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In-Depth Annotation of the Drosophila Bithorax-Complex Reveals the Presence of Several Alternative ORFs That Could Encode for Motif-Rich Peptides. Cells 2021; 10:cells10112983. [PMID: 34831206 PMCID: PMC8616405 DOI: 10.3390/cells10112983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/17/2021] [Accepted: 10/26/2021] [Indexed: 11/19/2022] Open
Abstract
It is recognized that a large proportion of eukaryotic RNAs and proteins is not produced from conventional genes but from short and alternative (alt) open reading frames (ORFs) that are not captured by gene prediction programs. Here we present an in silico prediction of altORFs by applying several selecting filters based on evolutionary conservation and annotations of previously characterized altORF peptides. Our work was performed in the Bithorax-complex (BX-C), which was one of the first genomic regions described to contain long non-coding RNAs in Drosophila. We showed that several altORFs could be predicted from coding and non-coding sequences of BX-C. In addition, the selected altORFs encode for proteins that contain several interesting molecular features, such as the presence of transmembrane helices or a general propensity to be rich in short interaction motifs. Of particular interest, one altORF encodes for a protein that contains a peptide sequence found in specific isoforms of two Drosophila Hox proteins. Our work thus suggests that several altORF proteins could be produced from a particular genomic region known for its critical role during Drosophila embryonic development. The molecular signatures of these altORF proteins further suggests that several of them could make numerous protein–protein interactions and be of functional importance in vivo.
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2
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Magray AR, Hafeez S, Ganai BA, Lone SA, Dar GJ, Ahmad F, Siriyappagouder P. Study on pathogenicity and characterization of disease causing fungal community associated with cultured fish of Kashmir valley, India. Microb Pathog 2021; 151:104715. [PMID: 33444698 DOI: 10.1016/j.micpath.2020.104715] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/19/2020] [Accepted: 12/21/2020] [Indexed: 01/21/2023]
Abstract
Cultured fisheries of developing countries are continously challenged by a number of pathogenic microbes. Among microbial diseases, fungal and fungal like pathogen outbreaks lead to negative social and economic impacts on stakeholders. The cultured fisheries of Kashmir valley are also facing challenge from fungal pathogens, leading to tremendous socio-economic lossess to the fish farmer community hence, yearns to boost the sector with efficient management strategy. Our study was aimed at investigating the diversity of fungal communities infecting cultured rainbow trout and carp fish species. We employed classical microbiology, macro and micro morphological characteristics, and molecular analysis (multilocus typing) for fungal identification. Also histopathological approach was used to examine the pathogenicity patterns of diverse fungal groups. The study revealed that the infection in fish was predisposed to both superficial as well as visceral organs. However, skin, gills and head were predominantly infected compared to internal organs. The microbiological investigation of infected fish by culture dependent approach helped us to obtain the total of 250 fungal isolates. Out of these isolates, 21 different species were identified belonging to three diverse fungal groups which mostly included 14 species among Ascomycetes, 03 species of Oomycetes and 04 species of Zygomycetes. The majority of fungi which were infectious to cultured fish of valley are biotrophic or opportunistic soil fungi, and some of them being exclusive pathogens of fish.
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Affiliation(s)
- Aqib Rehman Magray
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India.
| | - Sabira Hafeez
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India; Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Bashir Ahmad Ganai
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India; Department of Environmental Science, University of Kashmir, Srinagar, 190006, India.
| | - Showkat Ahmad Lone
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India
| | - Gulam Jeelani Dar
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India
| | - Fayaz Ahmad
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India; Department of Zoology, University of Kashmir, Srinagar, 190006, India
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3
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Hong WJ, Kim YJ, Chandran AKN, Jung KH. Infrastructures of systems biology that facilitate functional genomic study in rice. RICE (NEW YORK, N.Y.) 2019; 12:15. [PMID: 30874968 PMCID: PMC6419666 DOI: 10.1186/s12284-019-0276-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 03/06/2019] [Indexed: 05/08/2023]
Abstract
Rice (Oryza sativa L.) is both a major staple food for the worldwide population and a model crop plant for studying the mode of action of agronomically valuable traits, providing information that can be applied to other crop plants. Due to the development of high-throughput technologies such as next generation sequencing and mass spectrometry, a huge mass of multi-omics data in rice has been accumulated. Through the integration of those data, systems biology in rice is becoming more advanced.To facilitate such systemic approaches, we have summarized current resources, such as databases and tools, for systems biology in rice. In this review, we categorize the resources using six omics levels: genomics, transcriptomics, proteomics, metabolomics, integrated omics, and functional genomics. We provide the names, websites, references, working states, and number of citations for each individual database or tool and discuss future prospects for the integrated understanding of rice gene functions.
