Evidence for DNA loss as a determinant of genome size

Eukaryotic genome sizes range over five orders of magnitude. This variation cannot be explained by differences in organismic complexity (the C value paradox). To test the hypothesis that some variation in genome size can be attributed to differences in the patterns of insertion and deletion (indel) mutations among organisms, this study examines the indel spectrum in Laupala crickets, which have a genome size 11 times larger than that of Drosophila. Consistent with the hypothesis, DNA loss is more than 40 times slower in Laupala than in Drosophila.     

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.     

蜜蜂发育相关基因研究

蜜蜂是一种重要的授粉昆虫,也是研究人类疾病及社会行为的模式生物之一。由其基因组测序可知,蜜蜂基因组中(A+T)及CpG含量较高,其昼夜节律、RNAi和DNA甲基化基因更类似脊椎动物。先天免疫、表皮蛋白和味觉受体基因较少,气味受体基因较多。蜜蜂早期发育途径中的一些基因与果蝇的相似,功能却显著不同。本文综述了蜜蜂卵、幼虫、蛹和成虫期发育相关基因及其研究进展。     

The 1.2-megabase genome sequence of Mimivirus

We recently reported the discovery and preliminary characterization of Mimivirus, the largest known virus, with a 400-nanometer particle size comparable to mycoplasma. Mimivirus is a double-stranded DNA virus growing in amoebae. We now present its 1,181,404-base pair genome sequence, consisting of 1262 putative open reading frames, 10% of which exhibit a similarity to proteins of known functions. In addition to exceptional genome size, Mimivirus exhibits many features that distinguish it from other nucleocytoplasmic large DNA viruses. The most unexpected is the presence of numerous genes encoding central protein-translation components, including four amino-acyl transfer RNA synthetases, peptide release factor 1, translation elongation factor EF-TU, and translation initiation factor 1. The genome also exhibits six tRNAs. Other notable features include the presence of both type I and type II topoisomerases, components of all DNA repair pathways, many polysaccharide synthesis enzymes, and one intein-containing gene. The size and complexity of the Mimivirus genome challenge the established frontier between viruses and parasitic cellular organisms. This new sequence data might help shed a new light on the origin of DNA viruses and their role in the early evolution of eukaryotes.     

数量性状遗传基础研究的回顾与思考--后基因组时代数量遗传领域的挑战

回顾了100多年来数量性状遗传研究的发展。数量性状的遗传研究长期落后于质量性状的研究，主要是对其遗传基础缺乏必要的了解。20世纪80年代开始，DNA分子标记的大量开发，提供了遍布于基因组的位置参照点，促进了数量性状遗传基础研究的迅速发展。迄今至少已对68个生物种的很多数量性状(包括动、植物的重要经济性状和人类疾病)作过全基因组的数量性状座位(QTL)扫描，建立了QTL图谱。但是一般地说，QTL仍然是一个相当大的DNA片断，往往含有多个基因。遗传基础的进一步研究应当从QTL到数量性状基因(QTG)，再从QTG到相应于等位基因的数量性状核苷酸(QTN)，逐步深入下去。这是后基因组时代数量遗传领域的主要挑战。基因组上数以万计的DNA序列变异(例如SNP)以及模式生物全基因组测序的完成，已为这种准确的遗传剖分提供了必要的条件。     

The works of living social insects as pseudofossils and the age of the oldest known metazoa

Living organisms are known to create structures in ancient rocks that are indigenous but not primary and that have been mistaken for fossils. Examination of burrows recently reported as fossils from 10(9)-year-old sedimentary rocks indicates that they are not the same age as the rocks but were probably made by termites working down after water. The burrows are partially filled with material from a modern lateritic surface from which they descend into steeply dipping, decomposed silt-stones of the Zambian Copperbelt. In fact, no authentic record of Metazoa that are demonstrably coeval with rocks older than 680 million years is known.     

宁夏束颈蝗Cytb基因的Numt分析

核线粒体假基因Numt（Nuclear Mitochondrial pseudogene）的存在具有重大的进化意义,它为基因组进化和基因组间相互作用的动态研究打开了一个窗口。假基因是基因组上与编码基因序列非常相似的非功能性基因组DNA拷贝,一般情况都不被转录,且没有明确生理意义。Numts由于处于不同的突变压力下,与真正的线粒体序列相比具不同的进化模式,其进化速率比线粒体同源基因要慢的多,类似分子化石,在核苷酸序列上更接近现存mtDNA的祖先状态。本研究在前几年研究的基础上,通过PCR技术,旨在发现宁夏束颈蝗核基因组中所存在的线粒体Cytb基因的假基因（Numt）。通过对PCR产物的检测,推断宁夏束颈蝗存在Numt,在对目标片断进行测序并利用GeneBank的BLASTn序列比对后确定序列特征,进一步确定Numt的实验正在规化进行中。预期本研究的结果将为Numts来源和机制,基因组进化和基因组间相互作用、系统进化、横向基因转移和核序列突变等研究提供实验基础。     

