Endogenous viral elements in algal genomes
- PDF / 294,694 Bytes
- 6 Pages / 595.276 x 841.89 pts (A4) Page_size
- 61 Downloads / 195 Views
Endogenous viral elements in algal genomes WANG Liang1,3,4†, WU Shuangxiu1,3†, LIU Tao2, SUN Jing1,3,4, CHI Shan2, LIU Cui2, LI Xingang1,3 , YIN Jinlong1, WANG Xumin1,3*, YU Jun1,3* 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 2 College of Marine Life Science, Ocean University of China, Qingdao 266003, China 3 Beijing Key Laboratory of Functional Genomics for Dao-di Herbs, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China 4 University of Chinese Academy of Sciences, Beijing 100049, China Received 25 March 2013; accepted 1 August 2013 ©The Chinese Society of Oceanography and Springer-Verlag Berlin Heidelberg 2014
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. Key words: endogenous viral elements, algae, genome, transcriptome Citation: Wang Liang, Wu Shuangxiu, Liu Tao, Sun Jing, Chi Shan, Liu Cui, Li Xingang, Yin Jinlong, Wang Xumin, Yu Jun. 2014. Endogenous viral elements in algal genomes. Acta Oceanologica Sinica, 33(2): 102–107, doi: 10.1007/s13131-014-0446-1
1 Introduction The ocean covers more than 70% of the Earth's surface and contains 97% of the planet's water (Dean and Gorham, 1998). There are almost billions to tens-of-billions of free viruses per liter at the surface of the oceans (Wommack and Colwell, 2000). As the most abundant life form, viruses, especially marine viruses, play a major role in global ecosystem. For example, marine viruses could be one of the reasons, if not the major ones, to maintain the diversity of plankton (Fuhrman, 1999). They also
Data Loading...
