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Key message
We develop a set of universal genetic markers based on single-copy orthologous (COSII) genes in Poaceae.Abstract
Being evolutionary conserved, single-copy orthologous (COSII) genes are particularly useful in comparative mapping and phylogenetic investigation among species. In this study, we identified 2,684 COSII genes based on five sequenced Poaceae genomes including rice, maize, sorghum, foxtail millet, and brachypodium, and then developed 1,072 COSII markers whose transferability and polymorphism among five bamboo species were further evaluated with 46 pairs of randomly selected primers. 91.3 % of the 46 primers obtained clear amplification in at least one bamboo species, and 65.2 % of them produced polymorphism in more than one species. We also used 42 of them to construct the phylogeny for the five bamboo species, and it might reflect more precise evolutionary relationship than the one based on the vegetative morphology. The results indicated a promising prospect of applying these markers to the investigation of genetic diversity and the classification of Poaceae. To ease and facilitate access of the information of common interest to readers, a web-based database of the COSII markers is provided (http://www.sicau.edu.cn/web/yms/PCOSWeb/PCOS.html). 相似文献2.
Background
Orthology analysis is an important part of data analysis in many areas of bioinformatics such as comparative genomics and molecular phylogenetics. The ever-increasing flood of sequence data, and hence the rapidly increasing number of genomes that can be compared simultaneously, calls for efficient software tools as brute-force approaches with quadratic memory requirements become infeasible in practise. The rapid pace at which new data become available, furthermore, makes it desirable to compute genome-wide orthology relations for a given dataset rather than relying on relations listed in databases.Results
The program Proteinortho described here is a stand-alone tool that is geared towards large datasets and makes use of distributed computing techniques when run on multi-core hardware. It implements an extended version of the reciprocal best alignment heuristic. We apply Proteinortho to compute orthologous proteins in the complete set of all 717 eubacterial genomes available at NCBI at the beginning of 2009. We identified thirty proteins present in 99% of all bacterial proteomes.Conclusions
Proteinortho significantly reduces the required amount of memory for orthology analysis compared to existing tools, allowing such computations to be performed on off-the-shelf hardware. 相似文献3.
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Background
Reconstruction of evolutionary history of bacteriophages is a difficult problem because of fast sequence drift and lack of omnipresent genes in phage genomes. Moreover, losses and recombinational exchanges of genes are so pervasive in phages that the plausibility of phylogenetic inference in phage kingdom has been questioned.Results
We compiled the profiles of presence and absence of 803 orthologous genes in 158 completely sequenced phages with double-stranded DNA genomes and used these gene content vectors to infer the evolutionary history of phages. There were 18 well-supported clades, mostly corresponding to accepted genera, but in some cases appearing to define new taxonomic groups. Conflicts between this phylogeny and trees constructed from sequence alignments of phage proteins were exploited to infer 294 specific acts of intergenome gene transfer.Conclusion
A notoriously reticulate evolutionary history of fast-evolving phages can be reconstructed in considerable detail by quantitative comparative genomics.Open peer review
This article was reviewed by Eugene Koonin, Nicholas Galtier and Martijn Huynen. 相似文献8.
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Evolution of insect proteomes: insights into synapse organization and synaptic vesicle life cycle 下载免费PDF全文
Background
The molecular components in synapses that are essential to the life cycle of synaptic vesicles are well characterized. Nonetheless, many aspects of synaptic processes, in particular how they relate to complex behaviour, remain elusive. The genomes of flies, mosquitoes, the honeybee and the beetle are now fully sequenced and span an evolutionary breadth of about 350 million years; this provides a unique opportunity to conduct a comparative genomics study of the synapse.Results
We compiled a list of 120 gene prototypes that comprise the core of presynaptic structures in insects. Insects lack several scaffolding proteins in the active zone, such as bassoon and piccollo, and the most abundant protein in the mammalian synaptic vesicle, namely synaptophysin. The pattern of evolution of synaptic protein complexes is analyzed. According to this analysis, the components of presynaptic complexes as well as proteins that take part in organelle biogenesis are tightly coordinated. Most synaptic proteins are involved in rich protein interaction networks. Overall, the number of interacting proteins and the degrees of sequence conservation between human and insects are closely correlated. Such a correlation holds for exocytotic but not for endocytotic proteins.Conclusion
This comparative study of human with insects sheds light on the composition and assembly of protein complexes in the synapse. Specifically, the nature of the protein interaction graphs differentiate exocytotic from endocytotic proteins and suggest unique evolutionary constraints for each set. General principles in the design of proteins of the presynaptic site can be inferred from a comparative study of human and insect genomes. 相似文献11.