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Affiliation(s)
- Woo-Jong Hong
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Yu-Jin Kim
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | | | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea.
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4
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Zhang X, Shen Z, Zhang G, Shen Y, Chen M, Zhao J, Wu R. Short Exon Detection via Wavelet Transform Modulus Maxima. PLoS One 2016; 11:e0163088. [PMID: 27635656 PMCID: PMC5026382 DOI: 10.1371/journal.pone.0163088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/04/2016] [Indexed: 02/05/2023] Open
Abstract
The detection of short exons is a challenging open problem in the field of bioinformatics. Due to the fact that the weakness of existing model-independent methods lies in their inability to reliably detect small exons, a model-independent method based on the singularity detection with wavelet transform modulus maxima has been developed for detecting short coding sequences (exons) in eukaryotic DNA sequences. In the analysis of our method, the local maxima can capture and characterize singularities of short exons, which helps to yield significant patterns that are rarely observed with the traditional methods. In order to get some information about singularities on the differences between the exon signal and the background noise, the noise level is estimated by filtering the genomic sequence through a notch filter. Meanwhile, a fast method based on a piecewise cubic Hermite interpolating polynomial is applied to reconstruct the wavelet coefficients for improving the computational efficiency. In addition, the output measure of a paired-numerical representation calculated in both forward and reverse directions is used to incorporate a useful DNA structural property. The performances of our approach and other techniques are evaluated on two benchmark data sets. Experimental results demonstrate that the proposed method outperforms all assessed model-independent methods for detecting short exons in terms of evaluation metrics.
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Affiliation(s)
- Xiaolei Zhang
- Shantou University Medical College, Shantou, P.R. China
| | - Zhiwei Shen
- Department of Radiology, Second Affiliated Hospital of Shantou University Medical College, Shantou, P.R. China
| | - Guishan Zhang
- College of Engineering, Shantou University, Shantou, P.R. China
| | - Yuanyu Shen
- Department of Radiology, Second Affiliated Hospital of Shantou University Medical College, Shantou, P.R. China
| | - Miaomiao Chen
- Department of Radiology, Second Affiliated Hospital of Shantou University Medical College, Shantou, P.R. China
| | - Jiaxiang Zhao
- College of Electronic Information and Optical Engineering, Nankai University, Tianjin, P.R. China
- * E-mail: (JXZ); (RHW)
| | - Renhua Wu
- Department of Radiology, Second Affiliated Hospital of Shantou University Medical College, Shantou, P.R. China
- * E-mail: (JXZ); (RHW)
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5
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Albuquerque JP, Tobias-Santos V, Rodrigues AC, Mury FB, da Fonseca RN. small ORFs: A new class of essential genes for development. Genet Mol Biol 2015; 38:278-83. [PMID: 26500431 PMCID: PMC4612599 DOI: 10.1590/s1415-475738320150009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 03/30/2015] [Indexed: 12/02/2022] Open
Abstract
Genes that contain small open reading frames (smORFs) constitute a new group of eukaryotic genes and are expected to represent 5% of the Drosophila melanogaster transcribed genes. In this review we provide a historical perspective of their recent discovery, describe their general mechanism and discuss the importance of smORFs for future genomic and transcriptomic studies. Finally, we discuss the biological role of the most studied smORF so far, the Mlpt/Pri/Tal gene in arthropods. The pleiotropic action of Mlpt/Pri/Tal in D. melanogaster suggests a complex evolutionary scenario that can be used to understand the origins, evolution and integration of smORFs into complex gene regulatory networks.
