单击此处编辑母版标题样式,单击此处编辑母版文本样式,第二级,第三级,第四级,第五级,*,野生稻,O.rufipogon,W1943 1888条全长cDNA序列的数据分析,NCGR,2008-09-03,1,背景,野生稻,O.rufipogon,（AA genome）,是与栽培稻关系,最近,的祖先水稻品种,1,2,。,具有许多优于栽培稻的,农艺性状,，比如耐旱、耐盐等等,3,4,；,公共数据库中有大量栽培稻的,基因组序列信息,5,6,，同时也有大量的,cDNA,资源,7,8,；,极少,野生稻的序列和克隆资源，比较成规模的是,Oryza minuta,(BBCC genome),5,211条叶片,ests,9,。,2,现状与目的,NCGR,野生稻资源：克隆并精确测序了,1,888,个,unique,的,O.rufipogon,W1943 cDNA,克隆。,期望通过,W1943 cDNA,序列与籼、粳稻,cDNA,序列的比较：,汇总一些水稻,新基因,、潜在野生稻,特有的基因,、W1943,特有剪切方式,基因、,组织特异性高,表达的基因和与,microRNA,相关,的基因；,提供一些线索，供有兴趣者作进一步研究之用。,3,1888 W1943 cDNAs,BLAST against cultivated rice,genomic sequences and cDNAs,1888 W1943 cDNAs,SSR comparison,with indica and japonica cDNAs,4,一、未匹配粳稻基因组之基因,定义,：未能定位到,O.sativa,japonica Nipponbare genome sequences,，但与籼稻93-11基因组序列有同源或与水稻ests序列有同源或与其它禾本科ests序列有同源。且去除与细菌有同源的基因,解释,：或者落于粳稻基因组测序gap中，或者籼稻特有的基因，或者野生稻特有基因。,name,93-11 contigs,ESTs or mRNA hits,protein,name,93-11 contigs,ESTs or mRNA hits,protein,CT842002,Contig005912,AK241925,-,CU406895,Contig003011,CT859459,-,CT842007,Contig008507,CT856206,-,CU861744,Contig000750,AK099287,ring-box protein,CU405940,Contig001402,AK103326,-,CU405657,-,CT856885,-,CU406172,Contig014596,AK242967,-,CT841712,-,CA766528,-,CT842006,Contig000383,AK111647,GTP-binding protein,CU405768,-,CT836656,60S ribosomal protein L7A,CU861753,Contig000750,AK099287,ring-box protein,CU405675,-,CA756235,60S ribosomal protein L17,CU406308,Contig000444,AK070131,-,CU406202,-,NM_001063334,-,CT841996,Contig002576,CT834800,-,CU406924,-,AC145809,-,CU406568,Contig003848,AK064050,Bowman Birk trypsin inhibitor,CU405898,-,CN130755.1(,Sorghum bicolor,),ribulose-bisphosphate carboxylase,CU406582,Contig000444,AK107776,-,CU406778,-,BE429292.1(,Triticum turgidum,),-,CU406596,Contig001277,AK242711,-,CU861677,-,FF534517.1(,Manihot esculenta,),-,CT842008,Contig008507,CT856206,-,CT841912,-,EH277383.1(,Spartina alterniflora,),-,5,二、,水稻新,基因,定义：,能定位到栽培稻基因组序列的同源，但无任何已知水稻表达序列的同源。与rice MPSS搜索比较几乎没有找到匹配片段。,解释：,水稻新基因。或者在栽培稻中表达量过低难于克隆，或者野生稻特有。,name,Len(bp),Chr location,Identity(%),name,Len(bp),Chr location,Identity(%),Antisense,protein,CU406910,656,10,99,CU405785,727,05,99,CA764081,DNA-directed RNA polymerase 3,CU406138,568,02,99,CU861795,475,09,79,CT858901,-,CU406022,543,12,99,CU406355,837,12,97,AK107125,AP2 domain,putative,CU405757,477,04,100,CU406396,520,02,99,AK103485,-,CU406921,414,02,100,CT841800,941,11,99,AK121962,patatin,putative,CU406535,389,02,100,CU861688,693,08,99,AK109182,-,CU406832,530,10,92,CT841937,1552,08,98,AK106713,-,CU406871,458,01,84,注：该17个基因均没有找到任何蛋白同源匹配。右侧的7个基因与已知的水稻表达序列成反义RNA对。,CU861804,383,06,99,CU861721,554,01,100,6,三、,W1943,特有剪切方式基因,定义,：与栽培稻,japonica,基因组序列完全一致(,100%identity,)，同时与栽培稻表达序列同源但剪切方式独有(独特的AS剪切方式)。,解释,：或只是尚未克隆到该AS表达方式；或为野生稻所独具。,name,Len(bp),Chr location,No.of exon,protein,CT841942,978,07,6 (1st intron:GC-AG),-,CU406810,958,06,6(1st intron:GT-TG),dual-specificity phosphatase protein,CT841893,1011,01,6,drought-induced protein,CT841874,1369,01,4,vesicle transport protein,CU405853,1377,05,1,dehydration-responsive protein,CU405923,639,07,1,IAA amidohydrolase,CU406279,648,05,1,-,CU406025,839,02,1,-,CT841561,740,06,2,-,CU406579,468,09,2,-,CU406935,1345,01,2,-,CU406600,1107,01,2,-,CU405570,952,01,2,-,CU406091,893,01,3,-,CU406134,665,10,3,-,7,some W1943 cDNAs unique splicing pattern,:The expression level of every gene should exceed 100 tpm(times per million)of at least one tissue.,:If the gene expressed in several diverse tissues,then the percentage of the highest expression level should be more than 75%among all tissues.,:The ratio of the first two highest expression level should be over 10.,41 putative tissue-specific genes,10,exon,剪切出现,intron；intron中出现exon,exon,剪切出现,intron,intergenic区,出现,exon,2个exon合并成单exon,8,四、组织特异性高表达基因,name,len,ORF,tissue,protein,orw1943s101k15,619bp,51-434bp,leaf,light-regulated protein,orw1943c102c24,833bp,62-463bp,leaf,subunit of ribulose-1,5-bisphosphate carboxylase,orw1943s101p08,1544bp,111-650bp,leaf,glycolate oxidase,orw1943s101h18,912bp,120-752bp,leaf,H+-transporting ATP synthase chain 9-like protein,orw1943c113b17,837bp,108-623bp,leaf,retrotransposon protein,putative,unclassified,orw1943c002g13,843bp,58-576bp,leaf,alanine aminotransferase,orw1943c003d24,404bp,18-227bp,leaf,ferredoxin-NADP(H)oxidoreductase,orw1943c104a05,985bp,70-777bp,leaf,photosystem-1 F subunit precursor,orw1943c006o21,625bp,89-310bp,root,metallothionein-like protein type 1,orw1943c103g16,916bp,110-553bp,root,MAPEG family,orw1943c003o09,619bo,111-311bp,root,Potato inhibitor I family,orw1943c112g14,1008bp,58-825bp,root,receptor-like protein kinase,orw1943c104g04,805bp,115-618bp,root,pathogenesis-related protein PR-1a,orw1943c006h22,664bp,1-453bp,root,pathogenesis-related protein 4b,orw1943s101p06,512bp,36-353bp,root,N-carbamyl-L-amino acid amidohydrolase,orw1943c111d19,1399bp,59-1312bp,germinating seedling,putative alpha-galactosidase,orw1943c002o05,769bp,82-432bp,germinating seedling,nonspecific lipid-transfer protein 2 precursor,orw1943c002p22,518bp,92-331bp,meristematic tissue,metallothionein,