谈谈植物的性别 ——由一道选择题引起的思考

有这样一道选择题,题目如下：我国科学家在2002年独立完成了“水稻基因组”的测序工作,并且这些数据无偿对外开放,这表明我国在有关基因组测定中走在世界前列。二倍体水稻有24条染色体,我国科学家测定水稻基因组需要测定水稻细胞中多少条染色体DNA的碱基序列(\ )。     

水稻基因组测序的研究进展

水稻是最重要的粮食作物之一,世界上大约有一半的人口以水稻为主要粮食.作为基因组研究的模式植物,水稻基因组的测序工作已在世界范围内展开.此项研究工作不仅能破译水稻全基因组序列,还将有助于了解其他禾本科植物的基因组信息.本文对水稻基因组测序工作进展作一综述。 Abstract:Because of the importamce of rice as the staple food source for over half of the world population and since rice is a leading model plant for genomic studies,an international effort has now begun to sequence the rice genome.This project eventually will reveal all of the genomic sequence information of rice and be an indispensable aid in understanding the genomics of other grass species.In this paper,the development and research progress in sequencing of rice genome are reviewed.     

美国绘出玉米基因组草图

美国圣路易斯华盛顿大学基因组测序中心近日宣布,他们成功测序得出了玉米基因组草图,这是人类成功测序的第二种农作物基因组,第一种被测序的农作物是水稻。测序项目负责人理查德·威尔逊在“玉米遗传学会议”第50次年会上公布了玉米基因组草图。     

水稻(籼稻)全基因组框架序列研究简介

水稻为世界一半以上的人口提供了主要食物。水稻基因组的常染色质部分长约 43 0个ｍｂ ,是拟南芥基因组长度的 3 .7倍 ,约为人类基因组长度的七分之一。我们最近完成了水稻的籼亚种——— (ＯｒｙｚａｓａｔｉｖａＬ .ｓｓｐ .ｉｎｄｉｃａ)中的全基因组序列草图的绘制 (Ｓｃｉｅｎｃｅ ,2 96 :79～ 92 ,2 0 0 2 )。籼稻在中国与东南亚广泛种植。我们分析的籼稻品种 93＿1 1就是袁隆平院士培育的超级杂交水稻两优培 9(ＬＹＰ9)的父本。水稻基因组全长 46 6ｍｂ ,包含有 46 0 2 2～ 5 5 0 1 5个基因。在已测序的序列中功能区占 92 .0 %。通过…     

美科学家绘出玉米基因组草图

美国科学家2月28日在华盛顿宣布．他们成功测序得出了玉米基因组的草图,这是人类成功测序的第2种农作物基因组,第1种被测序的农作物是水稻。     

植物基因组研究进展（综述）

目前集中在模式植物拟南芥,水稻的基因组研究进展迅速,基因组测序和物理作图极大地便利于基于分子标记图的基因克隆,并增加了对植物基因组的组织,结构和进化的认识。     

水稻基因组测序及基因功能的鉴定

水稻是重要的粮食作物。作为单子叶模式植物,水稻基因组的大规模测序具有巨大的理论价值和现实意义。目前已获得了籼稻“93—11”和粳稻“日本晴”高质量的基因组数据,这为在基因组水平上深入研究其生长、发育、抗病和高产等的遗传机理提供了便利,从而为进一步解决世界粮食危机提供了新的突破口和契机。随着水稻基因组计划的顺利结束,其研究重心也已由建立高分辨率的遗传、物理和转录图谱为主的结构基因组学转向基因功能的研究。结构基因组学研究获得的大量序列数据为揭示和开发功能基因开辟了广阔的前景。目前,利用图位克隆和电子克隆等方法已成功分离了多个水稻抗病、抗虫、抗逆境、抗倒伏、高产、优质等重要农艺性状相关的基因,对培育水稻新品种,促进农业的可持续发展意义重大。据估计,水稻至少拥有3．7万个非转座因子相关的蛋白编码基因。因此,完成全基因组序列测定后,重要基因功能的鉴定已成为当前基因组学研究的主要目标。反向遗传学、大规模基因功能表达谱分析和蛋白质组研究等策略已在研究水稻重要基因的功能方面发挥了重要作用。文章综述了水稻基因组测序及基因功能研究的现状,并就新基因发掘和基因功能注释的方法作了评述,期待为水稻遗传工程和育种实践提供参考。     

毛竹基因组大小和序列构成的比较分析

毛竹(P. pubescens)是世界重要的竹类植物之一, 是中国分布范围最广、种植面积最大(占全国竹林总面积的2/3以上)、经济价值最高的竹种. 毛竹属于禾本科, 为四倍体(4x = 48), 是该科中特殊的草本植物. 禾本科中多个基因组已被或正在被测序, 但竹类植物基因组研究还未见报 道. 本研究以被测序的玉米(B73)和水稻(日本晴) 基因组作为内参, 利用流式细胞仪(FCM)获得大小约为2034 Mb毛竹基因组, 其与玉米基因组大小相仿, 远大于水稻基因组. 为了明确毛竹基因组是否与玉米基因组一样由大量重复序列组成, 进行了毛竹基因组随机测序, 获得近1000条基因组调查序列(GSS). 序列分析表明, 毛竹基因组的重复序列组成比例23.3%, 明显低于玉米(65.7%); 其重复序列主要由Ty1/Copia和Gypsy/DIRS1 2类LTR逆转座子(14.7%)构成, DNA转座子和其他重复序列比例均较低. 但由于测序数量等原因,该结果还有待今后更大规模的基因组测序分析. 本研究对毛竹和其他竹种的基因组学研究提供了一些有价值的基础数据, 同时该研究是第一次对竹类植物基因组的序列构成进行了初步描述.     