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Zhenzhong Wang Yu Cui Yongxing Chen Deyun Zhang Yong Liang Dong Zhang Qiuhong Wu Jingzhong Xie Shuhong Ouyang Delin Li Yinlian Huang Ping Lu Guoxin Wang Meihua Yu Shenghui Zhou Qixin Sun Zhiyong Liu 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2014,127(8):1741-1751
Key message
By applying comparative genomics analyses, a high-density genetic linkage map narrowed the powdery mildew resistance gene Pm41 originating from wild emmer in a sub-centimorgan genetic interval.Abstract
Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici, results in large yield losses worldwide. A high-density genetic linkage map of the powdery mildew resistance gene Pm41, originating from wild emmer (Triticum turgidum var. dicoccoides) and previously mapped to the distal region of chromosome 3BL bin 0.63–1.00, was constructed using an F5:6 recombinant inbred line population derived from a cross of durum wheat cultivar Langdon and wild emmer accession IW2. By applying comparative genomics analyses, 19 polymorphic sequence-tagged site markers were developed and integrated into the Pm41 genetic linkage map. Ultimately, Pm41 was mapped in a 0.6 cM genetic interval flanked by markers XWGGC1505 and XWGGC1507, which correspond to 11.7, 19.2, and 24.9 kb orthologous genomic regions in Brachypodium, rice, and sorghum, respectively. The XWGGC1506 marker co-segregated with Pm41 and could be served as a starting point for chromosome landing and map-based cloning as well as marker-assisted selection of Pm41. Detailed comparative genomics analysis of the markers flanking the Pm41 locus in wheat and the putative orthologous genes in Brachypodium, rice, and sorghum suggests that the gene order is highly conserved between rice and sorghum. However, intra-chromosome inversions and re-arrangements are evident in the wheat and Brachypodium genomic regions, and gene duplications are also present in the orthologous genomic regions of Pm41 in wheat, indicating that the Brachypodium gene model can provide more useful information for wheat marker development. 相似文献14.
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The COG database: an updated version includes eukaryotes 总被引:4,自引:0,他引:4
Roman L Tatusov Natalie D Fedorova John D Jackson Aviva R Jacobs Boris Kiryutin Eugene V Koonin Dmitri M Krylov Raja Mazumder Sergei L Mekhedov Anastasia N Nikolskaya B Sridhar Rao Sergei Smirnov Alexander V Sverdlov Sona Vasudevan Yuri I Wolf Jodie J Yin Darren A Natale 《BMC bioinformatics》2003,4(1):1-14
Background
The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies.Results
We describe here a major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs) from the sequenced genomes of prokaryotes and unicellular eukaryotes and the construction of clusters of predicted orthologs for 7 eukaryotic genomes, which we named KOGs after eukaryotic orthologous groups. The COG collection currently consists of 138,458 proteins, which form 4873 COGs and comprise 75% of the 185,505 (predicted) proteins encoded in 66 genomes of unicellular organisms. The eukaryotic orthologous groups (KOGs) include proteins from 7 eukaryotic genomes: three animals (the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster and Homo sapiens), one plant, Arabidopsis thaliana, two fungi (Saccharomyces cerevisiae and Schizosaccharomyces pombe), and the intracellular microsporidian parasite Encephalitozoon cuniculi. The current KOG set consists of 4852 clusters of orthologs, which include 59,838 proteins, or ~54% of the analyzed eukaryotic 110,655 gene products. Compared to the coverage of the prokaryotic genomes with COGs, a considerably smaller fraction of eukaryotic genes could be included into the KOGs; addition of new eukaryotic genomes is expected to result in substantial increase in the coverage of eukaryotic genomes with KOGs. Examination of the phyletic patterns of KOGs reveals a conserved core represented in all analyzed species and consisting of ~20% of the KOG set. This conserved portion of the KOG set is much greater than the ubiquitous portion of the COG set (~1% of the COGs). In part, this difference is probably due to the small number of included eukaryotic genomes, but it could also reflect the relative compactness of eukaryotes as a clade and the greater evolutionary stability of eukaryotic genomes.Conclusion
The updated collection of orthologous protein sets for prokaryotes and eukaryotes is expected to be a useful platform for functional annotation of newly sequenced genomes, including those of complex eukaryotes, and genome-wide evolutionary studies. 相似文献16.
