芸薹属A，B和C基因组之间关系研究进展

芸薹属A,B和C基因组之间的亲缘关系近年来取得了很大进展,大量细胞遗传学和分子生物学的研究结果表明A和C基因组之间的亲缘关系较A和B基因组以及B和C基因组之间更为接近。A,B和C基因组之间的比较基因组结果表明,这3个基因组是由更加原始物种进化而来的。在芸薹属基因组演化过程中发生了大量的染色体变异,如重复、缺失、重排等,从而造成了现在不同基因组之间的差别。最后,文章对芸薹属不同基因组和拟南芥基因组之间的亲缘关系进行了综述。     

芸薹属植物基因组学研究进展

芸薹属是十字花科植物300多个属中最为重要的一个属,是我国栽培面积最大的蔬菜作物。拟南芥和芸薹属在十字花科中两者的亲缘关系最近,通过它们之间的比较作图,两者之间的共线性被大量发现。模式植物拟南芥全基因组测序已经完成,这为芸薹属作物的基因组研究提供了便利条件。芸薹属作物的功能基因组学能够进一步明确不同发育时期基因的功能,为解释芸薹属的进化提供基因证据。就芸薹属植物在比较基因组学、功能基因组学最新进展,特别是芸薹属与模式植物拟南芥在基因组之间的相互关系进行了综述。     

芸薹属作物EST-SNP的发掘与分析

芸薹属作物是十字花科中重要的蔬菜和油用作物,经济价值和食用价值比较高。本研究通过生物信息学手段,从3个芸薹属物种EST序列中获得了大量的SNP和Indel资源,对SNP与EST的数量及拼接结果之间的关系、SNP碱基置换的偏好性、Indel碱基数量与发生频率之间的关系进行了分析。分析结果对深入研究芸薹属基因组特点具有一定的参考价值,为进一步通过试验验证预测的SNP位点、开发该作物高通量SNP分子标记奠定了基础。     

大豆重复序列的克隆,特性分析及在染色体上的定位

从大豆栽培品种Ｕｎｉｏｎ（Ｇ．ｍａｘ）基因组ｐＵＣ１８质粒文库中,以基因组ＤＮＡ为探针,筛选出一个重复序列家族。序列分析表明,此重复序列的重复单位为９１ｂｐ,拷贝数约为１０￣５,其序列约占基因组ＤＮＡ的０．９％。基因组ＤＮＡ不同限制酶片段Ｓｏｕｔｈｅｒｎ杂交分析和染色体原位杂交分析表明此重复序列主要以串联方式集中分布在Ｍ２和Ｍ１１号染色体的臂上,而另外一些则散布于整个Ｍ１２和Ｓｍ７号染色体上。以该序列为探针片大豆属不同亚属１３个种的１８个品系的Ｓｏｕｔｈｅｒｎ杂交结果表明,此重复序列为Ｓｏｊａ亚属所特有。这一Ｓｏｉａ亚属特异重复序列的发现,从另一个角度支持应把Ｓｏｊａ亚属的３个种Ｇ．ｓｏｊａ、Ｇ．ｇｒａｃｉｌｌｉｓ、Ｇ．ｍａｘ划分为一个种的观点。     

芸薹属蔬菜Chs基因序列多态性

为探讨我国芸薹属蔬菜的起源及遗传多样性,克隆、测序芸薹属不同种的Chs基因序列。A基因组二倍体、A基因组多倍体、B基因组多倍体和C基因组二倍体的Chs基因突变位点数分别为120、172、194和25个,Chs基因多态性表现为:B基因组多倍体A基因组二倍体A基因组多倍体C基因组多倍体。Tajima'D、Fu and Li'D和Fu and Li'F检验表明A基因组二倍体、C基因组二倍体Chs基因是中性进化基因。HKA平衡检验及误配分析表明A基因组多倍体和B基因组多倍体Chs基因进化中存在选择作用。A基因组和B基因组间存在较低的共有差异和较高的共有多态性,C基因组与A、B基因组存在较高的共有差异和较低的共有多态性。系统发育树将芸薹属Chs基因序列分成4个亚支、10个支系。网状分析表明,白菜可能是四倍体A基因组的供体,黑芥可能是四倍体B基因组的供体,甘蓝可能是四倍体C基因组的供体。中国芸薹属蔬菜在Chs基因位点有较高的遗传多态性,不同基因组间分化程度不一样,B基因组分化较大,A和C基因组分化较小。A和B基因组的亲缘关系较A和C基因组以及B和C基因组更为接近。建议根据基因组的不同将中国芸薹蔬菜分成白菜组、芥菜组和甘蓝组,研究结果支持芸薹属进化的禹式三角模型。     