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Affiliation(s)
- João Paulo Albuquerque
- Laboratório Integrado de Bioquímica Hatisaburo Masuda, Núcleo em Ecologia e Desenvolvimento Sócio-Ambiental, Universidade Federal de Rio de Janeiro, Macaé, RJ, Brazil
| | - Vitória Tobias-Santos
- Laboratório Integrado de Bioquímica Hatisaburo Masuda, Núcleo em Ecologia e Desenvolvimento Sócio-Ambiental, Universidade Federal de Rio de Janeiro, Macaé, RJ, Brazil
| | - Aline Cáceres Rodrigues
- Laboratório Integrado de Bioquímica Hatisaburo Masuda, Núcleo em Ecologia e Desenvolvimento Sócio-Ambiental, Universidade Federal de Rio de Janeiro, Macaé, RJ, Brazil
| | - Flávia Borges Mury
- Laboratório Integrado de Bioquímica Hatisaburo Masuda, Núcleo em Ecologia e Desenvolvimento Sócio-Ambiental, Universidade Federal de Rio de Janeiro, Macaé, RJ, Brazil. ; Entomologia Molecular, Instituto Nacional de Ciência e Tecnologia, Universidade Federal de Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Rodrigo Nunes da Fonseca
- Laboratório Integrado de Bioquímica Hatisaburo Masuda, Núcleo em Ecologia e Desenvolvimento Sócio-Ambiental, Universidade Federal de Rio de Janeiro, Macaé, RJ, Brazil. ; Entomologia Molecular, Instituto Nacional de Ciência e Tecnologia, Universidade Federal de Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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6
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Su M, Ling Y, Yu J, Wu J, Xiao J. Small proteins: untapped area of potential biological importance. Front Genet 2013; 4:286. [PMID: 24379829 PMCID: PMC3864261 DOI: 10.3389/fgene.2013.00286] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 11/27/2013] [Indexed: 01/13/2023] Open
Abstract
Polypeptides containing ≤100 amino acid residues (AAs) are generally considered to be small proteins (SPs). Many studies have shown that some SPs are involved in important biological processes, including cell signaling, metabolism, and growth. SP generally has a simple domain and has an advantage to be used as model system to overcome folding speed limits in protein folding simulation and drug design. But SPs were once thought to be trivial molecules in biological processes compared to large proteins. Because of the constraints of experimental methods and bioinformatics analysis, many genome projects have used a length threshold of 100 amino acid residues to minimize erroneous predictions and SPs are relatively under-represented in earlier studies. The general protein discovery methods have potential problems to predict and validate SPs, and very few effective tools and algorithms were developed specially for SPs identification. In this review, we mainly consider the diverse strategies applied to SPs prediction and discuss the challenge for differentiate SP coding genes from artifacts. We also summarize current large-scale discovery of SPs in species at the genome level. In addition, we present an overview of SPs with regard to biological significance, structural application, and evolution characterization in an effort to gain insight into the significance of SPs.
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Affiliation(s)
- Mingming Su
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China ; Graduate University of Chinese Academy of Sciences Beijing, China
| | - Yunchao Ling
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China ; Graduate University of Chinese Academy of Sciences Beijing, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China
| | - Jiayan Wu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China
| | - Jingfa Xiao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China
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7
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Abstract
Historically many genome annotation strategies have lacked experimental evidence at the protein level, which and have instead relied heavily on ab initio gene prediction tools, which consequently resulted in many incorrectly annotated genomic sequences. Proteogenomics aims to address these issues using mass spectrometry (MS)-based proteomics, genomic mapping, and providing statistical significance measures such as false discovery rates (FDRs) to validate the mapped peptides. Presented here is a tool capable of meeting this goal, the UCSD proteogenomic pipeline, which maps peptide-spectrum matches (PSMs) to the genome using the Inspect MS/MS database search tool and assigns a statistical significance to the match using a target-decoy search approach to assign estimated FDRs. This pipeline also provides the option of using a more reliable approach to proteogenomics by determining the precise false-positive rates (FPRs) and p-values of each PSM by calculating their spectral probabilities and rescoring each PSM accordingly. In addition to the protein prediction challenges in the rapidly growing number of sequenced plant genomes, it is difficult to extract high-quality protein samples from many plant species. For that reason, this chapter contains methods for protein extraction and trypsin digestion that reliably produce samples suitable for proteogenomic analysis.
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8
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Peyretaillade E, Parisot N, Polonais V, Terrat S, Denonfoux J, Dugat-Bony E, Wawrzyniak I, Biderre-Petit C, Mahul A, Rimour S, Gonçalves O, Bornes S, Delbac F, Chebance B, Duprat S, Samson G, Katinka M, Weissenbach J, Wincker P, Peyret P. Annotation of microsporidian genomes using transcriptional signals. Nat Commun 2012; 3:1137. [DOI: 10.1038/ncomms2156] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 09/20/2012] [Indexed: 12/24/2022] Open
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9
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Cheng H, Chan WS, Li Z, Wang D, Liu S, Zhou Y. Small open reading frames: current prediction techniques and future prospect. Curr Protein Pept Sci 2012; 12:503-7. [PMID: 21787300 DOI: 10.2174/138920311796957667] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 04/01/2011] [Accepted: 05/04/2011] [Indexed: 11/22/2022]
Abstract
Evidence is accumulating that small open reading frames (sORF, <100 codons) play key roles in many important biological processes. Yet, they are generally ignored in gene annotation despite they are far more abundant than the genes with more than 100 codons. Here, we demonstrate that popular homolog search and codon-index techniques perform poorly for small genes relative to that for larger genes, while a method dedicated to sORF discovery has a similar level of accuracy as homology search. The result is largely due to the small dataset of experimentally verified sORF available for homology search and for training ab initio techniques. It highlights the urgent need for both experimental and computational studies in order to further advance the accuracy of sORF prediction.
