从水稻基因组序列中挖掘生物信息

重点介绍了在水稻基因组序列分析方面取得的几项最新研究结果.内容主要包括:水稻基因组被证实曾发生过全基因组倍增;水稻基因组大小变化的趋势;水稻籼粳亚种的分化时间比以前估计的100万年前要迟得多;对水稻基因产生GC含量负梯度现象的解释.     

水稻基因组进化的研究进展

介绍了近年来在水稻基因组进化方面的研究进展,主要内容包括:水稻的核基因组至少经历了2次基因组复制过程,并从最初5条染色体形成了12条染色体;水稻籼粳两个亚种的分化估计发生在距今20～40万年前;在水稻驯化的研究方面,一方面克隆了一些控制重要驯化性状的基因,另一方面通过基因组分析发现了一些快速进化的基因组区段;片段复制、串联重复和逆转录转座等基因复制方式在水稻基因家族的物种特异性扩张方面起到了重要作用.通过整合以上研究成果,初步揭示了水稻基因进化的基本特点,为水稻功能基因组学和分子设计育种的进一步研究提供了新的切入点.     

基于全基因组测序构建水稻RIL群体遗传图谱

目的 以籼稻品种‘MDS’和‘R315’为亲本,构建一张高密度的遗传图谱,挖掘水稻Oryza sativa L.重要农艺性状相关基因并加快水稻品种选育。方法 对两亲本及其192个重组自交系(RILs)群体进行全基因组测序,筛选高质量单核苷酸多态性(SNPs),划分bin标记,针对每个连锁群使用JoinMap4.0对bin标记进行排序,用perl SVG模块绘制连锁图,并对标记在基因组和遗传图谱上的位置进行共线性分析。结果 两亲本间共筛选出221 494个高质量SNPs,构建了一张高密度遗传图谱,包含1 612个bin标记,总图距为1 327.82 cM,相邻标记间平均遗传图距为0.82 cM。共线性分析显示各连锁群上的大部分标记顺序与基因组保持一致,共线性较好,图谱质量高。结论 本研究构建的高密度遗传图谱质量较高,为后续功能基因的鉴定提供了基础。     

云南3种野生稻的花药离体培养研究

云南3种野生稻花药培养愈伤组织诱导能力差别较大,疣粒野生稻花药最易培养,愈伤组织诱导率为3.3%,其次是景洪普通野生稻为2.1%;元江普通野生稻再次之,为1.2%;药用野生稻诱导率最低,仅为0.8%。疣粒稻花药愈伤组织植株再生能力最强,再分化率在37.4%~52.6%,普通野生稻再分化率为19.2%~26.3%。本试验建立了疣粒野生稻、景洪类型和元江类型普通野生稻的花药培养离体无性系,为长期保存云南野生稻资源奠定了基础。     

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.     

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.     

Comparative analysis of the genome of the field isolate V86010 of the rice blast fungus Magnaporthe oryzae from Philippines

Genome dynamics of pathogenic organisms are driven by plant host and pathogenic organism co-evolution,in which pathogen genomes are used to overcome stresses imposed by hosts with various genetic backgrounds through generation of a range of field isolates. This model also applies to the rice host and its fungal pathogen Magnaporthe oryzae. To better understand genetic variation of M. oryzae in nature,the field isolate V86010 from the Philippines was sequenced and analyzed. Genome annotation found that the assembled V86010 genome was composed of 1 931 scaffolds with a combined length of 38.9 Mb. The average GC ratio is 51.3% and repetitive elements constitute 5.1% of the genome. A total of 11 857 genes including 616 effector protein genes were predicted using a combined analysis pipeline. All predicted genes and effector protein genes of isolate V86010 distribute on the eight chromosomes when aligned with the assembled genome of isolate 70-15. Effector protein genes are located disproportionately at several chromosomal ends. The Pot2 elements are abundant in V86010. Seven V86010-specific effector proteins were found to suppress programmed cell death induced by BAX in tobacco leaves using an Agrobacterium-mediated transient assay. Our results may provide useful information for further study of the molecular and genomic dynamics in the evolution of M. oryzae and rice host interactions,and for characterizing novel effectors and AVR genes in the rice blast pathogen.