Proteomics to study genes and genomes

Proteomics, the large-scale analysis of proteins, will contribute greatly to our understanding of gene function in the post-genomic era. Proteomics can be divided into three main areas: (1) protein micro-characterization for large-scale identification of proteins and their post-translational modifications; (2) 'differential display' proteomics for comparison of protein levels with potential application in a wide range of diseases; and (3) studies of protein-protein interactions using techniques such as mass spectrometry or the yeast two-hybrid system. Because it is often difficult to predict the function of a protein based on homology to other proteins or even their three-dimensional structure, determination of components of a protein complex or of a cellular structure is central in functional analysis. This aspect of proteomic studies is perhaps the area of greatest promise. After the revolution in molecular biology exemplified by the ease of cloning by DNA methods, proteomics will add to our understanding of the biochemistry of proteins, processes and pathways for years to come.     

The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes ( approximately 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.     

Evolution of genes and genomes on the Drosophila phylogeny

Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.     

Conservation and rearrangement of mitochondrial structural gene sequences

Mitochondria contain the simplest DNA molecules that are present in eukaryotes. Mitochondrial DNA (mtDNA) is easily purified, and is an important model system for studying eukaryote gene structure and basic molecular processes. The protein sequences of mitochondrial gene products have been shown to be conserved from yeast to man, and there are definite similarities at the DNA sequence level. In contrast, the overall organization of the mitochondrial genome is drastically different in these organisms. To understand this, we need to extend work on mtDNA to a wider range of species. We have chosen to study the mtDNA of Aspergillus nidulans because a particularly comprehensive analysis of this system can be achieved using genetics as well as biochemistry, and like most eukaryotes it is an obligate aerobe, whereas Saccharomyces cerevisiae is not. We have investigated whether defined pieces of particular yeast mitochondrial genes show enough homology to Aspergillus mtDNA fragments to enable the corresponding Aspergillus genes to be located on the physical map. The results reported here show that this is the case for all five genes tested, and present the first data on the physical organization of the structural genes in the mitochondrial genome of A. nidulans.     

蚜蝇科昆虫比较线粒体基因组分析

通过检索GenBank数据库(截止2018年9月)和查阅文献资料,对已知的6种蚜蝇线粒体基因组全序列进行了分析,其基本结构特点是:1)全序列在碱基组成中表现出很强的AT偏向性; 2)未出现基因重排现象; 3) tRNA基因的二级结构为典型的三叶草结构; 4)大多数线粒体蛋白编码基因的起始密码子都是ATN。同时基于8条线粒体基因组全序列(含3个外群)构建蚜蝇科系统发育关系,结果支持蚜蝇科的单系性。     

Advances in the study of helminth mitochondrial genomes and their associated applications

Helminths, including flatworms and roundworms, are abundant organisms that have a variety of life histories. Of these, the genera Schistosoma, Echinococcus, Trichinella are notable parasites of veterinary and medical importance, and cause substantial socio- economic losses throughout China and the rest of the world. Genetic markers in the mitochondrial (mt) genome have proven use- ful for systematic, ecological, evolutionary and population studies, and the growth of mt genomic research has increased in the last two decades. Technological improvements, such as the long-polymerase chain reaction method and high-throughput se- quencing have allowed minute amounts of DNA from single worms, biopsy samples or microscopic organisms to be used for whole mt genome characterization. To facilitate the retrieval, annotation and analyses of mitochondrial features, multiple data- bases and specific software have also been designed and established. This review focuses on current progress, applications and perspectives regarding helminth mt genomics. To date, the complete mt genomes for 93 species of helminths have been sequenced and analyzed. Analyses of the mt genes, including gene content, arrangement, composition and variation have revealed unique features among the helminths when compared with other metazoans. This provides important data concerning their functional and comparative mitochondrial genomics, molecular taxonomy and characterization, population genetics and systematics, and evolu- tionary history. Moreover, mt genome data for parasitic helminths are important for diagnosis, epidemiology and ecology of in- fections. Mitochondrial genome data offer a rich source of markers for the systematics and population genetics of socioeconomi- cally important parasitic helminths of humans and other animals.     

The longest ultraconserved sequences and evolution of vertebrate mitochondrial genomes

ULTRACONSERVED SEQUENCES (ULTRACONSERVED, 100% IDENTITY WITH NO INSERTIONS OR DELETIONS) AND SMALL RNA IN GENOMES OFTEN PLAY A SPECIAL ROLE IN LIFE AND EVOLU- TION OF MANY SPECIES[1-4]. WE COMPARED 753 GENOMESOF BACTERIA, ARCHAEA, AND MITOCHONDRIA (MORE T…     

Selfish genes, evolutionary games, and the adaptiveness of behaviour

The science of sociobiology, which began in principle with the work of Fisher and Haldane and has more recently been developed by Hamilton, Maynard Smith, Trivers, Wilson and others, has been the centre of both scientific and political controversy. Dr Parker discusses the strengths and weaknesses of the approach, and illustrates that behaviour can be adapted in a complex way in conformity with sociobiological theory.     

The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes

Angiosperms have dominated the Earth's vegetation since the mid-Cretaceous (90 million years ago), providing much of our food, fibre, medicine and timber, yet their origin and early evolution have remained enigmatic for over a century. One part of the enigma lies in the difficulty of identifying the earliest angiosperms; the other involves the uncertainty regarding the sister group of angiosperms among extant and fossil gymnosperms. Here we report a phylogenetic analysis of DNA sequences of five mitochondrial, plastid and nuclear genes (total aligned length 8,733 base pairs), from all basal angiosperm and gymnosperm lineages (105 species, 103 genera and 63 families). Our study demonstrates that Amborella, Nymphaeales and Illiciales-Trimeniaceae-Austrobaileya represent the first stage of angiosperm evolution, with Amborella being sister to all other angiosperms. We also show that Gnetales are related to the conifers and are not sister to the angiosperms, thus refuting the Anthophyte Hypothesis. These results have far-reaching implications for our understanding of diversification, adaptation, genome evolution and development of the angiosperms.     