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Affiliation(s)
- Haoyu Cheng
- Indiana University School of Informatics, Indiana University-Purdue University and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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10
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Hawkins T, Kihara D. FUNCTION PREDICTION OF UNCHARACTERIZED PROTEINS. J Bioinform Comput Biol 2011; 5:1-30. [PMID: 17477489 DOI: 10.1142/s0219720007002503] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Revised: 09/23/2006] [Accepted: 10/10/2006] [Indexed: 11/18/2022]
Abstract
Function prediction of uncharacterized protein sequences generated by genome projects has emerged as an important focus for computational biology. We have categorized several approaches beyond traditional sequence similarity that utilize the overwhelmingly large amounts of available data for computational function prediction, including structure-, association (genomic context)-, interaction (cellular context)-, process (metabolic context)-, and proteomics-experiment-based methods. Because they incorporate structural and experimental data that is not used in sequence-based methods, they can provide additional accuracy and reliability to protein function prediction. Here, first we review the definition of protein function. Then the recent developments of these methods are introduced with special focus on the type of predictions that can be made. The need for further development of comprehensive systems biology techniques that can utilize the ever-increasing data presented by the genomics and proteomics communities is emphasized. For the readers' convenience, tables of useful online resources in each category are included. The role of computational scientists in the near future of biological research and the interplay between computational and experimental biology are also addressed.
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Affiliation(s)
- Troy Hawkins
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
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11
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Arefian E, Kiani J, Soleimani M, Shariati SAM, Aghaee-Bakhtiari SH, Atashi A, Gheisari Y, Ahmadbeigi N, Banaei-Moghaddam AM, Naderi M, Namvarasl N, Good L, Faridani OR. Analysis of microRNA signatures using size-coded ligation-mediated PCR. Nucleic Acids Res 2011; 39:e80. [PMID: 21486750 PMCID: PMC3130289 DOI: 10.1093/nar/gkr214] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The expression pattern and regulatory functions of microRNAs (miRNAs) are intensively investigated in various tissues, cell types and disorders. Differential miRNA expression signatures have been revealed in healthy and unhealthy tissues using high-throughput profiling methods. For further analyses of miRNA signatures in biological samples, we describe here a simple and efficient method to detect multiple miRNAs simultaneously in total RNA. The size-coded ligation-mediated polymerase chain reaction (SL-PCR) method is based on size-coded DNA probe hybridization in solution, followed-by ligation, PCR amplification and gel fractionation. The new method shows quantitative and specific detection of miRNAs. We profiled miRNAs of the let-7 family in a number of organisms, tissues and cell types and the results correspond with their incidence in the genome and reported expression levels. Finally, SL-PCR detected let-7 expression changes in human embryonic stem cells as they differentiate to neuron and also in young and aged mice brain and bone marrow. We conclude that the method can efficiently reveal miRNA signatures in a range of biological samples.
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Affiliation(s)
- Ehsan Arefian
- Department of Molecular Biology and Genetic Engineering, Stem Cell Technology Research Center, Tehran 1585636473, Iran
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12
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BURRELL AMILLIE, TAYLOR KATHERINEG, WILLIAMS RYANJ, CANTRELL ROBERTT, MENZ MONICAA, PEPPER ALANE. A comparative genomic map for Caulanthus amplexicaulis and related species (Brassicaceae). Mol Ecol 2011; 20:784-98. [DOI: 10.1111/j.1365-294x.2010.04981.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Shinozuka H, Cogan NOI, Spangenberg GC, Forster JW. Comparative Genomics in Perennial Ryegrass (Lolium perenne L.): Identification and Characterisation of an Orthologue for the Rice Plant Architecture-Controlling Gene OsABCG5. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2011; 2011:291563. [PMID: 21941532 PMCID: PMC3173957 DOI: 10.1155/2011/291563] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 06/20/2011] [Indexed: 05/11/2023]
Abstract
Perennial ryegrass is an important pasture grass in temperate regions. As a forage biomass-generating species, plant architecture-related characters provide key objectives for breeding improvement. In silico comparative genomics analysis predicted colocation between a previously identified QTL for plant type (erect versus prostrate growth) and the ortholocus of the rice OsABCG5 gene (LpABCG5), as well as related QTLs in other Poaceae species. Sequencing of an LpABCG5-containing BAC clone identified presence of a paralogue (LpABCG6) in the vicinity of the LpABCG5 locus, in addition to three other gene-like sequences. Comparative genomics involving five other 5 grass species (rice, Brachypodium, sorghum, maize, and foxtail millet) revealed conserved microsynteny in the ABCG5 ortholocus-flanking region. Gene expression profiling and phylogenetic analysis suggested that the two paralogues are functionally distinct. Fourteen additional ABCG5 gene family members, which may interact with the LpABCG5 gene, were identified through sequencing of transcriptomes from perennial ryegrass leaf, anther, and pistils. A larger-scale phylogenetic analysis of the ABCG gene family suggested conservation between major branches of the Poaceae family. This study identified the LpABCG5 gene as a candidate for the plant type determinant, suggesting that manipulation of gene expression may provide valuable phenotypes for perennial ryegrass breeding.