Modular construction of early Ediacaran complex life forms

Newly discovered, exceptionally preserved, soft-bodied fossils near Spaniard's Bay in eastern Newfoundland exhibit features not previously described from Ediacaran (terminal Neoproterozoic) fossils. All of the Spaniard's Bay taxa were composed of similar architectural elements-centimeter-scale frondlets exhibiting three orders of fracticality in branching. Frondlets were combined as modules atop semi-rigid organic skeletons to form a wide array of larger constructions, including frondose and plumose structures. This architecture and construction define the "rangeomorphs," a biological clade that dominated the Mistaken Point assemblage (575 to 560 million years ago) but does not appear to be ancestral to any Phanerozoic or modern organisms.     

枣和酸枣基因组大小测定

本研究旨在找出最适合枣和酸枣的流式细胞术流程,进而测定它们的基因组大小。结果显示,在所对比的5 种裂解液中,WPB 最适合枣属植物细胞裂解。以毛果杨为内标,通过比较待测样品和内参G0/ G1 期峰,计算得出6 种枣属植物基因组大小。各枣品种的基因组大小有一定差异,平均基因组大小约为418.56 Mb,其中:‘冬枣爷的基 因组大小为(393.60 ±4.72)Mb,即C-值为(0.40 ±0.01)pg;‘鲁枣2 号爷的基因组大小为(428.00 ±3.61)Mb,即C- 值为(0.44 ±0.00)pg;‘金丝小枣爷的基因组大小为(424.00 ±5.81 )Mb,即C-值为(0.44 ±0.01)pg;‘孔府酥脆枣爷 的基因组大小为(429.60 ±5.03)Mb,即C-值为(0.44 ±0.01)pg;‘无核小枣爷的基因组大小为(413.60 ±7.07)Mb, 即C-值为(0.42 ±0.01 )pg;酸枣的基因组大小为(441.60 ±4.29)Mb,即C-值为(0.45 ±0.01)pg。优化的枣属植 物流式细胞术流程,为枣属植物的倍性鉴定奠定了基础      

Microbial genes in the human genome: lateral transfer or gene loss?

The human genome was analyzed for evidence that genes had been laterally transferred into the genome from prokaryotic organisms. Protein sequence comparisons of the proteomes of human, fruit fly, nematode worm, yeast, mustard weed, eukaryotic parasites, and all completed prokaryote genomes were performed, and all genes shared between human and each of the other groups of organisms were collected. About 40 genes were found to be exclusively shared by humans and bacteria and are candidate examples of horizontal transfer from bacteria to vertebrates. Gene loss combined with sample size effects and evolutionary rate variation provide an alternative, more biologically plausible explanation.     

利用水稻C0t-1 DNA和基因组DNA对栽培稻、药用野生稻和疣粒野生稻基因组的比较分析

【目的】研究中高度重复序列在稻属不同物种基因组进化中的作用。【方法】用栽培稻C0t-1 DNA和基因组DNA(gDNA)作为探针，分别对栽培稻、药用野生稻和疣粒野生稻进行荧光原位杂交(FISH)和比较基因组杂交(CGH)。【结果】C0t-1 DNA覆盖栽培稻、药用野生稻和疣粒野生稻基因组比例(%)和大小(Mb)分别为47.10±0.16，38.61±0.13，44.38±0.13和212.33±1.21，269.42±0.89以及532.56±1.68。栽培稻gDNA在药用野生稻和疣粒野生稻基因组中的覆盖率约为91.0%和93.6%，含量分别约为634 Mb和1123 Mb，各有365 Mb和591 Mb不属于源自栽培稻基因组的中高度重复序列，未被栽培稻gDNA所覆盖的部分，分别为64 Mb和78 Mb左右。此外，以C0t-1 DNA的组成为依据，对这3个种核型进行了同源性聚类。【结论】稻属中度和高度重复序列和功能基因一样，在不同种中也存在着高度同源性和保守性，并在进化过程中得以保存下来。药用野生稻和疣粒野生稻基因组增大的重要原因之一，可能是基因组中度和高度重复序列加倍的结果，药用野生稻这种序列扩增相对疣粒野生稻要缓和得多。另外，这两个野生种在长期进化过程中，由于存在加倍、重排和基因选择性丢失等现象，形成了具有自己种的特异性的基因组成分。     

Discoidal impressions and trace-like fossils more than 1200 million years old

The Stirling Range Formation of southwestern Australia contains discoidal impressions and trace-like fossils in tidal sandstones. The various disks have previously been linked to the Ediacaran biota, younger than 600 million years old. From this unit, we report U-Th-Pb geochronology of detrital zircon and monazite, as well as low-grade metamorphic monazite, constraining the depositional age to between 2016 +/- 6 and 1215 +/- 20 million years old. Although nonbiological origins for the discoidal impressions cannot be completely discounted, the structures resembling trace fossils clearly have a biological origin and suggest the presence of vermiform, mucus-producing, motile organisms.     

