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Comparative genomics in cyprinids: common carp ESTs help the annotation of the zebrafish genome

Alan Christoffels, Richard Bartfai, Hamsa Srinivasan, Hans Komen, Laszlo Orban
2006 BMC Bioinformatics  
The fact that common carp transcripts help the identification or confirmation of these coding regions in zebrafish exemplifies the usefulness of sequences from closely related species for the annotation  ...  The scarcity of genomic information from other cyprinids provides the impetus to leverage EST collections to understand gene structures in this diverse teleost group.  ...  They also acknowledge the help of Oliver Bezuidt, Cameron MacPherson and Vladimir Bajic for the comparative analysis of homologous 5'UTRs from common carp and zebrafish as well as Vladimir Bajic's helpful  ... 
doi:10.1186/1471-2105-7-s5-s2 pmid:17254304 pmcid:PMC1764476 fatcat:mmtvqyiq2ffobnfjiz4tmij7km

Comparative transcriptomics of cyprinid minnows and carp in a common wild setting: a resource for ecological genomics in freshwater communities

Trevor J Krabbenhoft, Thomas F Turner
2017 DNA Research  
Here, we demonstrate the utility and potential pitfalls of comparative transcriptomics of wild organisms, with an example from three cyprinid fish species (Teleostei:Cypriniformes).  ...  Comparative transcriptomics can now be conducted on organisms in natural settings, which has greatly enhanced understanding of genome-environment interactions.  ...  The availability of a (draft) genome for common carp 40 will eventually help identify Ohnologs that are silenced because pseudogenes of silenced genes may still be present in genomic DNA sequences; currently  ... 
doi:10.1093/dnares/dsx034 pmid:28985264 pmcid:PMC5824830 fatcat:nat5qlydtbgylpqndwfbvf4jme

Host microRNA analysis in cyprinid Herpesvirus-3 (CyHV-3) infected common carp

Michal Reichert, Anna Lukasik, Piotr Zielenkiewicz, Marek Matras, Joanna Maj-Paluch, Magdalena Stachnik, Ewa Borzym
2019 BMC Genomics  
The mechanism of latency and the ability of the cyprinid herpesvirus 3 (CyHV-3) to establish life-long infections in carp remains poorly understood.  ...  Conclusions: The results of our analysis expand the knowledge of common carp microRNAs engaged during CyHV-3 infection and provide a useful basis for the further study of the mechanism of CyHV-3 induced  ...  Since the common carp genome is available only in the preliminary (first) version without any annotation, the zebrafish RNA sequences, genome and its annotation were used additionally for this part of  ... 
doi:10.1186/s12864-018-5266-9 fatcat:uu5aakxmrvflvj3esmjvixe4jq

Different expression patterns of sperm motility-related genes in testis of diploid and tetraploid cyprinid fish†

Fangzhou Hu, Kang Xu, Yunfan Zhou, Chang Wu, Shi Wang, Jun Xiao, Min Wen, Rurong Zhao, Kaikun Luo, Min Tao, Wei Duan, Shaojun Liu
2017 Biology of Reproduction  
Clues of variations in tetraploid testis are characterized by comparative transcriptome analysis between tetraploid hybrid and common carp.  ...  In our previous study, we found that the diploid spermatozoa from allotetraploid hybrid (4nAT) had longer durations of rapid and slow progressive motility than haploid spermatozoa from common carp (COC  ...  Tetraploidization in fish during culture is most common in cyprinids, salmonids, and catostomids [51] [52] [53] .  ... 
doi:10.1093/biolre/iox010 pmid:28340181 pmcid:PMC5441299 fatcat:oj7qhnydfrb3pgctfrt4ye3qmu

Genome Wide Identification, Phylogeny, and Expression of Aquaporin Genes in Common Carp (Cyprinus carpio)

Chuanju Dong, Lin Chen, Jingyan Feng, Jian Xu, Shahid Mahboob, Khalid Al-Ghanim, Xuejun Li, Peng Xu, Graça Soveral
2016 PLoS ONE  
Comparative analysis was performed across five typical vertebrate genomes. We found that almost all of the aqp genes in common carp were duplicated in the evolution of the gene family.  ...  We postulated that the expansion of the aqp gene family in common carp was the result of an additional whole genome duplication event and that the aqp gene family in other teleosts has been lost in their  ...  ) [27] , Microsatellite analysis [28] and comparing common carp linkage map to zebrafish genome [29] provided critical evidence in support of the 4R WGD event in common carp [36] .  ... 
doi:10.1371/journal.pone.0166160 pmid:27935978 pmcid:PMC5147823 fatcat:qic3icgkh5frpawflh772sed2y