鹿科麂属动物基因组演化研究进展

鹿科麂属(Muntiacus, Cervidae)在近两三百万年内经历了快速物种辐射, 但其物种间核型差异巨大. 5个现生种核型数据显示, 该类群染色体数目范围从小麂(Muntiacus reevesi)的46条到赤麂(M. muntjak vaginalis)的6条. 该类群的基因组在较短时间内发生了快速演化, 使其成为进化生物学研究的理想材料. 40多年来, 技术的革新使该领域的研究不断深入, 染色体重排的类型、推动重排的分子机制及物种间的核型演化历程逐渐被阐释. 而且, 研究中发现, 雄性黑麂(M. crinifrons)1p+4染色体的演化途径与哺乳动物Y染色体的演化历程相似, 可成为哺乳动物性染色体演化研究的珍贵模型. 有关麂属动物基因组演化依然有许多问题等待更加全面、深入的探讨. 本文总结了该领域研究进展, 并对未来研究热点进行了展望.     

转座子在植物XY性染色体起源与演化过程中的作用

XY性染色体决定系统是决定植物性别的主要方式,但是对于其起源与演化机制却知之甚少。目前认为,携带控制雌蕊或雄蕊发育基因的一对常染色体由于某种未知原因的突变形成早期的neo-Y或neo-X性染色体,随着演化的进行,早期XY性染色体之间的重组逐渐受到抑制,非重组区域扩展最终形成异型的性染色体。研究发现,重复序列的累积以及DNA甲基化等因素都可能参与了XY性染色体的异染色质化、重组抑制及Y染色体体积增大过程。转座子作为一种基因组中含量最高的重复序列在性染色体演化中扮演了重要的角色,包括性染色体演化的起始激发,以及导致性染色体局部表观遗传修饰使其发生异染色质化扩展和重组抑制。文章综述了转座子在植物性染色体上的累积及其与性染色体异染色质化之间的关系,并简要分析了转座子在性染色体演化过程中的作用。     

利用栽培稻C0t-1DNA和基因组DNA比较分析斑点野生稻和短药野生稻基因组

通过荧光原位杂交(FISH)利用来源于A基因组栽培稻的中高度重复序列C0t-1DNA和基因组DNA作为探针,对栽培稻、斑点野生稻和短药野生稻进行了比较基因组分析。结果发现C0t-1DNA杂交信号主要分布在这3种染色体的着丝粒、近着丝粒和端粒区域,在斑点野生稻染色体上的信号多于短药野生稻,与gDNA作为探针FISH的结果相一致,说明A和B基因组间的亲缘关系明显近于A和F基因组。确定了含有中高度重复序列的C0t-1DNA用于属内种间关系研究的可行性,并根据C0t-1DNA的FISH结果进行了染色体核型分析。     

端粒酶(Telomerase)PCR ELISA——用于检测端粒酶活性的快速方法

宝灵曼公司最近推出了一种端粒酶PCR ELISA,它能对培养细胞或其他生物样品的细胞提取物中的端粒酶活性作高度灵敏的定性检测。 端粒是真核细胞染色体末端的特殊DNA-蛋白质结构,端粒DNA的特点是含有大量串连重复并富含G的重复序列,这些序列在进化中是高度保守的。端粒被认为可以阻止基因组DNA被降解或发生有害的重组,如:末端融合、重排、染色体易位和染色体缺失。由于     

