Endogenous viral elements in algal genomes

WANG Liang; WU Shuangxiu; LIU Tao; SUN Jing; CHI Shan; LIU Cui; LI Xingang; YIN Jinlong; WANG Xumin; YU Jun

doi:10.1007/s13131-014-0446-1

Endogenous viral elements in algal genomes

doi: 10.1007/s13131-014-0446-1

1.
CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China;Beijing Key Laboratory of Functional Genomics for Dao-di Herbs, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China;University of Chinese Academy of Sciences, Beijing 100049, China
2.
CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China;Beijing Key Laboratory of Functional Genomics for Dao-di Herbs, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
3.
College of Marine Life Science, Ocean University of China, Qingdao 266003, China
4.
CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China

基金项目: The National Natural Science Foundation of China under contract Nos 31140070, 31271397 and 41206116; the algal transcriptome sequencing was supported by 1KP Project (www.onekp.com).

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出版历程
- 收稿日期: 2013-03-25
- 修回日期: 2013-08-01

Endogenous viral elements in algal genomes

1.
CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China;Beijing Key Laboratory of Functional Genomics for Dao-di Herbs, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China;University of Chinese Academy of Sciences, Beijing 100049, China
2.
CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China;Beijing Key Laboratory of Functional Genomics for Dao-di Herbs, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
3.
College of Marine Life Science, Ocean University of China, Qingdao 266003, China
4.
CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China

摘要

摘要: Endogenous viral elements (EVEs) are host-genomic fragments originated from viral genomes. They have been found universally in animal and plant genomes. Here we carried out a systematic screening and analysis of EVEs in algal genomes and found that EVEs commonly exist in algal genomes. We classified the EVE fragments into three categories according to the length of EVE fragments. Due to the probability of sequence similarity by chance, we ignored the potential function of medium-length EVE fragments. However, longlength EVE fragments probably had capability to encode protein domains or even entire proteins, and some short-length EVE fragments had high similarity with host's siRNA sequences and possibly served functions of small RNAs. Therefore, short and long EVE fragments might provide regulomic and proteomic novelty to the host's metabolism and adaptation. We also found several EVE fragments shared by more than 3 algal genomes. By phylogenetic analysis of the shared EVEs and their corresponding species, we found that the integration of viral fragments into host genomes was an ancient event, possibly before the divergence of Chlorophytes and Ochrophytes. Our findings show that there is a frequent genetic flow from viruses to algal genomes. Moreover, study on algal EVEs shed light on the virus-host interaction in large timescale and could also help us understand the balance of marine ecosystems.
- endogenousviralelements /
- algae /
- genome /
- transcriptome
Abstract: Endogenous viral elements (EVEs) are host-genomic fragments originated from viral genomes. They have been found universally in animal and plant genomes. Here we carried out a systematic screening and analysis of EVEs in algal genomes and found that EVEs commonly exist in algal genomes. We classified the EVE fragments into three categories according to the length of EVE fragments. Due to the probability of sequence similarity by chance, we ignored the potential function of medium-length EVE fragments. However, longlength EVE fragments probably had capability to encode protein domains or even entire proteins, and some short-length EVE fragments had high similarity with host's siRNA sequences and possibly served functions of small RNAs. Therefore, short and long EVE fragments might provide regulomic and proteomic novelty to the host's metabolism and adaptation. We also found several EVE fragments shared by more than 3 algal genomes. By phylogenetic analysis of the shared EVEs and their corresponding species, we found that the integration of viral fragments into host genomes was an ancient event, possibly before the divergence of Chlorophytes and Ochrophytes. Our findings show that there is a frequent genetic flow from viruses to algal genomes. Moreover, study on algal EVEs shed light on the virus-host interaction in large timescale and could also help us understand the balance of marine ecosystems.
- endogenous viral elements /
- algae /
- genome /
- transcriptome

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参考文献(40)

Alexeyenko A, Tamas I, Liu Gang, et al. 2006. Automatic clustering of orthologs and inparalogs shared by multiple proteomes. Bioinformatics, 22(14): e9-15

Allen M J, Schroeder D C, Holden M T, et al. 2006. Evolutionary history of the Coccolithoviridae. Mol Biol Evol, 23(1): 86-92

Altschul S F, Gish W, Miller W, et al. 1990. Basic local alignment search tool. J Mol Biol, 215(3): 403-410

Boguski M S, Lowe T M, Tolstoshev C M. 1993. dbEST—database for “expressed sequence tags”. Nat Genet, 4(4): 332-333

Brussaard C P. 2004. Viral control of phytoplankton populations—a review. J Eukaryot Microbiol, 51(2): 125-138

Cerutti H, Ma Xinrong, Msanne J, et al. 2011. RNA-mediated silencing in Algae: biological roles and tools for analysis of gene function. Eukaryot Cell, 10(9): 1164-1172

Cock J M, Sterck L, Rouze P, et al. 2010. The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature, 465(7298): 617-621

Darriba D, Taboada G L, Doallo R, et al. 2011. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics, 27(8): 1164-1165

