葡萄生物学研究进入后基因组和系统生物学时代

目前,人类已经完成了拟南芥、葡萄、杨树、番木瓜、水稻、高粱和玉米等植物的基因组测序工作.果树分子生物学研究也因葡萄和番木瓜的基因组测序完成而步人后基因组学和系统生物学时代.以葡萄为例介绍并综述了葡萄基因组和后基因组学、比较基因组学、转录组学、蛋白质组学、代谢组学方面的研究进展,以及它们之间的关系.提出了葡萄生物学进入后...     

奶牛繁殖的遗传学和基因组学研究进展

繁殖性状是奶牛生产的重要经济性状。繁殖性状属于数量性状,受多基因的调节和环境的影响,并且遗传力低(一般不到0.05)。采用传统的选择方法提高奶牛繁殖力很难奏效,而基因组学的发展为有效提高繁殖力提供了可能。介绍了繁殖性状的遗传变异、繁殖性状与产奶量的关系,传统育种和基因辅助育种策略,奶牛繁殖的功能基因组学和基因组选择的研究进展和发展前景,特别是基因组和蛋白质组学的研究有望提高遗传选择的效率,预计在不久的将来,能对改善奶牛的繁殖性能发挥重要作用。     

猪生物医学模型研究进展

猪与人不仅在体重、生理特点、器官形成和疾病的发生方面都有高度的相似性,而且二者在基因组序列和染色体结构上有很高的同源性,所以猪已被作为人类研究中最主要的哺乳动物模型.目前,小型猪已被广泛应用于皮肤烧伤、肿瘤、免疫学、心血管病、糖尿病、畸形学和产期生物学、牙科、药理学等多方面的模式研究,以及对黑色素瘤和感染性疾病的基因组学研究中.在控制猪繁殖与呼吸系统综合征发生中的一些可行的基因组学方法,将为人类相似的病毒感染性疾病研究提供重要的参考.     

Microbial communities of the ant Formica exsecta and its nest material

In this study, we investigated the bacterial and fungal microbiomes of the ant Formica exsecta (Hymenoptera, Formicidae), and assessed whether the microbial communities inside the ants differ from those in their nest material. Furthermore, we investigated whether the microbial communities inside the ants are conserved across time. To achieve this, we sequenced the bacterial 16S rRNA, and the fungal ITS region in entire adult worker ants and their nest material by Illumina MiSeq. We found that both the bacterial, and the fungal microbiomes form communities discrete from those in the surrounding nest material. In addition to the differences in species composition, we also found that bacterial species diversity, species richness, ζ diversity, and evenness were lower in ants than in the nest material. For fungi, only species richness was lower in the ants than in the nest material. The rate of within-colony species turnover across sampling events was not statistically significant for bacteria, but highly significant for fungi. This suggests that the fungal communities in the ants are less stable than the bacterial ones. Four bacterial taxa (Alphaproteobacteria, Proteobacteria, Staphylococcus, and Streptococcus), and two fungal taxa (Davidiella and Cryptococcus) formed a core microbiome, being consistently present and more abundant in the ants, but absent in the nest material. In all other cases differences in community composition and structure were due to taxa that were more consistently present and more abundant in the nest material, and frequently absent in the ants. Furthermore, we found 36 unique OTUs identified as Proteobacteria, and 82 unique OTUs identified as Alphaproteobacteria in the ants, representing 2.5% and 5.8% of all bacterial OTUs and 24.6% and 41% of the total number of bacterial sequences. This suggests that F. exsecta harbours a considerable bacterial diversity that so far remains unexplored.     

萝卜抽薹开花相关基因的研究进展

通过构建萝卜抽薹开花相关基因的cDNA文库,获取大量的EST序列,并与十字花科模式植物拟南芥、白菜等进行比较基因组学研究,研究结果显示:萝卜与拟南芥、白菜等植物基因组具有很高的同源性,控制抽薹开花的相关基因在不同物种中具有保守性。拟南芥抽薹研究表明,抽薹开花过程受多基因控制,具有多种调控途径。抽薹开花是一个复杂的过程,其中FLC、FT、LFY等基因处于关键位置。目前这些关键基因在萝卜EST序列中已经发现了同源片段,并进行了一些基因克隆,结合萝卜基因组测序的完成,未来萝卜抽薹研究将进入基因功能验证和全基因组调控模式研究之中。     

Genome Reduction and Secondary Metabolism of the Marine Sponge-Associated Cyanobacterium Leptothoe