全基因组与串联复制后白菜基因的保留

全基因组复制与串联复制是两种重要的基因扩增途径,在生物进化过程中普遍存在.这两种复制方式相互关系的研究在拟南芥中已经取得很多成果.白菜(Brassica rapa)属于十字花科(Brassicaceae)芸薹属(Brassca),是一类重要的经济作物,也是研究基因组多倍化和形态演化的模式植物.白菜基因组的测序与组装工作已经取得了重大成就,运用比较基因组学的方法,通过比较白菜与模式植物拟南芥,可以清晰鉴定白菜基因组经历的全基因组三倍化事件.同时,白菜与拟南芥同属于十字花科,有较近的起源关系和良好的基因组共线性关系.因此,拟南芥可以作为外群研究白菜全基因组三倍化以及串联重复之后基因的偏向性保留.结果发现,在白菜中存在物种特有的偏向性保留基因,即与环境刺激相关的基因和与激素相关的基因.     

Karyotype and identification of all homoeologous chromosomes of allopolyploid Brassica napus and its diploid progenitors

Investigating recombination of homoeologous chromosomes in allopolyploid species is central to understanding plant breeding and evolution. However, examining chromosome pairing in the allotetraploid Brassica napus has been hampered by the lack of chromosome-specific molecular probes. In this study, we establish the identification of all homoeologous chromosomes of allopolyploid B. napus by using robust molecular cytogenetic karyotypes developed for the progenitor species Brassica rapa (A genome) and Brassica oleracea (C genome). The identification of every chromosome among these three Brassica species utilized genetically mapped bacterial artificial chromosomes (BACs) from B. rapa as probes for fluorescent in situ hybridization (FISH). With this BAC-FISH data, a second karyotype was developed using two BACs that contained repetitive DNA sequences and the ubiquitous ribosomal and pericentromere repeats. Using this diagnostic probe mix and a BAC that contained a C-genome repeat in two successive hybridizations allowed for routine identification of the corresponding homoeologous chromosomes between the A and C genomes of B. napus. When applied to the B. napus cultivar Stellar, we detected one chromosomal rearrangement relative to the parental karyotypes. This robust novel chromosomal painting technique will have biological applications for the understanding of chromosome pairing, homoeologous recombination, and genome evolution in the genus Brassica and will facilitate new applied breeding technologies that rely upon identification of chromosomes.     

Sequence-level analysis of the diploidization process in the triplicated FLOWERING LOCUS C region of Brassica rapa

Strong evidence exists for polyploidy having occurred during the evolution of the tribe Brassiceae. We show evidence for the dynamic and ongoing diploidization process by comparative analysis of the sequences of four paralogous Brassica rapa BAC clones and the homologous 124-kb segment of Arabidopsis thaliana chromosome 5. We estimated the times since divergence of the paralogous and homologous lineages. The three paralogous subgenomes of B. rapa triplicated 13 to 17 million years ago (MYA), very soon after the Arabidopsis and Brassica divergence occurred at 17 to 18 MYA. In addition, a pair of BACs represents a more recent segmental duplication, which occurred approximately 0.8 MYA, and provides an exception to the general expectation of three paralogous segments within the B. rapa genome. The Brassica genome segments show extensive interspersed gene loss relative to the inferred structure of the ancestral genome, whereas the Arabidopsis genome segment appears little changed. Representatives of all 32 genes in the Arabidopsis genome segment are represented in Brassica, but the hexaploid complement of 96 has been reduced to 54 in the three subgenomes, with compression of the genomic region lengths they occupy to between 52 and 110 kb. The gene content of the recently duplicated B. rapa genome segments is identical, but intergenic sequences differ.     

