Genetics. Transposons help sculpt a dynamic genome

New research is showing that the mobile genetic elements called transposons cause more extensive restructuring of the genome than previously thought. Researchers have known for about 20 years that transposons can expand the genome, resulting in the repetitive DNA sequences sometimes called "junk," but the new work indicates that transposons can also contribute to substantial DNA losses. What's more, these changes can be rapid--at least on an evolutionary scale--and may help organisms adapt to their environments.     

Prokaryotic chromosomes and disease

Recent insights into bacterial genome organization and function have improved our understanding of the nature of pathogenic bacteria and their ability to cause disease. It is becoming increasingly clear that the bacterial chromosome constantly undergoes structural changes due to gene acquisition and loss, recombination, and mutational events that have an impact on the pathogenic potential of the bacterium. Even though the bacterial genome includes additional genetic elements, the chromosome represents the most important entity in this context. Here, we will show that various processes of genomic instability have an influence on the many manifestations of infectious disease.     

Genetic analysis of the human malaria parasite Plasmodium falciparum

Malaria parasites are haploid for most of their life cycle, with zygote formation and meiosis occurring during the mosquito phase of development. The parasites can be analyzed genetically by transmitting mixtures of cloned parasites through mosquitoes to permit cross-fertilization of gametes to occur. A cross was made between two clones of Plasmodium falciparum differing in enzymes, drug sensitivity, antigens, and chromosome patterns. Parasites showing recombination between the parent clone markers were detected at a high frequency. Novel forms of certain chromosomes, detected by pulsed-field gradient gel electrophoresis, were produced readily, showing that extensive rearrangements occur in the parasite genome after cross-fertilization. Since patients are frequently infected with mixtures of genetically distinct parasites, mosquito transmission is likely to provide the principal mechanisms for generating parasites with novel genotypes.     

The composite genome of the legume symbiont Sinorhizobium meliloti

The scarcity of usable nitrogen frequently limits plant growth. A tight metabolic association with rhizobial bacteria allows legumes to obtain nitrogen compounds by bacterial reduction of dinitrogen (N2) to ammonium (NH4+). We present here the annotated DNA sequence of the alpha-proteobacterium Sinorhizobium meliloti, the symbiont of alfalfa. The tripartite 6.7-megabase (Mb) genome comprises a 3.65-Mb chromosome, and 1.35-Mb pSymA and 1.68-Mb pSymB megaplasmids. Genome sequence analysis indicates that all three elements contribute, in varying degrees, to symbiosis and reveals how this genome may have emerged during evolution. The genome sequence will be useful in understanding the dynamics of interkingdom associations and of life in soil environments.     

A "selfish" B chromosome that enhances its transmission by eliminating the paternal genome

In the parasitic wasp, Nasonia vitripennis, males are haploid and usually develop from unfertilized eggs, whereas females are diploid and develop from fertilized eggs. Some individuals in this species carry a genetic element, termed psr (paternal sex ratio), which is transmitted through sperm and causes condensation and subsequent loss of paternal chromosomes in fertilized eggs, thus converting diploid females into haploid males. In this report the psr trait was shown to be caused by a supernumerary chromosome. This B chromosome contains at least three repetitive DNA sequences that do not cross-hybridize to each other or to the host genome. The psr chromosome apparently produces a trans-acting product responsible for condensation of the paternal chromosomes, but is itself insensitive to the effect. Because the psr chromosome enhances its transmission by eliminating the rest of the genome, it can be considered the most "selfish" genetic element yet described.     

