Human genome ultraconserved elements are ultraselected

Ultraconserved elements in the human genome are defined as stretches of at least 200 base pairs of DNA that match identically with corresponding regions in the mouse and rat genomes. Most ultraconserved elements are noncoding and have been evolutionarily conserved since mammal and bird ancestors diverged over 300 million years ago. The reason for this extreme conservation remains a mystery. It has been speculated that they are mutational cold spots or regions where every site is under weak but still detectable negative selection. However, analysis of the derived allele frequency spectrum shows that these regions are in fact under negative selection that is much stronger than that in protein coding genes.     

Ancient noncoding elements conserved in the human genome

Cartilaginous fishes represent the living group of jawed vertebrates that diverged from the common ancestor of human and teleost fish lineages about 530 million years ago. We generated approximately 1.4x genome sequence coverage for a cartilaginous fish, the elephant shark (Callorhinchus milii), and compared this genome with the human genome to identify conserved noncoding elements (CNEs). The elephant shark sequence revealed twice as many CNEs as were identified by whole-genome comparisons between teleost fishes and human. The ancient vertebrate-specific CNEs in the elephant shark and human genomes are likely to play key regulatory roles in vertebrate gene expression.     

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.     

Insertional mutagenesis of the Drosophila genome with single P elements

A versatile genetic method for identifying and cloning Drosophila melanogaster genes affecting any recognizable phenotype is described. Strains are constructed in which the insertion of a single P transposable element has caused a new mutation, greatly simplifying the genetic and molecular analysis of the affected gene. Mutagenesis is initiated by crossing two strains, each of which contains a specially designed P element. One element (jumpstarter), encoding P element transposase, efficiently mobilizes the second nonautonomous transposon (mutator), whose structure facilitates selection and cloning of new insertion mutations. Random mutator transpositions are captured in individual stocks that no longer contain jumpstarter, where they remain stable. This method was used to construct 1300 single P element insertion stocks which were then screened for recessive mutations. A library of single-element insertion strains will allow the structure and function of Drosophila genes to be readily correlated, and should have many other applications in Drosophila molecular genetics.     

Mobile DNA in Old World monkeys: a glimpse through the rhesus macaque genome

The completion of the draft sequence of the rhesus macaque genome allowed us to study the genomic composition and evolution of transposable elements in this representative of the Old World monkey lineage, a group of diverse primates closely related to humans. The L1 family of long interspersed elements appears to have evolved as a single lineage, and Alu elements have evolved into four currently active lineages. We also found evidence of elevated horizontal transmissions of retroviruses and the absence of DNA transposon activity in the Old World monkey lineage. In addition, approximately 100 precursors of composite SVA (short interspersed element, variable number of tandem repeat, and Alu) elements were identified, with the majority being shared by the common ancestor of humans and rhesus macaques. Mobile elements compose roughly 50% of primate genomes, and our findings illustrate their diversity and strong influence on genome evolution between closely related species.     

Nonmethylated transposable elements and methylated genes in a chordate genome

The genome of the invertebrate chordate Ciona intestinalis was found to be a stable mosaic of methylated and nonmethylated domains. Multiple copies of an apparently active long terminal repeat retrotransposon and a long interspersed element are nonmethylated and a large fraction of abundant short interspersed elements are also methylation free. Genes, by contrast, are predominantly methylated. These data are incompatible with the genome defense model, which proposes that DNA methylation in animals is primarily targeted to endogenous transposable elements. Cytosine methylation in this urochordate may be preferentially directed to genes.     

The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism

Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for approximately 20% of global carbon fixation. We report the 34 million-base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand-base pair plastid and 44 thousand-base pair mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments.     

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.     

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。     

Comment on "Climate, critters, and cetaceans: Cenozoic drivers of the evolution of modern whales"

Marx and Uhen (Reports, 19 February 2010, p. 993) suggested that correlated diversity changes in the fossil record of whales and diatoms reflects secular evolutionary signals of underlying ecological drivers. We question the meaning of this association and outline avenues for more complete testing of correlations between productivity and marine consumers through geologic time.     

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.     

Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate

Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely nonadaptive. This rapidly evolving animal lineage thus offers unique perspectives on the level of genome plasticity. It also illuminates issues as fundamental as the mechanisms of intron gain.     

Radioactive elements on Mercury's surface from MESSENGER: implications for the planet's formation and evolution

The MESSENGER Gamma-Ray Spectrometer measured the average surface abundances of the radioactive elements potassium (K, 1150 ± 220 parts per million), thorium (Th, 220 ± 60 parts per billion), and uranium (U, 90 ± 20 parts per billion) in Mercury's northern hemisphere. The abundance of the moderately volatile element K, relative to Th and U, is inconsistent with physical models for the formation of Mercury requiring extreme heating of the planet or its precursor materials, and supports formation from volatile-containing material comparable to chondritic meteorites. Abundances of K, Th, and U indicate that internal heat production has declined substantially since Mercury's formation, consistent with widespread volcanism shortly after the end of late heavy bombardment 3.8 billion years ago and limited, isolated volcanic activity since.