A draft sequence of the rice genome (Oryza sativa L. ssp. indica)

We have produced a draft sequence of the rice genome for the most widely cultivated subspecies in China, Oryza sativa L. ssp. indica, by whole-genome shotgun sequencing. The genome was 466 megabases in size, with an estimated 46,022 to 55,615 genes. Functional coverage in the assembled sequences was 92.0%. About 42.2% of the genome was in exact 20-nucleotide oligomer repeats, and most of the transposons were in the intergenic regions between genes. Although 80.6% of predicted Arabidopsis thaliana genes had a homolog in rice, only 49.4% of predicted rice genes had a homolog in A. thaliana. The large proportion of rice genes with no recognizable homologs is due to a gradient in the GC content of rice coding sequences.     

The Release 5.1 annotation of Drosophila melanogaster heterochromatin

The repetitive DNA that constitutes most of the heterochromatic regions of metazoan genomes has hindered the comprehensive analysis of gene content and other functions. We have generated a detailed computational and manual annotation of 24 megabases of heterochromatic sequence in the Release 5 Drosophila melanogaster genome sequence. The heterochromatin contains a minimum of 230 to 254 protein-coding genes, which are conserved in other Drosophilids and more diverged species, as well as 32 pseudogenes and 13 noncoding RNAs. Improved methods revealed that more than 77% of this heterochromatin sequence, including introns and intergenic regions, is composed of fragmented and nested transposable elements and other repeated DNAs. Drosophila heterochromatin contains "islands" of highly conserved genes embedded in these "oceans" of complex repeats, which may require special expression and splicing mechanisms.     

A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)

The genome of the japonica subspecies of rice, an important cereal and model monocot, was sequenced and assembled by whole-genome shotgun sequencing. The assembled sequence covers 93% of the 420-megabase genome. Gene predictions on the assembled sequence suggest that the genome contains 32,000 to 50,000 genes. Homologs of 98% of the known maize, wheat, and barley proteins are found in rice. Synteny and gene homology between rice and the other cereal genomes are extensive, whereas synteny with Arabidopsis is limited. Assignment of candidate rice orthologs to Arabidopsis genes is possible in many cases. The rice genome sequence provides a foundation for the improvement of cereals, our most important crops.     

From sequence to chromosome: the tip of the X chromosome of D. melanogaster

One of the rewards of having a Drosophila melanogaster whole-genome sequence will be the potential to understand the molecular bases for structural features of chromosomes that have been a long-standing puzzle. Analysis of 2.6 megabases of sequence from the tip of the X chromosome of Drosophila identifies 273 genes. Cloned DNAs from the characteristic bulbous structure at the tip of the X chromosome in the region of the broad complex display an unusual pattern of in situ hybridization. Sequence analysis revealed that this region comprises 154 kilobases of DNA flanked by 1.2-kilobases of inverted repeats, each composed of a 350-base pair satellite related element. Thus, some aspects of chromosome structure appear to be revealed directly within the DNA sequence itself.     

水稻基因组序列研究进展

水稻是世界上最重要的粮食作物之一,是禾本科植物的模式植物。综述了基于图位克隆的水稻基因组序列,基因组大小为389 Mb,包括37 544个非转座因子相关蛋白的基因。95%的基因组序列被精确测定,包括全部的常染色质、2个完整的着丝点及6条完整的染色体。基因组中串联重复序列占14%,平均每Mb为51个SSR。SwaI光学限制性(酶切)图谱的构建使图距缩短了11%,使基因组大小变为382.17 Mb。     

5个水稻蛋白激酶的克隆、表达及活性研究

蛋白激酶在生长发育、表达调控、逆境反应、信号传导等几乎所有的生命过程中发挥着重要作用,蛋白激酶的研究具有重要的理论和应用价值。全基因组测序结果表明,水稻基因组中至少有1500个蛋白激酶。本研究利用已有的蛋白激酶序列,通过PCR扩增和重组克隆,将5个重要的蛋白激酶在酿酒酵母系统中进行了表达,它们的编号分别是:NM-189878,NM-194133,NM-190508,NM-197522和NM-197571,其中NM-194133具有较强的自我磷酸化活性。同源性分析表明,这些激酶在水稻中可能的作用包括:碳代谢的生物合成调控、种子形态发生、细胞分裂调控、生物和非生物刺激的反应调控等。这项工作为进一步的体外酶活分析及蛋白质-蛋白质相互作用研究等提供了基础,也为高通量克隆表达水稻蛋白激酶提供了一个有效的系统。     

The ecoresponsive genome of Daphnia pulex

We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.     