Mating systems of Cuphea laminuligera and Cuphea lutea

Summary A series of RFLP and isozyme markers were followed in the progenies of two alien addition lines of Brassica campestris-oleracea. One of the lines, carrying the C genome chromosome 4 as the alien chromosome, was surveyed for six markers. Fifty-four percent of the plants carrying alien chromosomes displayed all the expected makers, whereas the rest had one to five markers missing. The second line for C genome chromosome 5 displayed a similar behavior when surveyed for three markers. All three markers were transmitted together in 46% of the plants carrying alien chromosomes, whereas the rest carried only one or two of the markers. The loss of markers was associated with reduced chromosome size caused by deletions. The observed chromosome deficiencies permitted deletion analysis for a rough physical mapping and ordering of the markers on the two C genome chromosomes. The deletions observed may represent another mechanism for molding the chromosomes of the Brassica genomes during their evolution.     

甘蓝型油菜A基因组候选BAC克隆的筛选及其插入片段大小分析

选择甘蓝型油菜A基因组10个连锁群上特有的85个SSR分子标记,合成其引物序列,采用四维PCR法筛选甘蓝型油菜-新疆野生油菜二体异附加系BAC文库,成功筛选到甘蓝型油菜A基因组39个BAC克隆,其插入片段介于50～300 kb之间,平均为120 kb。甘蓝型油菜A基因组10个连锁群BAC克隆的获得,对后续开展甘蓝型油菜A基因组染色体识别、基因染色体定位、遗传距离与物理距离间关系分析等均具有重要价值。     

Identification of individual chromosomes and parental genomes in Brassica juncea using GISH and FISH

The three diploid (B. nigra, B. oleracea, B. campestris) and three allotetraploid (B. carinata, B. juncea, B. napus) species of Brassica, known as the "U-triangle" are one of the best model systems for the study of polyploidy. Numerous molecular investigations have provided a wealth of new insights into the polyploid origin and changes during the evolution of Brassica, but there are still many controversial aspects of their relationship and evolution. Interpretation of genome changes during evolution requires individual chromosome identification within the genome and clear distinction of genomes within the allotetraploid. The aim of this study was to identify individual chromosomes of B. juncea (genome AABB; 2n = 4x = 36) and to determine their genomic origin. Fluorescence in situ hybridization with 5S and 45S rDNA probes enabled discrimination of a substantial number of chromosomes, providing chromosomal landmarks for 20 out of 36 chromosomes of B. juncea. Additionally, along with double target genomic in situ hybridization, it allowed assignment of all chromosomes to either the A or B genomes.     

Simple sequence repeat-based comparative genomics between Brassica rapa and Arabidopsis thaliana: the genetic origin of clubroot resistance

An SSR-based linkage map was constructed in Brassica rapa. It includes 113 SSR, 87 RFLP, and 62 RAPD markers. It consists of 10 linkage groups with a total distance of 1005.5 cM and an average distance of 3.7 cM. SSRs are distributed throughout the linkage groups at an average of 8.7 cM. Synteny between B. rapa and a model plant, Arabidopsis thaliana, was analyzed. A number of small genomic segments of A. thaliana were scattered throughout an entire B. rapa linkage map. This points out the complex genomic rearrangements during the course of evolution in Cruciferae. A 282.5-cM region in the B. rapa map was in synteny with A. thaliana. Of the three QTL (Crr1, Crr2, and Crr4) for clubroot resistance identified, synteny analysis revealed that two major QTL regions, Crr1 and Crr2, overlapped in a small region of Arabidopsis chromosome 4. This region belongs to one of the disease-resistance gene clusters (MRCs) in the A. thaliana genome. These results suggest that the resistance genes for clubroot originated from a member of the MRCs in a common ancestral genome and subsequently were distributed to the different regions they now inhabit in the process of evolution.     