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Affiliation(s)
- Hiroshi Shinozuka
- Biosciences Research Division, Department of Primary Industries, Victorian AgriBiosciences Centre, La Trobe University Research and Development Park, 1 Park Drive, Bundoora, VIC 3083, Australia
- Molecular Plant Breeding Cooperative Research Centre, Bundoora, VIC 3083, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, VIC 3083, Australia
| | - Noel O. I. Cogan
- Biosciences Research Division, Department of Primary Industries, Victorian AgriBiosciences Centre, La Trobe University Research and Development Park, 1 Park Drive, Bundoora, VIC 3083, Australia
- Molecular Plant Breeding Cooperative Research Centre, Bundoora, VIC 3083, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, VIC 3083, Australia
| | - German C. Spangenberg
- Biosciences Research Division, Department of Primary Industries, Victorian AgriBiosciences Centre, La Trobe University Research and Development Park, 1 Park Drive, Bundoora, VIC 3083, Australia
- Molecular Plant Breeding Cooperative Research Centre, Bundoora, VIC 3083, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, VIC 3083, Australia
- La Trobe University, Bundoora, VIC 3086, Australia
| | - John W. Forster
- Biosciences Research Division, Department of Primary Industries, Victorian AgriBiosciences Centre, La Trobe University Research and Development Park, 1 Park Drive, Bundoora, VIC 3083, Australia
- Molecular Plant Breeding Cooperative Research Centre, Bundoora, VIC 3083, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, VIC 3083, Australia
- La Trobe University, Bundoora, VIC 3086, Australia
- *John W. Forster:
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Cibrián-Jaramillo A, De la Torre-Bárcena JE, Lee EK, Katari MS, Little DP, Stevenson DW, Martienssen R, Coruzzi GM, DeSalle R. Using phylogenomic patterns and gene ontology to identify proteins of importance in plant evolution. Genome Biol Evol 2010; 2:225-39. [PMID: 20624728 PMCID: PMC2997538 DOI: 10.1093/gbe/evq012] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2010] [Indexed: 01/01/2023] Open
Abstract
We use measures of congruence on a combined expressed sequenced tag genome phylogeny to identify proteins that have potential significance in the evolution of seed plants. Relevant proteins are identified based on the direction of partitioned branch and hidden support on the hypothesis obtained on a 16-species tree, constructed from 2,557 concatenated orthologous genes. We provide a general method for detecting genes or groups of genes that may be under selection in directions that are in agreement with the phylogenetic pattern. Gene partitioning methods and estimates of the degree and direction of support of individual gene partitions to the overall data set are used. Using this approach, we correlate positive branch support of specific genes for key branches in the seed plant phylogeny. In addition to basic metabolic functions, such as photosynthesis or hormones, genes involved in posttranscriptional regulation by small RNAs were significantly overrepresented in key nodes of the phylogeny of seed plants. Two genes in our matrix are of critical importance as they are involved in RNA-dependent regulation, essential during embryo and leaf development. These are Argonaute and the RNA-dependent RNA polymerase 6 found to be overrepresented in the angiosperm clade. We use these genes as examples of our phylogenomics approach and show that identifying partitions or genes in this way provides a platform to explain some of the more interesting organismal differences among species, and in particular, in the evolution of plants.
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Affiliation(s)
- Angélica Cibrián-Jaramillo
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA.
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15
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Poptsova MS, Gogarten JP. Using comparative genome analysis to identify problems in annotated microbial genomes. Microbiology (Reading) 2010; 156:1909-1917. [DOI: 10.1099/mic.0.033811-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genome annotation is a tedious task that is mostly done by automated methods; however, the accuracy of these approaches has been questioned since the beginning of the sequencing era. Genome annotation is a multilevel process, and errors can emerge at different stages: during sequencing, as a result of gene-calling procedures, and in the process of assigning gene functions. Missed or wrongly annotated genes differentially impact different types of analyses. Here we discuss and demonstrate how the methods of comparative genome analysis can refine annotations by locating missing orthologues. We also discuss possible reasons for errors and show that the second-generation annotation systems, which combine multiple gene-calling programs with similarity-based methods, perform much better than the first annotation tools. Since old errors may propagate to the newly sequenced genomes, we emphasize that the problem of continuously updating popular public databases is an urgent and unresolved one. Due to the progress in genome-sequencing technologies, automated annotation techniques will remain the main approach in the future. Researchers need to be aware of the existing errors in the annotation of even well-studied genomes, such as Escherichia coli, and consider additional quality control for their results.
