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

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Article Navigation > Acta Oceanologica Sinica > 2014 > 33(2): 102-107

WANG Liang, WU Shuangxiu, LIU Tao, SUN Jing, CHI Shan, LIU Cui, LI Xingang, YIN Jinlong, WANG Xumin, YU Jun. Endogenous viral elements in algal genomes[J]. Acta Oceanologica Sinica, 2014, 33(2): 102-107. doi: 10.1007/s13131-014-0446-1

Citation:

WANG Liang, WU Shuangxiu, LIU Tao, SUN Jing, CHI Shan, LIU Cui, LI Xingang, YIN Jinlong, WANG Xumin, YU Jun. Endogenous viral elements in algal genomes[J]. Acta Oceanologica Sinica, 2014, 33(2): 102-107. doi: 10.1007/s13131-014-0446-1

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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

Received Date: 2013-03-25
Rev Recd Date: 2013-08-01

Abstract

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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