Conservation of the microstructure of genome segments in Brassica napus and its diploid relatives

The cultivated Brassica species are the group of crops most closely related to Arabidopsis thaliana (Arabidopsis). They represent models for the application in crops of genomic information gained in Arabidopsis and provide an opportunity for the investigation of polyploid genome formation and evolution. The scientific literature contains contradictory evidence for the dynamics of the evolution of polyploid genomes. We aimed at overcoming the inherent complexity of Brassica genomes and clarify the effects of polyploidy on the evolution of genome microstructure in specific segments of the genome. To do this, we have constructed bacterial artificial chromosome (BAC) libraries from genomic DNA of B. rapa subspecies trilocularis (JBr) and B. napus var Tapidor (JBnB) to supplement an existing BAC library from B. oleracea. These allowed us to analyse both recent polyploidization (under 10,000 years in B. napus) and more ancient polyploidization events (ca. 20 Myr for B. rapa and B. oleracea relative to Arabidopsis), with an analysis of the events occurring on an intermediate time scale (over the ca. 4 Myr since the divergence of the B. rapa and B. oleracea lineages). Using the Arabidopsis genome sequence and clones from the JBr library, we have analysed aspects of gene conservation and microsynteny between six regions of the genome of B. rapa with the homoeologous regions of the genomes of B. oleracea and Arabidopsis. Extensive divergence of gene content was observed between the B. rapa paralogous segments and their homoeologous segments within the genome of Arabidopsis. A pattern of interspersed gene loss was identified that is similar, but not identical, to that observed in B. oleracea. The conserved genes show highly conserved collinearity with their orthologues across genomes, but a small number of species-specific rearrangements were identified. Thus the evolution of genome microstructure is an ongoing process. Brassica napus is a recently formed polyploid resulting from the hybridization of B. rapa (containing the Brassica A genome) and B. oleracea (containing the Brassica C genome). Using clones from the JBnB library, we have analysed the microstructure of the corresponding segments of the B. napus genome. The results show that there has been little or no change to the microstructure of the analysed segments of the Brassica A and C genomes as a consequence of the hybridization event forming natural B. napus. The observations indicate that, upon polyploid formation, these segments of the genome did not undergo a burst of evolution discernible at the scale of microstructure.     

Patterns of genome duplication within the Brassica napus genome.

The progenitor diploid genomes (A and C) of the amphidiploid Brassica napus are extensively duplicated with 73% of genomic clones detecting two or more duplicate sequences within each of the diploid genomes. This comprehensive duplication of loci is to be expected in a species that has evolved through a polyploid ancestor. The majority of the duplicate loci within each of the diploid genomes were found in distinct linkage groups as collinear blocks of linked loci, some of which had undergone a variety of rearrangements subsequent to duplication, including inversions and translocations. A number of identical rearrangements were observed in the two diploid genomes, suggesting they had occurred before the divergence of the two species. A number of linkage groups displayed an organization consistent with centric fusion and (or) fission, suggesting this mechanism may have played a role in the evolution of Brassica genomes. For almost every genetically mapped locus detected in the A genome a homologous locus was found in the C genome; the collinear arrangement of these homologous markers allowed the primary regions of homoeology between the two genomes to be identified. At least 16 gross chromosomal rearrangements differentiated the two diploid genomes during their divergence from a common ancestor.     

Rapid divergence of repetitive DNAs in Brassica relatives

Centromeric, subtelomeric, and telomeric repetitive DNAs were characterized in Brassica species and the related Raphanus sativus and Arabidopsis thaliana. In general, rapid divergence of the repeats was found. The centromeric tandem satellite repeats were differentially distributed in the species studied, suggesting that centromeric repeats have diverged during the evolution of the A/C and B genome lineages. Sequence analysis of centromeric repeats suggested rapid evolution. Pericentromere-associated retrotransposons were identified and showed divergence during the evolution of the lineages as centromeric repeats. A novel subtelomeric tandem repeat from B. nigra was found to be conserved across the diploid Brassica genomes; however, this sequence was not identified in the related species. In contrast to previous studies, interstitial telomere-like repeats were identified in the pericentromeres of Brassica chromosomes, and these repeats may be associated with genomic stability. These results provide insight into genome evolution during polyploidization in Brassica and divergence within the Brassicaceae.