植物特异DNA序列应用研究进展

植物特异DNA序列是指在某些植物属、种、基因组或染色体上单独具有的特异存在的DNA序列。几乎所有的高等生物基因组中都有一些物种或基因组特异(有)的DNA序列。研究这些特定序列,对研究物种间在进化过程中的关系及现有物种间的亲缘关系、特异性状表达等方面有着重要的意义。简述了植物特异DNA序列的种类,总结了利用特异DNA序列作为与某一性状基因连锁的分子标记的应用情况,以及特异DNA序列在鉴定外源染色体的来源、某一染色体组或基因组、某一物种或属植物等方面的应用情况,提出了存在的问题与应用前景。     

植物染色体重排在作物遗传改良中的应用研究进展

染色体重排是一种可能导致DNA片段丢失、重复、易位和倒位的机制,从而改变基因组结构,为创造新的变异性状提供可能。植物染色体重排事件的准确鉴定有助于更深入地理解植物基因组的结构、功能及它们在植物演化和作物育种中的作用。该文深入探讨了植物染色体重排的基本概念,介绍了植物染色体重排的自然发生和人工诱导的技术方法,阐述了植物染色体重排的细胞生物学、分子遗传学和高通量测序鉴定方法。同时,系统总结了植物染色体重排技术在作物遗传育种中的应用,结合具体实践,着重强调了染色体重排技术在提高农作物的遗传多样性、改良农作物的重要性状、增强农作物的环境适应性等方面极具优越性。然而,目前染色体重排的发生概率较低,技术上仍存在挑战,需要更多精准的工具和策略来实现染色体片段的精准定位和重排。通过全面了解染色体重排及其相关技术,研究人员和育种家可以更好地利用植物基因组,为全球粮食安全和环境可持续发展提供创新解决方案。相关研究不仅为深入认识植物基因组提供新途径,也为未来创新作物育种奠定坚实基础。通过挖掘植物基因组的多样性和可塑性,染色体重排技术有望为培育高产、优质、多抗的农作物新品种提供更多可能性,对解决全球日益严峻的...     

基因组编辑技术及其安全管理

基因组编辑技术利用核酸酶对生物体内的DNA双链进行断裂,并以非同源末端连接或同源重组的方式对基因组DNA特定位点进行突变、缺失或者基因的插入与替换。锌指核酸酶、转录激活因子样效应物核酸酶、成簇规律间隔短回文重复序列是目前基因组编辑技术应用中的3种关键核酸酶。基因组编辑技术已在植物基因功能、育种等领域广泛应用,特别是基于成簇规律间隔短回文重复序列的基因编辑技术CRISPR-Cas9。具有优良性状的基因组编辑大豆、玉米等产品已逐步从实验室走向田间,基因组编辑作物展现了较传统转基因作物更为优越的应用前景。本文简要概述了主要使用的3种基因组编辑技术及其原理。对这些技术的优缺点进行了分析,并依据物种分类梳理了利用上述3种技术在动物、植物中突变体建立、基因功能研究、分子育种等方面的研究进展。同时,针对基因编辑产物的产业化应用前景,讨论了基因编辑技术及其产品较传统转基因技术产品的优势,分析了基因编辑技术及其产品可能因脱靶效应而引发的生物安全风险,介绍了美国、欧盟等国家对基因编辑技术及其产品安全管理和商业化应用的政策。文章结合中国现行法规对转基因生物的定义及安全评价(实质等同、个案分析)原则,讨论了基因编辑技术及其产品的安全管理,初步提出了基于传统转基因生物安全评价框架的基因编辑产品的安全评价和管理思路。针对基因编辑产品需要按照个案原则进行评价和管理,安全评价重点开展分子特征及食用安全评价;同时需要针对基因编辑技术的特点建立更加有效、特异的检测新方法,实现对基因编辑产品的有效监测,以促进基因组编辑产品的商业化应用。     

华山新麦草属间杂种细胞间遗传物质的转移及其在物种演化中的意义

本文描述了华山新麦草同纤毛鹅观草、鹅观草、普通小麦和节节麦属间杂种小孢子发生过程中，细胞间通过接合管或接合孔转移遗传物质的现象。遗传物质的转移引起多核细胞的出现和染色体数目的变化。这些变化为生物进化提供了重要的物质基础。初步证明细胞间遗传物质的转称是受基因系统控制的，华山新麦草的Ｎｂ染色体组上可能存在控制细胞间遗传物质转移的基因系统。并讨论了细胞间遗传物质转移后，在物种演化过程中的意义和作用。     