Sponges form symbiotic relationships with diverse and abundant microbial communities. Cyanobacteria are among the most important members of the microbial communities that are associated with sponges. Here, we performed a genus-wide comparative genomic analysis of the newly described marine benthic cyanobacterial genus Leptothoe (Synechococcales). We obtained draft genomes from Le. kymatousa TAU-MAC 1615 and Le. spongobia TAU-MAC 1115, isolated from marine sponges. We identified five additional Leptothoe genomes, host-associated or free-living, using a phylogenomic approach, and the comparison of all genomes showed that the sponge-associated strains display features of a symbiotic lifestyle. Le. kymatousa and Le. spongobia have undergone genome reduction; they harbored considerably fewer genes encoding for (i) cofactors, vitamins, prosthetic groups, pigments, proteins, and amino acid biosynthesis; (ii) DNA repair; (iii) antioxidant enzymes; and (iv) biosynthesis of capsular and extracellular polysaccharides. They have also lost several genes related to chemotaxis and motility. Eukaryotic-like proteins, such as ankyrin repeats, playing important roles in sponge-symbiont interactions, were identified in sponge-associated Leptothoe genomes. The sponge-associated Leptothoe stains harbored biosynthetic gene clusters encoding novel natural products despite genome reduction. Comparisons of the biosynthetic capacities of Leptothoe with chemically rich cyanobacteria revealed that Leptothoe is another promising marine cyanobacterium for the biosynthesis of novel natural products.     

Biotechnological and Ecological Potential of Micromonospora provocatoris sp. nov., a Gifted Strain Isolated from the Challenger Deep of the Mariana Trench

A Micromonospora strain, isolate MT25^T, was recovered from a sediment collected from the Challenger Deep of the Mariana Trench using a selective isolation procedure. The isolate produced two major metabolites, n-acetylglutaminyl glutamine amide and desferrioxamine B, the chemical structures of which were determined using 1D and 2D-NMR, including ¹H-¹⁵N HSQC and ¹H-¹⁵N HMBC 2D-NMR, as well as high resolution MS. A whole genome sequence of the strain showed the presence of ten natural product-biosynthetic gene clusters, including one responsible for the biosynthesis of desferrioxamine B. Whilst 16S rRNA gene sequence analyses showed that the isolate was most closely related to the type strain of Micromonospora chalcea, a whole genome sequence analysis revealed it to be most closely related to Micromonospora tulbaghiae 45142^T. The two strains were distinguished using a combination of genomic and phenotypic features. Based on these data, it is proposed that strain MT25^T (NCIMB 15245^T, TISTR 2834^T) be classified as Micromonospora provocatoris sp. nov. Analysis of the genome sequence of strain MT25^T (genome size 6.1 Mbp) revealed genes predicted to responsible for its adaptation to extreme environmental conditions that prevail in deep-sea sediments.     

生物信息学在畜禽基因组研究中的应用

生物信息学已成为整个生命科学发展的重要组成部分，是生命科学研究的前沿领域。作者简述了畜禽基因组学和畜禽生物信息学的研究概况，着重阐述了生物信息学在畜禽基因组研究中的应用现状，并展望其发展前景。     

Agricultural Genomics: An Approach to Plant Protection

Genomics studies, focused on whole-genome analysis, have opened up a new era for biology in general, and for agriculture in particular. Along with the use of genetic plant models and the progress in sequencing agriculturally important organisms, the combination of bioinformatics and functional genomics globally enhances agricultural genomics. These studies are likely to pave the way towards better understanding of plant–pathogen biological networks, and eventually to lead to breakthroughs in the promotion of plant resistance to agricultural pests.     

新的禾本科模式植物——二穗短柄草

水稻（Oryza sativa）是禾本科中目前唯一已完成基因组测序的模式植物,但由于它很早从冷季型禾本科中进化分离出来,故其作为禾本科其他亚科的模式植物有一定局限性,因此,需要一种新的、更适合的模式植物。二穗短柄草（Brachypodium distachyon）是一种温带禾草,归属禾本科早熟禾亚科短柄草族短柄草属,具有基因组小、株型小、自花授粉、一年生、生命周期短、有二倍体和一系列多倍体、易培植、易转化等诸多优点,尤其是与很多重要的谷类作物如小麦、大麦、燕麦、玉米、水稻、高梁等以及许多牧草与草坪草有较近的亲缘关系,因而是温带禾本科植物功能基因纽学以及生物能源作物（如柳枝稷）研究的理想模式植物,作者例举二穗短柄草之所以成为新模式植物系统的依据,并介绍其在遗传进化、基因组特点、功能基因组及形态特征等方面的研究进展。