Self-splicing introns in tRNA genes of widely divergent bacteria.

The organization of eukaryotic genes into exons separated by introns has been considered as a primordial arrangement but because it does not exist in eubacterial genomes it may be that introns are relatively recent acquisitions. A self-splicing group I intron has been found in cyanobacteria at the same position of the same gene (that encoding leucyl transfer RNA, UAA anticodon) as a similar group I intron of chloroplasts, which indicates that this intron predates the invasion of eukaryotic cells by cyanobacterial endosymbionts. But it is not clear from this isolated example whether introns are more generally present in different genes or in more diverse branches of the eubacteria. Many mitochondria have intron-rich genomes and were probably derived from the alpha subgroup of the purple bacteria (or Proteobacteria), so ancient introns might also have been retained in these bacteria. We describe here the discovery of two small (237 and 205 nucleotides) self-splicing group I introns in members of two proteobacterial subgroups, Agrobacterium tumefaciens (alpha) and Azoarcus sp. (beta). The introns are inserted in genes for tRNA(Arg) and tRNA(Ile), respectively, after the third anticodon nucleotide. Their occurrence in different genes of phylogenetically diverse bacteria indicates that group I introns have a widespread distribution among eubacteria.     

Duplication and divergent evolution of the CHS and CHS-like genes in the chalcone synthase （CHS） superfamily

CHALCONE SYNTHASE (CHS) IS A KEY ENZYME OF FLA- VONOID BIOSYNTHESIS. IT CATALYSES THE CONDENSATION OF THREE MOLECULES OF MALONYL-COA WITH ONE MOLECULE OF 4-COUMAROYL-COA TO FORM NARINGENIN CHALCONE, THE PRECURSOR FOR A LARGE NUMBER OF FLAVONOIDS WHICH ARE WIDELY DISTRIBUTED IN THE PLANT KINGDOM AND HAVE IM- PORTANT ROLES IN FLOWER PIGMENTATION, PROTECTION AGAINST UV LIGHT A…     

Rearranged mitochondrial genes in the yeast nuclear genome

We have found a contiguous DNA sequence in the yeast nuclear genome with extensive homology to non-contiguous yeast mitochondrial DNA sequences. Closely linked to this nuclear sequence in some, but not all, yeast strains is a tandem pair of transposable (Ty) elements. Certain features of the content and organization of this nuclear DNA sequence suggest that it may have originated from petite mitochondrial DNA which integrated into the nuclear genome.     

Complex evolutionary history of the vertebrate sweet/umami taste receptor genes

Adaptive evolution plays a role in the functional divergence and specialization of taste receptors and the sense of taste is thought to be closely related to feeding ecology.To examine whether feeding ecology has shaped the evolution of taste receptor genes in vertebrates,we here focus on Tas1r gene family that encodes umami(Tas1r1 and Tas1r3 heterodimer) and sweet(Tas1r2 and Tas1r3 heterodimer) taste receptors.By searching currently available genome sequences in 48 vertebrates that contain 38 mammals,1 reptile,3 birds,1 frog,and 5 fishes,we found all three members of Tas1rs are intact in most species,suggesting umami and sweet tastes are maintained in most vertebrates.Interestingly,the absence and pseudogenization of Tas1rs were also discovered in a number of species with diverse feeding preferences and distinct phylogenetic positions,indicating widespread losses of umami and/or sweet tastes in these animals,irrespective of their diet.Together with previous findings showing losses of tastes in other vertebrates,we failed to identify common dietary factors that could result in the taste losses.Our results report here suggest the evolution of Tas1rs is more complex than we previously appreciated and highlight the caveat of analyzing sequences predicted from draft genome sequences.Future work for a better understanding of taste receptor function would help uncover what ecological factors have driven the evolution history of Tas1rs in vertebrates.     

Construction and initial analysis of five Fosmid libraries of mitochondrial genomes of cotton （Gossypium）

Cotton （Gossypium） is an important crop providing textile fiber and edible oil. To gain the insights into mechanism of the cyto- plasmic male sterility （CMS） inheritance, we constructed five fosmid libraries of mitochondrial genomes from mitotype of G. harknessii Brandegee. （one CMS line and its restorer）, mitotype of G. hirsutum L. （one CMS line and its maintainer）, and G. bar- badense L. The numbers of the clones in these libraries ranged from 1152 to 2016 with an average insert size of 36.2 to 38.4 kb, equivalent to 70-119.3 mitogenomes. The libraries were screened with 28 markers derived from the conservative sequences and yielded 22, 19, 26, 21, and 23 positive clones, respectively. These positive clones were used to construct the physical map of G. harknessii Brandegee. CMS line and G. barbadense L. mitogenomes that shared six syntenis regions. A total of 30 genes in nine clusters showed conservative and had high similarity with those in the mitochondrial genomes of cotton, Carica papaya, Cucur- bita pepo and Nicotiana tabacum. Further investigation indicated that gene rrn26 had two copies in all five cotton mitogenomes, while genes atpl, rrn5 and rrn18 had two copies only in G. barbadense L. The positive clones and physical map are considered being useful resources in cotton genomics research.