基因组数据的处理

随着人类基因组计划、小鼠基因组计划、各种微生物基因组计划、水稻基因组计划以及各种动植物基因组计划的顺利实施 ,基因数据不断增加。 1995年第一条全基因组数据 (Ｈａｅｍｏｐｈｉｌｕｓｉｎｆｌｕｅｎｚａｅ ,流感嗜血杆菌全基因组序列 )公布。以ＧｅｎＢａｎｋ收录的基因组数据为例 ,1996年 ,ＧｅｎＢａｎｋ仅收录了 2条全基因组数据 ,1997年就增加到 6条全基因组数据 ,到目前为止 ,ＧｅｎＢａｎｋ已收录了包括大肠杆菌在内的 10条全基因组数据。此外 ,至少有 32条微生物全基因组即将测序完毕 ,不久将收录ＧｅｎＢａｎｋ中[1] 。基因…     

复杂基因组测序技术研究进展

复杂基因组指的是无法使用常规测序和组装手段直接解析的一类基因组,通常指包含高比例重复序列、高杂合度、极端GC含量、存在难消除异源DNA污染的基因组。为了解决复杂基因组的测序和组装问题,需要分别从基因组测序实验方法、测序技术平台、组装算法与策略3个方面进行深入研究。本文详细介绍了复杂基因组测序组装相关的现有技术与方法,并结合复杂基因组经典实例介绍了复杂基因组测序的技术解决途径和发展历程,可为制订合适的复杂基因组测序策略提供参考。     

In silico comparative analysis reveals a mosaic conservation of genes within a novel colinear region in wheat chromosome 1AS and rice chromosome 5S

Comparative RFLP mapping has revealed extensive conservation of marker order in different grass genomes. However, microcolinearity studies at the sequence level have shown rapid genome evolution and many exceptions to colinearity. Most of these studies have focused on a limited size of genomic fragment and the extent of microcolinearity over large distances or across entire genomes remains poorly characterized in grasses. Here, we have investigated the microcolinearity between the rice genome and a total of 1,500 kb from physical BAC contigs on wheat chromosome 1AS. Using ESTs mapped in wheat chromosome bins as an additional source of physical data, we have identified 27 conserved orthologous sequences between wheat chromosome 1AS and a region of 1,210 kb located on rice chromosome 5S. Our results extend the orthology described earlier between wheat chromosome group 1S and rice chromosome 5S. Microcolinearity was found to be frequently disrupted by rearrangements which must have occurred after the divergence of wheat and rice. At the Lr10 orthologous loci, microrearrangements were due to the insertion of mobile elements, but also originated from gene movement, amplification, deletion and inversion. These mechanisms of genome evolution are at the origin of the mosaic conservation observed between the orthologous regions. Finally, in silico mapping of wheat genes identified an intragenomic colinearity between fragments from rice chromosome 1L and 5S, suggesting an ancestral segmental duplication in rice.Electronic Supplementary Material Supplementary material is available in the online version of this article at     

Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.)

In order to enhance the resolution of an existing genetic map of rice, and to obtain a comprehensive picture of marker utility and genomic distribution of microsatellites in this important grain species, rice DNA sequences containing simple sequence repeats (SSRs) were extracted from several small-insert genomic libraries and from the database. One hundred and eighty eight new microsatellite markers were developed and evaluated for allelic diversity. The new simple sequence length polymorphisms (SSLPs) were incorporated into the existing map previously containing 124 SSR loci. The 312 microsatellite markers reported here provide whole-genome coverage with an average density of one SSLP per 6 cM. In this study, 26 SSLP markers were identified in published sequences of known genes, 65 were developed based on partial cDNA sequences available in GenBank, and 97 were isolated from genomic libraries. Microsatellite markers with different SSR motifs are relatively uniformly distributed along rice chromosomes regardless of whether they were derived from genomic clones or cDNA sequences. However, the distribution of polymorphism detected by these markers varies between different regions of the genome. Received: 5 May 1999 / Accepted: 16 August 1999     

Whole genome survey and microsatellite motif identification of Artemia franciscana

Artemia is an industrially important genus used in aquaculture as a nutritious diet for fish and as an aquatic model organism for toxicity tests. However, despite the significance of Artemia, genomic research remains incomplete and knowledge on its genomic characteristics is insufficient. In particular, Artemia franciscana of North America has been widely used in fisheries of other continents, resulting in invasion of native species. Therefore, studies on population genetics and molecular marker development as well as morphological analyses are required to investigate its population structure and to discriminate closely related species. Here, we used the Illumina Hi-Seq platform to estimate the genomic characteristics of A. franciscana through genome survey sequencing (GSS). Further, simple sequence repeat (SSR) loci were identified for microsatellite marker development. The predicted genome size was ∼867 Mb using K-mer (a sequence of k characters in a string) analysis (K = 17), and heterozygosity and duplication rates were 0.655 and 0.809%, respectively. A total of 421467 SSRs were identified from the genome survey assembly, most of which were dinucleotide motifs with a frequency of 77.22%. The present study will be a useful basis in genomic and genetic research for A. franciscana.     