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Affiliation(s)
- Maria S. Poptsova
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3125, USA
| | - J. Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3125, USA
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16
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Hahn Y. Molecular evolution of TEPP protein genes in metazoans. Biochem Genet 2009; 47:651-64. [PMID: 19548082 DOI: 10.1007/s10528-009-9261-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Accepted: 06/03/2009] [Indexed: 10/20/2022]
Abstract
TEPP is a gene expressed in human reproductive organs such as testis, prostate, and placenta. Here, identification and molecular evolutionary analysis of TEPP proteins in various metazoan animals including deuterostomes (chordates, hemichordates, and echinoderms), lophotrochozoans (mollusks and annelids), and cnidarians (sea anemone and coral) are reported. A multiple sequence alignment revealed two highly conserved regions in TEPP proteins that had no similarity to any other known domains or proteins. Genomic sequence analysis showed frequent shifting of the splice sites of intron 1 in mammalian TEPP genes. A comparison of the intron positions in the coding region showed that the exon/intron structure of the TEPP gene was established in an early metazoan ancestor and that independent loss of a single intron occurred in echinoderms and in vertebrates. The urochordate tunicate TEPP genes are intronless, possibly due to replacement of the original gene by a retrogene. No homolog was detected in birds, insects, nematodes, and teleost fishes despite the extensive sequence data of these species, implying that the TEPP gene might be lost in these lineages.
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Affiliation(s)
- Yoonsoo Hahn
- Department of Life Science (BK21 Program) and Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Korea.
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Zhou J, Zhu T, Hu C, Li H, Chen G, Xu G, Wang S, Zhou J, Ma D. Comparative genomics and function analysis on BI1 family. Comput Biol Chem 2008; 32:159-62. [PMID: 18440869 DOI: 10.1016/j.compbiolchem.2008.01.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Revised: 01/29/2008] [Accepted: 01/31/2008] [Indexed: 11/17/2022]
Abstract
Bax inhibitor-1 (BI1) family contains six known genes in human. Some members of BI1 family have been proved to play important roles in cell death. Here we discuss the similarities and differences among the members of BI1 family by comparative genomics and proteomics, and report here the discovery of a novel member, tmbim1b, in Bos taurus. BI1 family is evolutionarily conserved as integral membrane proteins containing multiple membrane-spanning segments and predominantly localized to intracellular membranes, similar to Bcl-2 family proteins. They share multiple motifs and transcriptional factors within the promoter and the coding regions. They may represent regulators of cell death pathways, which are concluded from structure conservation of BI1 family.
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Affiliation(s)
- Jinhua Zhou
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave., Wuhan, Hubei, PR China
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18
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Cogburn LA, Porter TE, Duclos MJ, Simon J, Burgess SC, Zhu JJ, Cheng HH, Dodgson JB, Burnside J. Functional genomics of the chicken--a model organism. Poult Sci 2007; 86:2059-94. [PMID: 17878436 DOI: 10.1093/ps/86.10.2059] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Since the sequencing of the genome and the development of high-throughput tools for the exploration of functional elements of the genome, the chicken has reached model organism status. Functional genomics focuses on understanding the function and regulation of genes and gene products on a global or genome-wide scale. Systems biology attempts to integrate functional information derived from multiple high-content data sets into a holistic view of all biological processes within a cell or organism. Generation of a large collection ( approximately 600K) of chicken expressed sequence tags, representing most tissues and developmental stages, has enabled the construction of high-density microarrays for transcriptional profiling. Comprehensive analysis of this large expressed sequence tag collection and a set of approximately 20K full-length cDNA sequences indicate that the transcriptome of the chicken represents approximately 20,000 genes. Furthermore, comparative analyses of these sequences have facilitated functional annotation of the genome and the creation of several bioinformatic resources for the chicken. Recently, about 20 papers have been published on transcriptional profiling with DNA microarrays in chicken tissues under various conditions. Proteomics is another powerful high-throughput tool currently used for examining the dynamics of protein expression in chicken tissues and fluids. Computational analyses of the chicken genome are providing new insight into the evolution of gene families in birds and other organisms. Abundant functional genomic resources now support large-scale analyses in the chicken and will facilitate identification of transcriptional mechanisms, gene networks, and metabolic or regulatory pathways that will ultimately determine the phenotype of the bird. New technologies such as marker-assisted selection, transgenics, and RNA interference offer the opportunity to modify the phenotype of the chicken to fit defined production goals. This review focuses on functional genomics in the chicken and provides a road map for large-scale exploration of the chicken genome.