基于Perl脚本的大豆核苷酸序列高通量提取

自从大豆全基因组测序完成和序列公布之后,阐明每个基因的生物学功能和调控网络成为当前的主要任务。基于Perl脚本开发了一套可以高通量、快速提取序列的程序,该程序可以批量提取大豆染色体某个区间的核苷酸序列并利用其他工具进行批量分析,还可用于某个基因在全基因组中的所有序列分析。本研究分别对大豆第4染色体Glyma04g00930.1～Glyma04g01740.1区间的基因序列和水通道蛋白基因家族成员TIP(液泡膜水通道蛋白)序列进行提取。结果发现:Glyma04g00930.1～Glyma04g01740.1区间共含有112个基因序列;大豆全基因组共有91个TIP基因,在20条染色体上均有分布,且在第12染色体上分布最多,多达10个,暗示该染色体可能对大豆的水分利用效率起着重要作用,基因所含内含子数为1～8个。序列提取所用的2个脚本程序可以从http://www.zlhyd.com/sxbi/soybean_strict.rar下载。     

Stomatal size in fossil plants: evidence for polyploidy in majority of angiosperms

Three published estimates of the frequency of polyploidy in angiosperms (30 to 35 percent, 47 percent, and 70 to 80 percent) were tested by estimating the genome size of extinct woody angiosperms with the use of fossil guard cell size as a proxy for cellular DNA content. The inferred chromosome numbers of these extinct species suggest that seven to nine is the primitive haploid chromosome number of angiosperms and that most angiosperms (approximately 70 percent) have polyploidy in their history.     

禾谷类作物的比较基因组研究

 水稻是基因组最小的禾谷类作物,饱和遗传连锁图谱的构建,以及在此基础上开展的标记辅助选择和抗病基因克隆,表明水稻基因组研究已经领先于其他禾谷类作物。比较基因组研究表明：小麦、玉米、高粱、谷子和甘蔗的基因组均可由水稻染色体区段重新排列而成，这些区段上DNA标记的排列顺序在各个种之间保留。各种作物基因组大小的差异可能由于各个区段内基因间重复顺序扩增的程度不同所致。根据这些区段在各种作物染色体的排列顺序，有人提出根据水稻染色体区段排列单个原始禾谷类染色体的设想，为深入研究禾谷类作物的进化遗传提出了全新的思路。禾谷类作物基因组之间的共线性有利于在小基因组内克隆大基因组作物的同源基因，使生物技术在作物育种中发挥更大的作用。     

染色体涂染技术与动物分子细胞遗传学的建立和发展

染色体涂染 （ Ｃｈｒｏｍ ｓｏｍ ｅ ｐａｉｎｔｉｎｇ） 是一项在分子细胞遗传学水平上检测染色体重组和畸变的新技术, 包括染色体涂染 Ｄ Ｎ Ａ 探针制备和荧光标记原位杂交两部分。制备染色体涂染 Ｄ Ｎ Ａ 探针可通过流式细胞分类法, 克隆基因库或体细胞杂交株, 以及染色体显微切割和 Ｐ Ｃ Ｒ 扩增等途径, 现侧重综述近几年国际上用染色体显微切割和 Ｐ Ｃ Ｒ 扩增的方法制备探针进行家畜染色体涂染的实验技术和主要成果。研究结果表明,用该技术进行家畜染色体涂染具有很高的特异性和分辨力, 可用来检测家畜染色体畸变、性别鉴定、显微克隆等, 提高了对家畜染色体 Ｄ Ｎ Ａ 研究和分析的能力, 从而促进了动物分子细胞遗传学这一新的边缘学科的建立和发展。     