野生稻细胞核DNA提取的研究

药用野生稻是中国最具利用价值的野生稻资源之一,具有许多优良的性状和有利基因,是改良栽培稻培育新品种的宝贵基因库,而其CC基因组的优良基因有望以大片段形式通过BIBAC等载体转化到栽培稻中.BIBAC文库不仅能作为大片段基因组文库的载体,而且能通过根癌农杆菌介导将克隆片段导入植物基因组直接进行转化,可用于筛选分离基因等研究.如何获得基因组DNA大片段非常关键,本研究采取 琼脂糖包埋基因组的方法获得大片段DNA,并对其中的一些步骤进行了优化,为构建药用野生稻BIBAC文库打下了很好的基础,值得在其它植物类似研究中参考.     

水稻dirigent基因家族生物信息学分析

摘　要：利用现有的水稻生物信息资源,共鉴定出了53个水稻dirigent (OsDIR)基因,它们分布在8条水稻染色体上;基因结构分析显示,有32个OsDIR基因不含内含子,占总数的60.4%;保守功能区域预测表明,OsDIR基因至少含有1个保守的DIR功能域;模块预测显示,水稻DIR蛋白拥有至少10个大小不同的保守模块,且不同模块在基因家族成员中出现的频率有较大的差异;蛋白序列比对表明,该基因家族蛋白保守序列均位于DIR功能域内;蛋白功能预测表明,大多数OsDIR蛋白为稳定的疏水性蛋白,表达于大多数细胞器中,且在细胞壁中表达最为丰富;同源基因分子遗传进化分析表明,OsDIR基因可分为5个亚类,功能域片段与基因的复制特征表明,OsDIR基因可能起源于共同的祖先(基因)。     

水稻多逆境响应基因OsMsr13的克隆与功能分析

为了深入研究作物耐逆境胁迫的分子机制和发现新的水稻耐逆基因,采用Affymetrix基因芯片技术与水稻表达芯片(含51,279个转录本),分析了培矮64S不同生长发育时期、不同组织器官全基因组在低温、干旱、高温逆境胁迫下的表达水平变化,筛选出一批耐多逆境候选功能基因.OsMsr13是其中一个受低温、高温与干旱诱导,在各生长发育时期与组织器官均显著上调的基因.根据序列生物信息学分析,OsMsr13含有7个外显子和6个内含子,cDNA全长序列为1603bp,完整的ORF为1317bp,编码一个含438个氨基酸残基的蛋白质;在OsMsr13启动子区域发现多个与逆境应答相关的顺武作用元件;数据库查找和蛋白质多序列的比对表明Os Msr13的预测蛋白属于钙调素结合蛋白家族.为了进一步研究OsMsr13基因的功能,通过RT-PCR方法扩增到包含OsMsr13完整ORF的cDNA克隆,构建了含有OsMsr13重组基因的过量表达载体pCAM-JIT-OsMsr13,并经农杆菌介导法将重组基因导入到水稻中.转OsMsr13株系苗期的抗逆性试验表明OsMsr13过量表达能显著地提高水稻的耐寒性,但在抗旱和耐高温方面,转基因植株和野生型9311没有观察到多大差别.     

A physical map of the 1-gigabase bread wheat chromosome 3B

As the staple food for 35% of the world's population, wheat is one of the most important crop species. To date, sequence-based tools to accelerate wheat improvement are lacking. As part of the international effort to sequence the 17-billion-base-pair hexaploid bread wheat genome (2n = 6x = 42 chromosomes), we constructed a bacterial artificial chromosome (BAC)-based integrated physical map of the largest chromosome, 3B, that alone is 995 megabases. A chromosome-specific BAC library was used to assemble 82% of the chromosome into 1036 contigs that were anchored with 1443 molecular markers, providing a major resource for genetic and genomic studies. This physical map establishes a template for the remaining wheat chromosomes and demonstrates the feasibility of constructing physical maps in large, complex, polyploid genomes with a chromosome-based approach.     

富含γ-氨基丁酸(GABA)的巨胚功能稻研究进展

富含γ-氨基丁酸(GABA)的巨胚稻米具有降血压、治疗癫痫病等功效,是水稻品质改良的研究热点之一。通过诱变和杂交转育技术,已经育成了“Haim inori”、“巨胚1号”、“6601”、“W 025”、“伽马-1”、“龙特浦geA”和“98-14geA”等10余个巨胚水稻品种(系),并摸索出了巨胚稻的栽培调控管理措施。经高效液相色谱(HPLC)及氨基酸组成分析,富集后巨胚稻米的GABA含量达到3500-4000mg/100g,其它许多营养成分也比普通稻米高。水稻巨胚受一隐性基因控制,控制稻米巨胚的3个等位基因gem、ge、ges已被定位在水稻第7染色体上,多个与胚大小有关的QTL也被检测。对巨胚稻米GABA的富集条件、加工工艺、市场开发前景也进行了综述。     