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Affiliation(s)
- L A Cogburn
- Department of Animal and Food Sciences, University of Delaware, Newark 19717, USA.
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Liu X, Lu T, Yu S, Li Y, Huang Y, Huang T, Zhang L, Zhu J, Zhao Q, Fan D, Mu J, Shangguan Y, Feng Q, Guan J, Ying K, Zhang Y, Lin Z, Sun Z, Qian Q, Lu Y, Han B. A collection of 10,096 indica rice full-length cDNAs reveals highly expressed sequence divergence between Oryza sativa indica and japonica subspecies. PLANT MOLECULAR BIOLOGY 2007; 65:403-15. [PMID: 17522955 DOI: 10.1007/s11103-007-9174-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Accepted: 04/13/2007] [Indexed: 05/05/2023]
Abstract
Relatively few indica rice full-length cDNAs were available to aid in the annotation of rice genes. The data presented here described the sequencing and analysis of 10,096 full-length cDNAs from Oryza sativa subspecies indica Guangluai 4. Of them, 9,029 matched rice genomic sequences in publicly-available databases, and 1,200 were identified as new rice genes. Comparison with the knowledge-based Oryza Molecular Biological Encyclopedia japonica cDNA collection indicated that 3,316 (41.6%) of the 7,965 indica-japonica cDNA pairs showed no distinct variations at protein level (2,117 indica-japonica cDNA pairs showed fully identical and 1,199 indica-japonica cDNA pairs showed no frame shift). Moreover, 3,645 (45.8%) of the indica-japonica pairs showed substantial differences at the protein level due to single nucleotide polymorphisms (SNPs), insertions or deletions, and sequence-segment variations between indica and japonica subspecies. Further experimental verifications using PCR screening and quantitative reverse transcriptional PCR revealed unique transcripts for indica subspecies. Comparative analysis also showed that most of rice genes were evolved under purifying selection. These variations might distinguish the phenotypic changes of the two cultivated rice subspecies indica and japonica. Analysis of these cDNAs extends known rice genes and identifies new ones in rice.
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Affiliation(s)
- Xiaohui Liu
- National Center for Gene Research & Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China
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Affiliation(s)
- Ivano Bertini
- Magnetic Resonance Center (CERM) and Department of Chemistry – University of Florence, via L. Sacconi 6, 50019 Sesto Fiorentino, Italy, Fax: +39‐055‐457‐4271
| | - Antonio Rosato
- Magnetic Resonance Center (CERM) and Department of Chemistry – University of Florence, via L. Sacconi 6, 50019 Sesto Fiorentino, Italy, Fax: +39‐055‐457‐4271
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21
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Jain M, Shrager J, Harris EH, Halbrook R, Grossman AR, Hauser C, Vallon O. EST assembly supported by a draft genome sequence: an analysis of the Chlamydomonas reinhardtii transcriptome. Nucleic Acids Res 2007; 35:2074-83. [PMID: 17355987 PMCID: PMC1874618 DOI: 10.1093/nar/gkm081] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Clustering and assembly of expressed sequence tags (ESTs) constitute the basis for most genomewide descriptions of a transcriptome. This approach is limited by the decline in sequence quality toward the end of each EST, impacting both sequence clustering and assembly. Here, we exploit the available draft genome sequence of the unicellular green alga Chlamydomonas reinhardtii to guide clustering and to correct errors in the ESTs. We have grouped all available EST and cDNA sequences into 12 063 ACEGs (assembly of contiguous ESTs based on genome) and generated 15 857 contigs of average length 934 nt. We predict that roughly 3000 of our contigs represent full-length transcripts. Compared to previous assemblies, ACEGs show extended contig length, increased accuracy and a reduction in redundancy. Because our assembly protocol also uses ESTs with no corresponding genomic sequences, it provides sequence information for genes interrupted by sequence gaps. Detailed analysis of randomly sampled ACEGs reveals several hundred putative cases of alternative splicing, many overlapping transcription units and new genes not identified by gene prediction algorithms. Our protocol, although developed for and tailored to the C. reinhardtii dataset, can be exploited by any eukaryotic genome project for which both a draft genome sequence and ESTs are available.