家猪(Sus scrofa domestica L.)染色体G-带核型的研究

本文对经外周血淋巴细胞培养的猪染色体标本,运用胰酶 G-带技术,进行了核型分析,描述了早、中、晚不同时期中期染色体的 G-带型。将家猪中期染色体 G-带型划分成64个区。共488条带纹,比较了染色体 X 和9的带型差别。     

鼻咽癌高淋巴道转移裸鼠移植瘤的细胞遗传学研究

研究鼻咽癌克隆株ＣＮＥ－２Ｚ－Ｈ５高淋巴道转移裸鼠移植瘤离体培养细胞的细胞遗传学改变并探讨这种改变与肿瘤生物学特性之间的关系。方法染色体Ｇ显带后按人类细胞遗传学国际命名体制进行核型分析。     

The mosaic genome of warm-blooded vertebrates

Most of the nuclear genome of warm-blooded vertebrates is a mosaic of very long (much greater than 200 kilobases) DNA segments, the isochores; these isochores are fairly homogeneous in base composition and belong to a small number of major classes distinguished by differences in guanine-cytosine (GC) content. The families of DNA molecules derived from such classes can be separated and used to study the genome distribution of any sequence which can be probed. This approach has revealed (i) that the distribution of genes, integrated viral sequences, and interspersed repeats is highly nonuniform in the genome, and (ii) that the base composition and ratio of CpG to GpC in both coding and noncoding sequences, as well as codon usage, mainly depend on the GC content of the isochores harboring the sequences. The compositional compartmentalization of the genome of warm-blooded vertebrates is discussed with respect to its evolutionary origin, its causes, and its effects on chromosome structure and function.     

Homoploid hybrid speciation in an extreme habitat

According to theory, homoploid hybrid speciation, which is hybrid speciation without a change in chromosome number, is facilitated by adaptation to a novel or extreme habitat. Using molecular and ecological data, we found that the alpine-adapted butterflies in the genus Lycaeides are the product of hybrid speciation. The alpine populations possess a mosaic genome derived from both L. melissa and L. idas and are differentiated from and younger than their putative parental species. As predicted, adaptive traits may allow for persistence in the environmentally extreme alpine habitat and reproductively isolate these populations from their parental species.     

A genetic map and recombination parameters of the human malaria parasite Plasmodium falciparum

Genetic investigations of malaria require a genome-wide, high-resolution linkage map of Plasmodium falciparum. A genetic cross was used to construct such a map from 901 markers that fall into 14 inferred linkage groups corresponding to the 14 nuclear chromosomes. Meiotic crossover activity in the genome proved high (17 kilobases per centimorgan) and notably uniform over chromosome length. Gene conversion events and spontaneous microsatellite length changes were evident in the inheritance data. The markers, map, and recombination parameters are facilitating genome sequence assembly, localization of determinants for such traits as virulence and drug resistance, and genetic studies of parasite field populations.     

大黄鱼与黄姑鱼杂交F1及其双亲的核型分析

研究了大黄鱼与黄姑鱼正反交F1原肠早期胚胎细胞及其亲本头肾细胞的染色体核型,为深入剖析大黄鱼与黄姑鱼杂交后代的基因组构成提供了细胞遗传学证据.大黄鱼与黄姑鱼染色体组均含有48条端部着丝粒染色体,染色体组型公式均为2n=48 t,染色体臂数均为NF=48,组内染色体长度分布连续.两亲本物种间核型很相似,未找到鉴别两物种的细胞遗传标志.正反交F1原肠期胚胎细胞的染色体众数也均为48,均可较好地配为24对.结合前期AFLP分析结果可以推断,正反交胚胎细胞均同时含有一个大黄鱼染色体组和一个黄姑鱼染色体组.此外,杂交F1中的非整倍体比例与两亲本没有明显区别,初步表明杂交胚胎细胞未发生明显的染色体丢失.在黄姑鱼♀与大黄鱼♂杂交F1中出现4对非t-染色体,原因尚待查明.