Two novel gene-specific markers at the Pik locus facilitate the application of rice blast resistant alleles in breeding

Blast, a disease caused by Magnaporthe oryzae, is a major constraint for rice production worldwide. Introgression of durable blast resistance genes into high-yielding rice cultivars has been considered a priority to control the disease. The blast resistance Pik locus, located on chromosome 11, contains at least six important resistance genes, but these genes have not been widely employed in resistance breeding since existing markers hardly satisfy current breeding needs due to their limited scope of application. In this study, two PCR-based markers, Pikp-Del and Pi1-In, were developed to target the specific In Del(insertion/deletion) of the Pik-p and Pi-1 genes, respectively. The two markers precisely distinguished Pik-p, Pi-1, and the K-type alleles at the Pik locus, which is a necessary element for functional genes from rice varieties. Results also revealed that only several old varieties contain the two genes, of which nearly half carry the K-type alleles. Therefore, these identified varieties can serve as new gene sources for developing blast resistant rice. The two newly developed markers will be highly useful for the use of Pik-p, Pi-1 and other resistance genes at the Pik locus in markerassisted selection(MAS) breeding programs.     

水稻幼苗响应褐飞虱和稻瘿蚊的转录组分析

【目的】筛选出同时响应褐飞虱和稻瘿蚊取食的基因,揭示水稻幼苗应对2种害虫时基因表达层面的差异,为后续挖掘广谱抗虫基因和解析水稻抗虫机制打下理论基础。【方法】以水稻品种9311为供试植物,分别对15日龄的水稻幼苗进行褐飞虱和稻瘿蚊接虫处理,观测幼苗表型,并通过转录组测序技术分别对褐飞虱接入后24 h和稻瘿蚊接入后7 d的水稻幼苗进行转录组测序。以水稻日本晴基因组作为参考基因组进行对比,利用FPKM法计算基因表达量,设定参数（|log₂ FC|>1且P<0.05）筛选差异表达基因。结合基因差异表达分析和功能富集分析,研究水稻响应2种害虫的机制异同点。【结果】鉴定出响应褐飞虱取食的差异表达基因3963个,响应稻瘿蚊取食的差异表达基因1206个,有251个差异表达基因同时响应2种害虫,其中108个具有相同表达模式,143个具有相反表达模式。GO功能注释分析表明,褐飞虱取食显著影响植物体内细胞壁合成和缺水响应,而稻瘿蚊取食则对植物光合作用的影响更显著,具有相同表达模式的差异表达基因主要富集在光合作用、水杨酸合成、茉莉酸信号转导和伤害响应等生物学功能,而具有相反表达模式的差异表达基因仅富集在乙醛酸循环。KEGG信号通路富集分析表明,褐飞虱和稻瘿蚊取食均显著影响植物体内次生代谢物的合成,相同表达模式的差异表达基因富集到MAPK信号通路、植物激素信号转导通路及光合作用等6个通路,而相反表达模式的差异表达基因没有富集的通路。【结论】水稻应对褐飞虱和稻瘿蚊的基因表达调控存在相同点和不同之处,共响应2种害虫的调控通路可能在水稻抗虫过程中发挥重要作用。     

普通野生稻凝集素基因的克隆及序列分析

以我国普通野生稻基因组ＤＮＡ为模板以特异引物经聚事酶链反应方法扩增出凝集素基因并克隆到Ｅ．ｃｏｌｉ质粒ｐＢｌｕｅｓｃｒｉｐｔＳＫ（＋）的ＳｍａＩ位点。序列分析表明,克隆到的基因片段大小为７８１ｂｐ,没有内含子,编码一条长２２７个氨基酸、分子量约２３ＫＤ的肽链,其中Ｎ－端２８个氨基酸是信号肽。与报道的栽培稻凝集素ＣＤＮＡ序列进行顺序同源性比较,发现他们 很高的同源性（９９．４８％）,其非编码区第２３     

籼型红米具有的恢复性及其基因定位

经四川农业大学水稻研究所良繁研究室发现,（G46A、D702A、珍汕97A）D 62A／红宝石的F1代,植株基本全不育,但在回交过程中育性发生分离,可育株数明显增多,猜想红宝石具有对G46A、D702A、珍汕97A和D62A育性恢复的特性。为了验证该猜想,笔者构建遗传群体对其恢复性进行分析,并用SSLP对红宝石的恢复基因加以定位。     

