Mobile elements: drivers of genome evolution

Mobile elements within genomes have driven genome evolution in diverse ways. Particularly in plants and mammals, retrotransposons have accumulated to constitute a large fraction of the genome and have shaped both genes and the entire genome. Although the host can often control their numbers, massive expansions of retrotransposons have been tolerated during evolution. Now mobile elements are becoming useful tools for learning more about genome evolution and gene function.     

Genomic islands and the ecology and evolution of Prochlorococcus

Prochlorococcus ecotypes are a useful system for exploring the origin and function of diversity among closely related microbes. The genetic variability between phenotypically distinct strains that differ by less that 1% in 16S ribosomal RNA sequences occurs mostly in genomic islands. Island genes appear to have been acquired in part by phage-mediated lateral gene transfer, and some are differentially expressed under light and nutrient stress. Furthermore, genome fragments directly recovered from ocean ecosystems indicate that these islands are variable among cooccurring Prochlorococcus cells. Genomic islands in this free-living photoautotroph share features with pathogenicity islands of parasitic bacteria, suggesting a general mechanism for niche differentiation in microbial species.     

The Chlamydomonas genome reveals the evolution of key animal and plant functions

Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.     

紫貂线粒体基因组全序列结构及其进化

利用PCR方法和直接测序技术获得的紫貂线粒体基因组全长为16523bp,包含13个蛋白质编码基因、2个rRNA基因、22个tRNA基因和1个非编码基因控制区(D-Loop区),碱基组成为A32.0%、C27.6%、G14.7%、T25.8%;在编码蛋白质基因的密码子第3位点处具有AC高偏向性(72.6%),并且频繁利用不完全终止密码子T或TA(7个)。将紫貂线粒体基因组序列提交到GenBank,并获得检索号为FJ429093。结合GenBank中已公布的鼬科其他6种动物的线粒体基因组全序列及貂属6种D-Loop区部分序列,分别以虎和狗獾为外类群,应用最大简约法构建鼬科和貂属物种的系统进化树。结果表明:鼬科7个物种分成3大支系,分别为水獭亚科和臭鼬亚科群、日本貂和貂熊群以及紫貂和狗獾群,说明鼬科并非是一个单系群,紫貂与鼬科中的獾亚科亲缘关系较近,而与貂属中的美洲貂和石貂亲缘关系最近。     

The human genome project: past, present, and future

This article presents a short discussion of the development of the human genome program in the United States, a summary of the current status of the organization and administration of the National Institutes of Health component of the program, and some prospects for the future directions of the program and the applications of genome information.     

Genomics. Painting a picture of genome evolution

A new analysis of the genome sequences of two bacteria shows that genes can be lost as well as gained during evolution. Even more intriguingly, the work provides snapshots capturing gene decay in the act and thus illuminates the actual genomic changes that occurred over tens of millions of years of evolution. The research, which is described on page 2093, focuses on two pathogenic bacteria: Rickettsia conorii, the culprit in Mediterranean spotted fever, and R. prowazekii, which causes typhus.     

灵芝属真菌线粒体基因组特征及进化

【目的】分析灵芝属（Ganoderma）真菌的线粒体基因组特征及进化,为灵芝属物种分类、分子进化和系统发育分析提供理论依据。【方法】基于灵芝属真菌15个线粒体基因组序列,利用MEGA X、MISA、mVISTA、MAFFT、DnaSP、PAML X和IQ-TREE等生物信息学软件对基因组特征、序列多态性、简单重复序列（SSR）、基因进化和系统发育进行分析。【结果】灵芝属真菌线粒体基因组全长为50603~124588 bp,GC含量为25.4%~27.3%,含有15个保守的蛋白编码基因（PCG）、2个rRNA基因和25~29个tRNA基因。SSR主要由AT构成,单核苷酸重复类型比例最高,其次为三核苷酸重复和四核苷酸重复。种间线粒体基因组序列差异较大,非编码区的变异水平高于编码区,nad6、nad3和cob基因编码序列的变异度较高,内含子长度与线粒体基因组大小呈显著正相关。15个保守的线粒体蛋白编码基因主要受纯化选择影响,其中cob、cox1和nad2基因含有正选择位点。基因编码偏好A/T含量高的密码子,27个高频密码子中,13个以A结尾,14个以T结尾。系统发育分析结果显示,灵芝属真菌主要分为2个聚类组,其中紫芝、狭长孢灵芝和G.wiiroense聚为一组;喜热灵芝、白肉灵芝和铁杉灵芝聚成一支,与树舌灵芝、梅氏灵芝、四川灵芝和亮盖灵芝构成姊妹类群,共同构成另一组。【结论】灵芝属真菌的线粒体基因组在进化过程中发生明显的遗传变异,基因组长度主要与内含子插入和删除有关,蛋白编码基因密码子使用偏性强。     

OrchidBase 3.0:一个兰花基因功能和基因组进化研究的数据库

兰科为被子植物的最大科,兰科植物是经济价值非常高的世界性观赏植物,其基因组学和转录组学数据可为进一步推动兰花育种和研究提供帮助.本研究团队在建立的OrchidBase 1.0、2.0数据库的基础上,利用小兰屿蝴蝶兰的全基因组数据建立了基于网页版的OrchidBase 3.0数据库.OrchidBase 3.0数据库包含了小兰屿蝴蝶兰基因组拼接支架序列的信息以及基因注释、基因定位、基因结构、KEGG途径和BLAST搜索等内容;此外,该数据库也提供了小兰屿蝴蝶兰的基因序列和每千碱基读数每百万映射读数(RPKM).OrchidBase 3.0数据库的在线资源可以通过网页浏览、文本和BLAST搜索获取,搜索结果会显示在网站上并可供下载,用户可通过该数据库下载小兰屿蝴蝶兰的基因组拼接支架序列及预测的基因和蛋白质序列.http://orchidbase.itps.ncku.edu.tw为OrchidBase3.0数据库的免费网站链接.     

Gender,ecology, and the science of survival: Stories and lessons from Kenya

Sustainable development and biodiversity initiatives increasingly include ethnoscience, yet the gendered nature of rural people's knowledge goes largely unrecognized. The paper notes the current resurgence of ethnoscience research and states the case for including gendered knowledge and skills, supported by a brief review of relevant cultural ecology and ecofeminist field studies. The author argues the case from the point of view of better, more complete science as well as from the ethical imperative to serve women's interests as the “daily managers of the living environment”. In the interests of both objectives the paper advocates an ethnoscience research approach based on empowerment of rural people, rather than simple extraction of their knowledge. The Kenyan case study of women's agroforestry work follows their response to the drought and famine of 1985 and chronicles the unfolding discovery of women's ecological, political, and social science as gendered survival skills. The case is re-counted as a story, in keeping with an explicit choice to learn through participation and to report through storytelling. The experience of rural women and researchers during the drought provides several lessons for both groups about their respective knowledge systems, their agroforestry work, and the relationship of both to local and national political economy.