Dean W E, Gorham E. 1998. Magnitude and significance of carbon burial in lakes, reservoirs, and peatlands. Geology, 26(6): 535-538

Delaroque N, Boland W. 2008. The genome of the brown alga Ectocarpus siliculosus contains a series of viral DNA pieces, suggesting an ancient association with large dsDNA viruses. BMC Evol Biol, 8: 110

Delaroque N, Muller D G, Bothe G, et al. 2001. The complete DNA sequence of the Ectocarpus siliculosus Virus EsV-1 genome. Virology, 287(1): 112-132

Do C B, Mahabhashyam M S, Brudno M, et al. 2005. ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res, 15(2): 330-340

Dunigan D D, Fitzgerald L A, Van Etten J L. 2006. Phycodnaviruses: a peek at genetic diversity. Virus Res, 117(1): 119-132

Emerman M, Malik H S. 2010. Paleovirology—modern consequences of ancient viruses. PLoS Biol, 8(2): e1000301

Essoussi N, Boujenfa K, Limam M. 2008. A comparison of MSA tools. Bioinformation, 2(10): 452-455

Fitzgerald L A, Graves M V, Li Xiao, et al. 2007. Sequence and annotation of the 369-kb NY-2A and the 345-kb AR158 viruses that infect Chlorella NC64A. Virology, 358(2): 472-484

Fuhrman J A. 1999. Marine viruses and their biogeochemical and ecological effects. Nature, 399(6736): 541-548

Gifford R, Tristem M. 2003. The evolution, distribution and diversity of endogenous retroviruses. Virus Genes, 26(3): 291-315

Goodstein D M, Shu Shengqiang, Howson R, et al. 2012. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res, 40(Database issue): D1178-1186

Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol, 52(5): 696-704

International Committee on Taxonomy of Viruses, King A M Q, Societies I U o M. 2012. Virus Taxonomy: Classification and Nomenclature of Viruses: Ninth Report of the International Committee on Taxonomy of Viruses. Amsterdam: Elsevier/Academic Press, 1327

Katzourakis A, Gifford R J. 2010. Endogenous viral elements in animal genomes. PLoS Genet, 6(11): e1001191

Kent W J. 2002. BLAT—the BLAST-like alignment tool. Genome Res, 12(4): 656-664

Langmead B, Trapnell C, Pop M, et al. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol, 10(3): R25

Lavrukhin O V, Fortune J M, Wood T G, et al. 2000. Topoisomerase II from Chlorella virus PBCV-1. Characterization of the smallest known type II topoisomerase. J Biol Chem, 275(10): 6915-6921

Meints R H, Ivey R G, Lee A M, et al. 2008. Identification of two virus integration sites in the brown alga Feldmannia chromosome. J Virol, 82(3): 1407-1413

Mette M F, Kanno T, Aufsatz W, et al. 2002. Endogenous viral sequences and their potential contribution to heritable virus resistance in plants. EMBO J, 21(3): 461-469

Monier A, Pagarete A, de Vargas C, et al. 2009. Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus. Genome Res, 19(8): 1441-1449

Muller D G, Sengco M, Wolf S, et al. 1996. Comparison of two DNA viruses infecting the marine brown algae Ectocarpus siliculosus and E. fasciculatus. J Gen Virol, 77(Pt 9): 2329-2333

O'Brien K P, Remm M, Sonnhammer E L. 2005. Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res, 33(Database issue): D476-480

Punta M, Coggill P C, Eberhardt R Y, et al. 2012. The Pfam protein families database. Nucleic Acids Res, 40(Database issue): D290-301

Raoult D, Audic S, Robert C, et al. 2004. The 1.2-megabase genome sequence of Mimivirus. Science, 306(5700): 1344-1350

Ribet D, Harper F, Dupressoir A, et al. 2008. An infectious progenitor for the murine IAP retrotransposon: emergence of an intracellular genetic parasite from an ancient retrovirus. Genome Res, 18(4): 597-609

Staginnus C, Richert-Poggeler K R. 2006. Endogenous pararetroviruses: two-faced travelers in the plant genome. Trends Plant Sci, 11(10): 485-491

Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22(21): 2688-2690

Van Etten J L, Graves M V, Muller D G, et al. 2002. Phycodnaviridae—large DNA algal viruses. Arch Virol, 147(8): 1479-1516

Wilson W H, Schroeder D C, Allen M J, et al. 2005. Complete genome sequence and lytic phase transcription profile of a Coccolithovirus. Science, 309(5737): 1090-1092

Wommack K E, Colwell R R. 2000. Virioplankton: viruses in aquatic ecosystems. Microbiol Mol Biol Rev, 64(1): 69-114

Yanai-Balser G M, Duncan G A, Eudy J D, et al. 2010. Microarray analysis of Paramecium bursaria chlorella virus 1 transcription. J Virol, 84(1): 532-542

Zdobnov E M, Apweiler R. 2001. InterProScan—an integration platform for the signature-recognition methods in InterPro. Bioinformatics, 17(9): 847-848

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Endogenous viral elements in algal genomes

doi: 10.1007/s13131-014-0446-1

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Endogenous viral elements in algal genomes

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