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Sequence analysis of mRNA polyadenylation signals of rice genes

Chinese Science Bulletin 2006年第9期51卷 1069-1077页

作者： lu ying1, 2. gao chenxi1,{2.,{3., shanghai institutes for biological Sciences, Chinese Academy of Sciences, shanghai 2.02.3. china 2. Graduate School of the Chinese Academy of Sciences, Beijing 10003., china 3. Institute of Plant Physiology and Ecology, shanghai institutes for biological Sciences, Chinese Academy of Sciences, shanghai 2.003.2} china national center for {2.{3. Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China Graduate School of the Chinese Academy of Sciences Beijing China Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China

The formation of eukaryotic mRNAs involves the cleavage and polyadenylation of pre- mRNAs. To investigate the sequence requirement of putative polyadenylation signals (PASs), poly(A) sites and downstream elements (DUEs) in 3.-end-pro- cessing in rice, we compared expressed sequences tags (ESTs) with poly(A) extremity to full-length cDNA sequences and constructed a database of 12.69 pre- mRNA sequences in ?40―+40 nt surrounding the poly(A) sites, which were from 9953.genes. The al- ternative poly(A) sites were revealed in approxi- mately 2.% of mRNAs. Nearly 80% of pre-mRNAs showed stringent requirement of the YA (CA or UA) at poly (A) sites for polyadenylation. About 7.9% had the AAUAAA signals on ?40―?1 nt upstream of the poly(A) sites. Over 60% of mRNAs probably used the one- or two-base variants of AAUAAA hexamers as their PASs in 3. fragments. The single-base variants of AAUGAA revealed the high frequency in 11.5% of 3. fragments. The DUEs were detected in 90% of pre- mRNAs, especially more t{3. half of the pre-mRNAs with multi-base variants of AAUAAA had the DUEs surrounding the poly(A) site. The location of DUE is also important for defining the cleavage site. Al- though most of the rice pre-mRNAs did not contain AAUAAA signal, the existence of downstream ele- ments ensured the efficiency of cleavage-polyade-

关键词：多聚腺苷酸序列分析 mRNA 水稻基因工程

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Anaerobic Induction of Isocitrate Lyase and Malate Synthase in Submerged Rice Seedlings Indicates the Important Metabolic Role of the Glyoxylate Cycle

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Acta Biochimica et Biophysica Sinica 2005年第6期37卷 406-414页

作者： ying lu~(1.2. Yong-Rui WU~(1.2. {2. han~(1.3. 1 national center for gene {2.. shanghai institutes for biological Sciences. Chinese Academy of Sciences.{13.. 2.Graduate School of the Chinese Academy of Sciences. Beijing 10003..{12. 3.Institute of Plant Physiology and Ecology. shanghai institutes for biological Sciences. Chinese Academy of Sciences. shanghai 2.003.2} {12. national center for {2.{3. Shanghai Institutes for Biological Sciences Chinese Academy of SciencesShanghai 200233 China Graduate School of the Chinese Academy of SciencesBeijing 10003. China Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of SciencesShanghai 200032 China

The glyoxylate cycle is a modified form of the tricarboxylic acid cycle that converts C2.ompounds into C4 dicarboxylic acids at plant developmental *** studying submerged rice seedlings,we revealed the activation of the glyoxylate cycle by identifying the increased transcripts of mRNAs of the{2.s of isocitrate lyase(ICL)and malate synthase(MS),two characteristic enzymes of the *** blot analysis showed that ICL and MS were activated in the prolonged anaerobic *** activity assay of pyruvate decarboxylase and ICL in the submerged seedlings indicated an 8.8-fold and3.5-fold increase over that in the unsubmerged seedlings,*** activity assay of acetyl-coen-zyme A synthetase in the submerged seedlings indicated a 3.fold increase over that in the unsubmergedseedlings,which is important for initiating acetate ***,we concluded that the glyoxylatecycle was involved in acetate metabolism under anaerobic conditions.

关键词： Oryza sativa glyoxylate cycle isocitrate lyase malate synthase acetyl-coenzyme A synthetase anoxia

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Genome Sequences Provide Insights into the Reticulate Origin and Unique Traits of Woody Bamboos

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Molecular Plant 2019年第10期12卷 1353-1365页

作者： Zhen-Hua Guo Peng-Fei Ma Guo-Qian Yang Jin-Yong Hu Yun-Long Liu En-Hua Xia Mi-Cai Zhong Lei Zhao Gui-Ling Sun Yu-Xing Xu You-Jie Zhao Yi-Chi Zhang Yu-Xiao Zhang Xue-Mei Zhang Meng-Yuan Zhou {3. Guo Cen Guo Jing-Xia Liu Xia-{3. Ye Yun-Mei Chen Yang Yang bin han Choun-Sea Lin {3. lu De-Zhu Li Germplasm Bank of Wild Species Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan 650201China Key Laboratory for Plant Diversity and Biogeography in East Asia Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan 650201China State Key Laboratory of Tea Plant Biology and Utilization Anhui Agricultural UniversityHefeiAnhui 230036China Kunming College of Life Science University of Chinese Academy of SciencesKunmingYunnan 650201China lnstitute of Plant Stress Biology State Key Laboratory of Cotton BiologyDepartment of BiologyHenan UniversityKaifengHenan 475001China College of Big Data and Intelligent Engineering Southwest Forestry UniversityKunmingYunnan 650224China Yunnan Academy of Biodiversity Southwest Forestry UniversityKunmingYunnan 650224China national center for {2.{3. Shanghai Institute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai 200032China Agricultural Biotechnology research center Academia SinicaTaipei College of Fisheries and Life Science Shanghai Ocean UniversityShanghai 201306China

Polyploidization is a major driver of speciation and its importance to plant evolution has been well *** comprise one diploid herbaceous and three polyploid woody lineages,and are members of the only major subfamily in grasses that diversified in forests,with the woody members having a tree-like lignified *** this study,we generated four draft genome assemblies of major bamboo lineages with three different ploidy levels(diploid,tetraploid,and hexaploid).We also constructed a high-density genetic linkage map for a hexaploid species of bamboo,and used a linkage-map-based strategy for genome assembly and identification of subgenomes in *** phylogenomic analyses using a large dataset of syntenic genes with expected copies based on ploidy levels revealed that woody bamboos originated subsequent to the divergence of the herbaceous bamboo lineage,and experienced complex reticulate evolution through three independent allopolyploid events involving four extinct diploid ancestors.A shared but distinct subgenome was identified in all polyploid forms,and the progenitor of this subgenome could have been critical in ancient polyploidizations and the origin of woody *** genetic clues to the unique flowering behavior and woody trait in bamboos were also *** together,our study provides significant insights into ancient reticulate evolution at the subgenome level in the absence of extant donor species,and offers a potential model scenario for broad-scale study of angiosperm origination by allopolyploidization.

关键词： Bambusoideae polyploidization comparative genomics subgenome evolution flowering

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