芸薹属植物比较基因组学研究进展

芸薹属(Brassica)植物是双子叶植物比较基因组学研究的重点对象。经过十几年的研究, 芸薹属植物比较基因组学研究已取得很大进展。宏观共线性和微观共线性两个层次的研究均发现, 芸薹属植物之间以及芸薹属和拟南芥之间都存在广泛的共线性, 表明拟南芥信息在芸薹属中具有重要应用价值。芸薹属作物基因组内存在着多个拷贝的共线性区域, 支持二倍体芸薹属作物起源于多倍体祖先的假设。     

芸薹属植物比较基因组学研究进展

芸薹（Brassica）植物是双子叶植物比较基因组学研究的重点对象。经过十几年的研究,芸薹属植物比较基因组学研究已取得很大进膜。宏观共线性和微观共线性两个层次的研究均发现,芸薹属植物之间以及芸薹属和拟南芥之间都存在广泛的共线性,表明拟南芥信息在芸薹属中具有重要应用价值。芸薹属作物基因组内存在着多个拷贝的共线性区域,支持二倍体芸薹属作物起源于多倍体祖先的假设。     

Background and Overview of Comparative Genomics

Comparative genomics---the cross-referencing of information on genome organization between species---provides an additional dimension to the Human Genome Project and can derive much information from it for the benefit of animal health and animal breeding. Arrangements of genes and other DNA sequences may be determined by a variety of genetic and physical techniques, at resolutions from the gross cytological level to the level of the single base pair. Gross arrangements and rearrangements can also be charted by comparative chromosome painting. Genome organization may then be compared across mammal---and other vertebrate---species. Genetic mapping is well advanced in several livestock species as well as rodent model species, and outline maps are available for at least 30 mammal species in eight orders. At the time of this writing, maps are being rapidly constructed for chicken and fish species. Comparisons, even over vast evolutionary time scales, show that the mammal genome---indeed, the vertebrate genome---has been highly conserved. Thus, information about location and function of genes is directly transferable across species and should greatly accelerate the search for genes that specify inherited diseases in domestic mammals and humans as well as genes that specify economically important traits.     

Reference-Free Validation of Short Read Data

Background

High-throughput DNA sequencing techniques offer the ability to rapidly and cheaply sequence material such as whole genomes. However, the short-read data produced by these techniques can be biased or compromised at several stages in the sequencing process; the sources and properties of some of these biases are not always known. Accurate assessment of bias is required for experimental quality control, genome assembly, and interpretation of coverage results. An additional challenge is that, for new genomes or material from an unidentified source, there may be no reference available against which the reads can be checked.

Results

We propose analytical methods for identifying biases in a collection of short reads, without recourse to a reference. These, in conjunction with existing approaches, comprise a methodology that can be used to quantify the quality of a set of reads. Our methods involve use of three different measures: analysis of base calls; analysis of k-mers; and analysis of distributions of k-mers. We apply our methodology to wide range of short read data and show that, surprisingly, strong biases appear to be present. These include gross overrepresentation of some poly-base sequences, per-position biases towards some bases, and apparent preferences for some starting positions over others.

Conclusions

The existence of biases in short read data is known, but they appear to be greater and more diverse than identified in previous literature. Statistical analysis of a set of short reads can help identify issues prior to assembly or resequencing, and should help guide chemical or statistical methods for bias rectification.     

Comparative Genomics of Cluster O Mycobacteriophages

Mycobacteriophages – viruses of mycobacterial hosts – are genetically diverse but morphologically are all classified in the Caudovirales with double-stranded DNA and tails. We describe here a group of five closely related mycobacteriophages – Corndog, Catdawg, Dylan, Firecracker, and YungJamal – designated as Cluster O with long flexible tails but with unusual prolate capsids. Proteomic analysis of phage Corndog particles, Catdawg particles, and Corndog-infected cells confirms expression of half of the predicted gene products and indicates a non-canonical mechanism for translation of the Corndog tape measure protein. Bioinformatic analysis identifies 8–9 strongly predicted SigA promoters and all five Cluster O genomes contain more than 30 copies of a 17 bp repeat sequence with dyad symmetry located throughout the genomes. Comparison of the Cluster O phages provides insights into phage genome evolution including the processes of gene flux by horizontal genetic exchange.     

玉米比较基因组学研究进展

玉米是世界上重要的粮食作物 ,长期以来一直是遗传学、分子生物学和基因组学研究的重点对象。近十多年来 ,涉及到玉米的基因组学研究取得了很大进展。不仅在利用比较遗传作图方法方面发现玉米和其它植物 (尤其是禾谷类作物 )的基因组存在广泛的共线性 ,在较小的DNA区域上也发现存在微共线性。尽管还存在一些共线性的例外情形 ,进一步的比较基因组学研究将深入阐明玉米基因组的结构和进化 ,并把这些研究成果应用于基因发掘中。     

植物比较基因组学的研究进展

评述植物比较基因组学最新的发展及应用状况。     

比较基因组学和人类基因组研究

在人类基因组计划突飞猛进地开展的同时,模式生物基因组计划也在轰轰烈烈地进行,并取得许多实质性的进展,是人类对于模式生物基因组有了更广泛更深刻的认识。这些知识的积累,从根本上推动了人类基因组计划的进行。     

比较基因组学及其应用

比较基因组学是利用某些基因组图谱和测序获得的信息推测其他生物基因组的基因数目、位置、功能、表达机制和物种进化的学科。比较基因组学的发展与序列数据的积累密切相关,目前该学科已经成为研究生物基因组的最主要手段之一。利用FASTA、BLAST和CLUSTAL W等序列比对工具,种间的比较基因组学能够让人们了解物种间在基因组结构上的差异,发现基因的功能、物种的进化关系,以及进行功能基因的克隆。种内的比较基因组学研究主要涉及个体或群体基因组内诸如SNP、CNP等变异和多态现象。比较基因组学的研究结果不但有助于深入了解生命体的遗传机制,也有助于阐明人类复杂疾病的致病机制,揭示生命的本质规律。