Background
The ubiquitin 26S/proteasome system (UPS), a serial cascade process of protein ubiquitination and degradation, is the last step for most cellular proteins. There are many genes involved in this system, but are not identified in many species. The accumulating availability of genomic sequence data is generating more demands in data management and analysis. Genomics data of plants such as Populus trichocarpa, Medicago truncatula, Glycine max and others are now publicly accessible. It is time to integrate information on classes of genes for complex protein systems such as UPS.Results
We developed a database of higher plants' UPS, named 'plantsUPS'. Both automated search and manual curation were performed in identifying candidate genes. Extensive annotations referring to each gene were generated, including basic gene characterization, protein features, GO (gene ontology) assignment, microarray probe set annotation and expression data, as well as cross-links among different organisms. A chromosome distribution map, multi-sequence alignment, and phylogenetic trees for each species or gene family were also created. A user-friendly web interface and regular updates make plantsUPS valuable to researchers in related fields.Conclusion
The plantsUPS enables the exploration and comparative analysis of UPS in higher plants. It now archives > 8000 genes from seven plant species distributed in 11 UPS-involved gene families. The plantsUPS is freely available now to all users at http://bioinformatics.cau.edu.cn/plantsUPS. 相似文献17.
Matthias Westhues Tobias A. Schrag Claas Heuer Georg Thaller H. Friedrich Utz Wolfgang Schipprack Alexander Thiemann Felix Seifert Anita Ehret Armin Schlereth Mark Stitt Zoran Nikoloski Lothar Willmitzer Chris C. Schön Stefan Scholten Albrecht E. Melchinger 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2017,130(9):1927-1939
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Neil R Hackett Marcus W Butler Renat Shaykhiev Jacqueline Salit Larsson Omberg Juan L Rodriguez-Flores Jason G Mezey Yael Strulovici-Barel Guoqing Wang Lukas Didon Ronald G Crystal 《BMC genomics》2012,13(1):1-31
Background
The feline genome is valuable to the veterinary and model organism genomics communities because the cat is an obligate carnivore and a model for endangered felids. The initial public release of the Felis catus genome assembly provided a framework for investigating the genomic basis of feline biology. However, the entire set of protein coding genes has not been elucidated.Results
We identified and characterized 1227 protein coding feline sequences, of which 913 map to public sequences and 314 are novel. These sequences have been deposited into NCBI's genbank database and complement public genomic resources by providing additional protein coding sequences that fill in some of the gaps in the feline genome assembly. Through functional and comparative genomic analyses, we gained an understanding of the role of these sequences in feline development, nutrition and health. Specifically, we identified 104 orthologs of human genes associated with Mendelian disorders. We detected negative selection within sequences with gene ontology annotations associated with intracellular trafficking, cytoskeleton and muscle functions. We detected relatively less negative selection on protein sequences encoding extracellular networks, apoptotic pathways and mitochondrial gene ontology annotations. Additionally, we characterized feline cDNA sequences that have mouse orthologs associated with clinical, nutritional and developmental phenotypes. Together, this analysis provides an overview of the value of our cDNA sequences and enhances our understanding of how the feline genome is similar to, and different from other mammalian genomes.Conclusions
The cDNA sequences reported here expand existing feline genomic resources by providing high-quality sequences annotated with comparative genomic information providing functional, clinical, nutritional and orthologous gene information. 相似文献19.
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Cloning of seed dormancy genes (TaSdr) associated with tolerance to pre-harvest sprouting in common wheat and development of a functional marker 总被引:1,自引:0,他引:1
Yingjun Zhang Xilei Miao Xianchun Xia Zhonghu He 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2014,127(4):855-866