Identification of Common Carp Innate Immune Genes with Whole-Genome Sequencing and RNA-Seq Data

Yanju Zhang, Elia Stupka, Christiaan V. Henkel, Hans J. Jansen, Herman P. Spaink, Fons J. Verbeek
2011 Journal of Integrative Bioinformatics  
Currently, our aim is to identify carp genes involved in the development of the innate immune response, particularly TIR domaincontaining genes, from a preliminary genome assembly.  ...  The common carp is a candidate model system for immunology research.  ...  Wiegertjes from the Cell Biology and Immunology Group, Wageningen University for providing the zebrafish immune gene sequences.  ... 
doi:10.1515/jib-2011-169 fatcat:2fm5daurjzcqbbthgo3jexh6su

Identification of common carp innate immune genes with whole-genome sequencing and RNA-Seq data

Yanju Zhang, Elia Stupka, Christiaan V Henkel, Hans J Jansen, Herman P Spaink, Fons J Verbeek
2011 Journal of Integrative Bioinformatics  
Currently, our aim is to identify carp genes involved in the development of the innate immune response, particularly TIR domain-containing genes, from a preliminary genome assembly.  ...  The common carp is a candidate model system for immunology research.  ...  Wiegertjes from the Cell Biology and Immunology Group, Wageningen University for providing the zebrafish immune gene sequences.  ... 
doi:10.2390/biecoll-jib-2011-169 pmid:21908900 fatcat:madyll3vkzbvxihssx4o3yt62a

A Dense Genetic Linkage Map for Common Carp and Its Integration with a BAC-Based Physical Map

Lan Zhao, Yan Zhang, Peifeng Ji, Xiaofeng Zhang, Zixia Zhao, Guangyuan Hou, Linhe Huo, Guiming Liu, Chao Li, Peng Xu, Xiaowen Sun, Laszlo Orban
2013 PLoS ONE  
in the common carp genome.  ...  Comparative analysis between common carp and zebrafish genomes was performed based on the integrated map, providing more insights into the common carp specific whole genome duplication and segmental rearrangements  ...  Comparative Analysis between Zebrafish and Common Carp Genomes Common carp has 100 chromosomes (2n) [48, 49] , which is double of that of diploid cyprinids, such as the zebrafish.  ... 
doi:10.1371/journal.pone.0063928 pmid:23704958 pmcid:PMC3660343 fatcat:g5t2ezeuljft5ibhmayxi3yhqq

Genetic evolution and diversity of common carp Cyprinus carpio L

Dimitry Chistiakov, Natalia Voronova
2009 Open Life Sciences  
The genome duplication event has resulted in tetraploidy since the common carp currently harbors a substantial portion of duplicated loci in its genome and twice the number of chromosomes (n = 100–104)  ...  Of those, microsatellites and mitochondrial DNA were most frequently used in the analysis of genetic diversity and genome evolution of common carp.  ...  Also, as with any cyprinid fish, there is great potential in applying information from the zebrafish genome [79] to the carp, as this provides a putative sequence source for the majority of coding genes  ... 
doi:10.2478/s11535-009-0024-2 fatcat:q4ik6kel5bda3mzmqxupqzpzli

Ancient and modern duplication events and the evolution of stearoyl-CoA desaturases in teleost fishes

Helen Evans, Tony De Tomaso, Mike Quail, Jane Rogers, Andrew Y. Gracey, Andrew R. Cossins, Michael Berenbrink
2008 Physiological Genomics  
Using syntenically aligned chromosomal fragments from large-insert clones of common carp and grass carp together with those from genomically sequenced model species, we show that the ancient and modern  ...  Critical support for this interpretation comes from comparison across all vertebrate groups of the gene order in the genomic environments of the SCD isoforms.  ...  , and Spencer Polley (London School of Health and Tropical Medicine, London, UK) for helpful discussions.  ... 
doi:10.1152/physiolgenomics.90266.2008 pmid:18593860 pmcid:PMC2536826 fatcat:rnjkppvfkfh4zlzqawm7xd5qay

Construction, De-Novo Assembly and Analysis of Transcriptome for Identification of Reproduction-Related Genes and Pathways from Rohu, Labeo rohita (Hamilton)