应用软件Fgenesh预测水稻基因

 【目的】为生物基因组序列注释提供一定科学依据,加快序列注释进度和精确性。【方法】以粳稻日本晴（Oryza sativa L. ssp. japonica cv. Nipponbare）较长的6号染色体的序列为例,采用生物信息学手段,详细探索了Fgenesh（v2.0）对单子叶模式植物水稻基因的预测。【结果】预测的基因数涵盖了注释的基因数且两者相差不大;预测的基因以多外显子基因为主,占总基因的77.52%;预测基因的长度变化幅度很大;从显著匹配数上来看,Fgenesh对多外显子基因预测准确性较高,其中TIGR注释支持度达到100%,cDNA的支持度也在78%以上;从Fgenesh对多外显子基因不同位置的外显子预测来看,居间外显子和末端外显子的cDNA支持度较高;高支持度的多外显子基因中居间外显子的长度较短,而起始外显子和末端外显子较长;高支持度的单外显子基因长度多数较短;从外显子数目上看,高支持度多外显子基因的外显子数目主要集中在5以下。【结论】Fgenesh对水稻基因的预测有较高的准确性,但需要将预测结果与cDNA数据库进行序列比对,根据cDNA的支持情况对预测结果做必要的修订。     

禾谷类作物的比较基因组研究

 水稻是基因组最小的禾谷类作物,饱和遗传连锁图谱的构建,以及在此基础上开展的标记辅助选择和抗病基因克隆,表明水稻基因组研究已经领先于其他禾谷类作物。比较基因组研究表明：小麦、玉米、高粱、谷子和甘蔗的基因组均可由水稻染色体区段重新排列而成，这些区段上DNA标记的排列顺序在各个种之间保留。各种作物基因组大小的差异可能由于各个区段内基因间重复顺序扩增的程度不同所致。根据这些区段在各种作物染色体的排列顺序，有人提出根据水稻染色体区段排列单个原始禾谷类染色体的设想，为深入研究禾谷类作物的进化遗传提出了全新的思路。禾谷类作物基因组之间的共线性有利于在小基因组内克隆大基因组作物的同源基因，使生物技术在作物育种中发挥更大的作用。     

Comparison and analysis of QTLs for grain and hull thickness related traits in two recombinant inbred line(RIL) populations in rice(Oryza sativa L.)

Grain traits are major constraints in rice production, which are key factors in determining grain yield and market values. This study used two recombinant inbred line(RIL) populations, RIL-JJ(japonica/japonica) and RIL-IJ(indica/japonica) derived from the two crosses Shennong 265/Lijiangxintuanheigu(SN265/LTH) and Shennong 265/Luhui 99(SN265/LH99). Sixty-eight quantitative trait loci(QTLs) associated with 10 grain traits were consistently detected on the 12 chromosomes across different populations and two environments. Although 61.75% of the QTLs clustered together across two populations, only 16.17% could be detected across two populations. Eight major QTLs were detected on the 9, 10 and 12 chromosomes in RIL-JJ under two environments, a novel QTL clustered on the 10 chromosome, q GT10, q BT10 and q TGW10, have a higher percentage of explained phenotypic variation(PVE) and additive effect; 15 major QTLs were detected on the 5, 8, 9, and 11 chromosomes in RIL-IJ under two environments, a novel clustered QTL, q GT8 and q TGW8, on the 8 chromosome have a higher additive effect. Finally, the analysis of major QTL-BSA mapping narrowed the q TGW10 to a 1.47-Mb region flanked by simple sequence repeat markers RM467 and RM6368 on chromosome 10. A comparison of QTLs for grain traits in two different genetic backgrounds recombinant inbred line populations confirmed that genetic background had a significant impact on grain traits. The identified QTLs were stable across different populations and various environments, and 29.42% of QTLs controlling grain traits were reliably detected in different environments. Fewer QTLs were detected for brown rice traits than for paddy rice traits, 7 and 17 QTLs for brown rice out of 25 and 43 QTLs under RIL-JJ and RILIJ populations, respectively. The identification of genes constituting the QTLs will help to further our understanding of the molecular mechanisms underlying grain shape.     

水稻与拟南芥全基因组丝氨酸羧肽酶类蛋白家族比较分析(英文)

    基于水稻与拟南芥全基因组序列,在基因组与蛋白质组水平上对这2种模式植物的丝氨酸羧肽酶 (SCPs)基因家族进行比较分析.利用隐马可夫模型(hidden Markov models,HMM),发现水稻与拟南芥中分别存在71个与54个丝氨酸羧肽酶类(serine carboxypeptidases like,SCPL)蛋白编码基因,它们广泛分布于基因组中各条染色体上,并且存在多个基因簇聚区.基因结构分析显示,拟南芥的SCPL基因存在广泛的交替剪接方式,而这种现象在水稻SCPL基因中却不常见.蛋白结构分析表明,所有SCPL家族成员均具有α/β水解酶折叠亚族与S10家族典型的保守结构域与二级结构特征.系统进化分析表明,这125个SCPL蛋白可以分成3大类,与水稻不同,大多数拟南芥SCPL (88.9%)可归属于双链羧肽酶Ⅰ或Ⅱ.