions. Surprisingly, the three cultivated rice species contained substantially lower numbers of TE associated with genes as compared to their wild relatives. The cultivated rice species contained 9.7 to 11.2% of the total TE inserted in gene regions, while their wild relatives contained 17.8 to 21.9% of their TE in genes.Moreover, we quantified TE within the 2 kb regions upstream and downstream of the genes. Notably, these regions did not have any substantial differences in TE content, i.e.similar levels of TE were found in these regions in the cultivated and in the rice species and their wild relatives. We found strong support for lower levels of TE associated with genes in the cultivated vs wild rice species. These findings indicate that the cultivated rice species deprive TE from their gene regions, suggesting that TE may promote certain environmental adaptation of genes in the wild rice species. Gene ontology and homology analyses revealed that while certain genes contained TE in all the wild species, the closest homologs in the cultivated species were devoid of them. GO terms enrich in the cultivated rice such as "cell wall" "flower development" and "cell death". Likewise,the wild rice species displayed their own set of GO terms affected by TE, including the GO terms"response to biotic stimuli" and "kinase activity".In this study, comparative genomic analyses among closely related rice species enhance understanding of plant genes and genome evolution. The cultivation of rice has led to distinct genomic distributions of TE. Some rice traits are closely associated with specific TE distribution patterns. Hence, these results provide means to better understanding of TE-dependent rice traits and the potential to genetically engineer rice for better agronomic performance.Concerns about global climate change and shortage of energy supply promote exploitation of non-fossile fuels. Use of cellulosic-ethanol offers several benefits towards reduction of the greenhouse gas emission and preventing of the competition with food supplies.Lignocellulosic biomass is a natural complex primarily consisting of three biopolymers: cellulose, hemicelluloses, and lignin. Biomass recalcitrance is the largest obstacle for cellulosic ethanol production.Miscanthus is a C4 perennial grass, including 14 species. They are distributed in eastern and south-eastern Asia and the Pacific islands. There are four major Miscanthus species in China, including M. sinensis, M. saccharforus Benth, Anderss M. floridulus Warb and M. lutarioriparius Spp.In this study, a total of 171 natural Miscanthus accessions were geographically mapped using the public database (cite website). According to the equation [P(H/L| East)?P(H/LflEast)/P(East)], the probability (P) parameters were calculated on the relationships between geographical distributions of Miscanthus accessions in the East of China, and related factors with high(H) or low(L) values including biomass saccahrification under 1% NaOH and 1% H2SO4 pretreatments, lignocellulose features and climate conditions. Based on the maximum P value, a golden cutting line was generated from 42°25' N, 108°22' E to 22058' N, 116028' E at the original locations of Miscanthus accessions with high P(H|East) values (0.800-0.813), indicating that more than 90% Micanthus accessions were originally located in the East with high biomass saccharification. Furthermore, the average insolation showed high P(H|East) and P(East|H)values at 0.782 and 0.754, whereas other climate factors had low P(East|H) values,suggesting that the average insolation is a unique factor on Miscanthus distribution for biomass saccharification. In terms of cell wall compositions and wall polymer features,both hemicellulose level and cellulose crystallinity (CrI) of Miscanthus accessions exhibited relative high P values, suggesting that they should be the major factors accounting for geographic distribution of Miscanthus accessions with high biomass digestibility.Miscanthus accessions with high biomass saccharification are mainly distributed in the east of China divided by a golden cutting-line, where the average insolation is the major related climate factor on biomass digestibility. Hence, this study has suggested strategy for developing dedicated bioenergy Miscanthus crops in China and over the world by appropriate cell wall modifications. |
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