Dinesh Kumar Sahu, Soumya Prasad Panda, Prem Kumar Meher, Paramananda Das, Padmanav Routray, Jitendra Kumar Sundaray, Pallipuram Jayasankar, Samiran Nandi, John A Craft
2015 PLoS ONE  
Unlike common carp the monsoon breeding habit of rohu restricts its seed production beyond season indicating strong genetic control over spawning. Genetic information is limited in this regard.  ...  The problem is exacerbated by the lack of genomic-resources.  ...  Acknowledgments This work was supported by Indian Council of Agricultural Research (ICAR) and Central Institute of Freshwater Aquaculture (CIFA), Government of India.  ... 
doi:10.1371/journal.pone.0132450 pmid:26148098 pmcid:PMC4509579 fatcat:5t264ytssrdy5eiaobzo32o3pu

CXCL8 Chemokines in Teleost Fish: Two Lineages with Distinct Expression Profiles during Early Phases of Inflammation

Lieke M. van der Aa, Magdalena Chadzinska, Edwin Tijhaar, Pierre Boudinot, B. M. Lidy Verburg-van Kemenade, Kathleen A. Kelly
2010 PLoS ONE  
During the inflammatory process, chemokine CXCL8 plays a pivotal role in recruitment of human neutrophilic granulocytes.  ...  A diversity of sequences similar to CXCL8 was reported in fish, but their evolutionary relationships and functional homology with their human homolog remain unclear.  ...  Mark Huising for HI-treatments, Maria de Boer for the help with the in vitro chemotaxis assay, Pierre Pontarroti for helpful discussions, and Didier Chevret for the analysis of the recombinant CXCa_L1  ... 
doi:10.1371/journal.pone.0012384 pmid:20865040 pmcid:PMC2928728 fatcat:cbkyhbrgy5g3teupoltsofo7ua

Computational identification of Y-linked markers and genes in the grass carp genome by using a pool-and-sequence method

Aidi Zhang, Rong Huang, Liangming Chen, Lv Xiong, Libo He, Yongming Li, Lanjie Liao, Zuoyan Zhu, Yaping Wang
2017 Scientific Reports  
Comparative analysis of the zebrafish genome revealed that the LG24 linkage group of grass carp corresponds to chromosomes 10 and 22 of zebrafish, suggesting that the grass carp genome underwent chromosome  ...  These findings provided an abundant resource for the Y chromosome of grass carp, and may help elucidate sex chromosome evolution in cyprinid fish.  ...  During the breeding season of grass carp and common carp (late April to early May), 1 female grass carp, 1 male grass carp, and 1 male common carp parents were randomly selected from the Guanqiao Experimental  ... 
doi:10.1038/s41598-017-08476-y pmid:28811564 pmcid:PMC5557828 fatcat:tao3bqv77je6fmuonqlnypypue

Lineage-Specific Expansion of IFIT Gene Family: An Insight into Coevolution with IFN Gene Family

Ying Liu, Yi-Bing Zhang, Ting-Kai Liu, Jian-Fang Gui, Nicolas Salamin
2013 PLoS ONE  
In the present study, IFIT genes are identified in the genome databases from the jawed vertebrates including the cartilaginous elephant shark but not from non-vertebrates such as lancelet, sea squirt and  ...  Our results are helpful for understanding of evolution of vertebrate IFN system.  ...  Wrote the paper: YBZ YL JFG.  ... 
doi:10.1371/journal.pone.0066859 pmid:23818968 pmcid:PMC3688568 fatcat:mvsgbhi7gbh2xox2ficushmrtu

Transcriptome Analysis of Crucian Carp (Carassius auratus), an Important Aquaculture and Hypoxia-Tolerant Species

Xiaolin Liao, Lei Cheng, Peng Xu, Guoqing Lu, Michael Wachholtz, Xiaowen Sun, Songlin Chen, Marc Robinson-Rechavi
2013 PLoS ONE  
The gene expression analysis revealed more genes expressed in brain, more up-regulated genes in muscle and more down-regulated genes in liver as compared with gene expression profiles of other tissues.  ...  The crucian carp is an important aquaculture species and a potential model to study genome evolution and physiological adaptation.  ...  We are grateful to Mary Christman for proofreading the manuscript. Author Contributions Conceived and designed the experiments: XL PX XS SC. Performed the experiments: XL LC.  ... 
doi:10.1371/journal.pone.0062308 pmid:23630630 pmcid:PMC3632525 fatcat:mux7qfqdkrawxhekwf3nzsgfby
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