Genomics of the filamentous fungi - moving from the shadow of the bakers yeast

Fungi have now well and truly entered the genomic age. We currently know the complete DNA sequence for 18 fungal species and many more fungal genome sequencing projects are in progress. Whilst yeasts dominated the early genomic years, recently there has been a dramatic increase in filamentous fungal genome projects. The implications of this wealth of genetic information for mycologists worldwide is immense. In this review we summarise the background to fungal genome projects with an emphasis on the filamentous fungi. We discuss efforts to determine gene function and to compare genomes from different species. Since this is such a fast-moving field, useful web sites are listed that will enable the reader to keep up to date with developments.     

RGAAT: A Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes

The rapid development of high-throughput sequencing technologies has led to a dramatic decrease in the money and time required for de novo genome sequencing or genome resequencing projects, with new genome sequences constantly released every week. Among such projects, the plethora of updated genome assemblies induces the requirement of version-dependent annotation files and other compatible public dataset for downstream analysis. To handle these tasks in an efficient manner, we developed the reference-based genome assembly and annotation tool (RGAAT), a flexible toolkit for resequencing-based consensus building and annotation update. RGAAT can detect sequence variants with comparable precision, specificity, and sensitivity to GATK and with higher precision and specificity than Freebayes and SAMtools on four DNA-seq datasets tested in this study. RGAAT can also identify sequence variants based on cross-cultivar or cross-version genomic alignments. Unlike GATK and SAMtools/BCFtools, RGAAT builds the consensus sequence by taking into account the true allele frequency. Finally, RGAAT generates a coordinate conversion file between the reference and query genomes using sequence variants and supports annotation file transfer. Compared to the rapid annotation transfer tool (RATT), RGAAT displays better performance characteristics for annotation transfer between different genome assemblies, strains, and species. In addition, RGAAT can be used for genome modification, genome comparison, and coordinate conversion. RGAAT is available at https://sourceforge.net/projects/rgaat/ and https://github.com/wushyer/RGAAT_v2 at no cost.     

A BAC Library Constructed to the Rice Cultivar

"Minghui 63" is the restorer line for a number of the most important commercial rice hybrids varieties in China. To facilitate long-term commitment in genetic analysis and molecular cloning of the superior genes in the genome of "Minghui 63", the authors have constructed a largeinsert genomic DNA library using the bacterial artificial chromosome (BAC) cloning vector (pBe- loBAC 11). Size fractionated Hind m digest of genomic DNA was ligated to the BAC vector, and the ligation mixture was used to transform the bacterial strain DH10B. A total of over 26 000 clones were obtained with the average insert size of about 150 kb, ranging from 90 to 240 kb. These clones thus represent 9 x rice haploid genome equivalents. The library is now being used for physical mapping of several genomic regions for map-based gene cloning.     

Centromeric retrotransposon lineages predate the maize/rice divergence and differ in abundance and activity

Centromeric retrotransposons (CR) are located almost exclusively at the centromeres of plant chromosomes. Analysis of the emerging Zea mays inbred B73 genome sequence revealed two novel subfamilies of CR elements of maize (CRM), bringing the total number of known CRM subfamilies to four. Orthologous subfamilies of each of these CRM subfamilies were discovered in the rice lineage, and the orthologous relationships were demonstrated with extensive phylogenetic analyses. The much higher number of CRs in maize versus Oryza sativa is due primarily to the recent expansion of the CRM1 subfamily in maize. At least one incomplete copy of a CRM1 homolog was found in O. sativa ssp. indica and O. officinalis, but no member of this subfamily could be detected in the finished O. sativa ssp. japonica genome, implying loss of this prolific subfamily in that subspecies. CRM2 and CRM3, as well as the corresponding rice subfamilies, have been recently active but are present in low numbers. CRM3 is a full-length element related to the non-autonomous CentA, which is the first described CRM. The oldest subfamily (CRM4), as well as its rice counterpart, appears to contain only inactive members that are not located in currently active centromeres. The abundance of active CR elements is correlated with chromosome size in the three plant genomes for which high quality genomic sequence is available, and the emerging picture of CR elements is one in which different subfamilies are active at different evolutionary times. We propose a model by which CR elements might influence chromosome and genome size. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

SNP标记与大豆基因组作图

大豆是重要的粮油作物,在农业和经济中具有重要地位,因此对大豆基因的研究具有重要的意义。利用分子标记构建的遗传图谱是植物基因组结构和功能分析的有力工具。本文综述了SNP标记在大豆基因组中的开发、大豆基因组作图的研究概况及SNP标记在其中的应用。