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Affiliation(s)
- Monica Jain
- The Carnegie Institution, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305, USA, Biology Department, Duke University, Durham, NC 27708, USA, Institut de Biologie Physico-Chimique, UMR7141 CNRS/Université Pierre et Marie Curie-Paris6, 13 Rue Pierre et Marie Curie, 75005 Paris, France and St. Edwards University, Department of Biology, Austin, TX 78704, USA
| | - Jeff Shrager
- The Carnegie Institution, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305, USA, Biology Department, Duke University, Durham, NC 27708, USA, Institut de Biologie Physico-Chimique, UMR7141 CNRS/Université Pierre et Marie Curie-Paris6, 13 Rue Pierre et Marie Curie, 75005 Paris, France and St. Edwards University, Department of Biology, Austin, TX 78704, USA
| | - Elizabeth H. Harris
- The Carnegie Institution, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305, USA, Biology Department, Duke University, Durham, NC 27708, USA, Institut de Biologie Physico-Chimique, UMR7141 CNRS/Université Pierre et Marie Curie-Paris6, 13 Rue Pierre et Marie Curie, 75005 Paris, France and St. Edwards University, Department of Biology, Austin, TX 78704, USA
| | - Renee Halbrook
- The Carnegie Institution, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305, USA, Biology Department, Duke University, Durham, NC 27708, USA, Institut de Biologie Physico-Chimique, UMR7141 CNRS/Université Pierre et Marie Curie-Paris6, 13 Rue Pierre et Marie Curie, 75005 Paris, France and St. Edwards University, Department of Biology, Austin, TX 78704, USA
| | - Arthur R. Grossman
- The Carnegie Institution, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305, USA, Biology Department, Duke University, Durham, NC 27708, USA, Institut de Biologie Physico-Chimique, UMR7141 CNRS/Université Pierre et Marie Curie-Paris6, 13 Rue Pierre et Marie Curie, 75005 Paris, France and St. Edwards University, Department of Biology, Austin, TX 78704, USA
| | - Charles Hauser
- The Carnegie Institution, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305, USA, Biology Department, Duke University, Durham, NC 27708, USA, Institut de Biologie Physico-Chimique, UMR7141 CNRS/Université Pierre et Marie Curie-Paris6, 13 Rue Pierre et Marie Curie, 75005 Paris, France and St. Edwards University, Department of Biology, Austin, TX 78704, USA
| | - Olivier Vallon
- The Carnegie Institution, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305, USA, Biology Department, Duke University, Durham, NC 27708, USA, Institut de Biologie Physico-Chimique, UMR7141 CNRS/Université Pierre et Marie Curie-Paris6, 13 Rue Pierre et Marie Curie, 75005 Paris, France and St. Edwards University, Department of Biology, Austin, TX 78704, USA
- *To whom correspondence should be addressed. +33 1 5841 5058+33 1 5841 5022
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Abstract
Zinc is one of the metal ions essential for life, as it is required for the proper functioning of a large number of proteins. Despite its importance, the annotation of zinc-binding proteins in gene banks or protein domain databases still has significant room for improvement. In the present work, we compiled a list of known zinc-binding protein domains and of known zinc-binding sequence motifs (zinc-binding patterns), and then used them jointly to analyze the proteome of 57 different organisms to obtain an overview of zinc usage by archaeal, bacterial, and eukaryotic organisms. Zinc-binding proteins are an abundant fraction of these proteomes, ranging between 4% and 10%. The number of zinc-binding proteins correlates linearly with the total number of proteins encoded by the genome of an organism, but the proportionality constant of Eukaryota (8.8%) is significantly higher than that observed in Bacteria and Archaea (from 5% to 6%). Most of this enrichment is due to the larger portfolio of regulatory proteins in Eukaryota.
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Affiliation(s)
- Claudia Andreini
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
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Ryan MT, Sweeney T. Integrating molecular biology into the veterinary curriculum. JOURNAL OF VETERINARY MEDICAL EDUCATION 2007; 34:658-673. [PMID: 18326779 DOI: 10.3138/jvme.34.5.658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The modern discipline of molecular biology is gaining increasing relevance in the field of veterinary medicine. This trend must be reflected in the curriculum if veterinarians are to capitalize on opportunities arising from this field and direct its development toward their own goals as a profession. This review outlines current applications of molecular-based technologies that are relevant to the veterinary profession. In addition, the current techniques and technologies employed within the field of molecular biology are discussed. Difficulties associated with teaching a subject such as molecular biology within a veterinary curriculum can be alleviated by effectively integrating molecular topics throughout the curriculum, pitching the subject at an appropriate depth, and employing varied teaching methods throughout.
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Affiliation(s)
- Marion T Ryan
- College of Life Sciences, School of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Dublin, Ireland.
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