红麻叶绿体DNA非编码区扩增及PCR-RFLP多态性分析

为研究红麻叶片叶绿体DNA(cpDNA)非编码区的序列特征,采用改良CTAB方法提取红麻总DNA,以8份红麻光钝感突变体及其4份近缘种基因组DNA为模板,应用8对植物cpDNA通用引物对红麻cpDNA非编码区序列进行PCR扩增,优化cpDNA非编码序列PCR的扩增条件,应用4种限制性内切酶(EcoRⅠ、HindⅢ、TaqⅠ、AulⅠ)酶切扩增片段.结果表明:所筛选的通用引物适用于红麻cpDNA非编码序列扩增,扩增产物经1.5%琼脂糖电泳检测,片段大小为400-2000 bp,共扩增cpDNA片段大小约13000 bp.将PCR扩增产物进行酶切,每个片段均有相同的酶切位点,只有cp4引物对cpDNA的扩增产物经AluⅠ酶切获得多态性片段,红麻光钝感突变体及其对照的cpDNA存在部分变异,该结果可为进一步探讨红麻叶绿体基因组种内的变异情况提供理论依据.     

Ringlike structure of the Deinococcus radiodurans genome: a key to radioresistance?

The bacterium Deinococcus radiodurans survives ionizing irradiation and other DNA-damaging assaults at doses that are lethal to all other organisms. How D. radiodurans accurately reconstructs its genome from hundreds of radiation-generated fragments in the absence of an intact template is unknown. Here we show that the D. radiodurans genome assumes an unusual toroidal morphology that may contribute to its radioresistance. We propose that, because of restricted diffusion within the tightly packed and laterally ordered DNA toroids, radiation-generated free DNA ends are held together, which may facilitate template-independent yet error-free joining of DNA breaks.     

Trace fossil evidence for late ordovician animals on land

Fossil burrows within newly recognized buried soils in the Late Ordovician Juniata Formation, near Potters Mills in central Pennsylvania, represent the oldest reported nonmarine trace fossils. They are thought to have been an original part of the soil because their greater density toward the top of the paleosols corresponds with mineralogical, microstructural, and chemical changes attributed to ancient weathering and because about half the burrows are encrusted with nodular carbonate, interpreted as caliche. Associated fossil caliche, the size distribution of the burrows, and their W-shaped backfills are evidence that the burrows may have been excavated by bilaterally symmetrical organisms that grew in well-defined growth increments and were able to withstand desiccation. Among well-known soil organisms, millipedes are burrowing animals that satisfy these requirements, but have a fossil record not quite this old. This trace fossil evidence for animals on land, together with recent palynological evidence for land plants of a bryophytic grade of evolution during Late Ordovician time, are indications of terrestrial ecosystems of slightly greater antiquity and complexity than hitherto suspected.     

Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota

Ecosystems are shaped by complex communities of mostly unculturable microbes. Metagenomes provide a fragmented view of such communities, but the ecosystem functions of major groups of organisms remain mysterious. To better characterize members of these communities, we developed methods to reconstruct genomes directly from mate-paired short-read metagenomes. We closed a genome representing the as-yet uncultured marine group II Euryarchaeota, assembled de novo from 1.7% of a metagenome sequenced from surface seawater. The genome describes a motile, photo-heterotrophic cell focused on degradation of protein and lipids and clarifies the origin of proteorhodopsin. It also demonstrates that high-coverage mate-paired sequence can overcome assembly difficulties caused by interstrain variation in complex microbial communities, enabling inference of ecosystem functions for uncultured members.     

高等植物线粒体基因组研究进展

高等植物线粒体基因组在目前已知生物中是最大、最复杂的, 阐述了高等植物线粒体基因组的最新研究进展。从全基因组的测序方法开始,重点介绍了高等植物线粒体基因组的组成和结构特点,特别是基因含量、内含子、基因间隔序列、RNA编辑、重复序列、叶绿体和细胞核与线粒体之间的DNA交换以及线粒体基因的遗传起源和进化等热点问题,以期为更好的了解核质互作、植物进化等科学问题奠定基础。     

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。     

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.