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Report on Marine Life Genomics 44 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 12 December 2018 doi:10.20944/preprints201812.0156.v1 The report of marine life genomic research Guangyi Fan1,2, Jianwei Chen1, Tao Jin1, Chengcheng Shi1, Xiao Du1, He Zhang1, Yaolei Zhang1, Hanbo Li1, Ting Luo1, Pengxu Yan1, Guang Liu1, Xiangqun Chi1, Xiaoxuan Tan1, Liangwei Li1, Guilin Liu1, Xiaochuan Liu1, Shijie Hao1, Kai Han1, Xiaoyun Huang1, Shuai Sun1, Jing Zhou1, Mengjun Yu1, Lingfeng Meng1, Yue Chang1, Rui Zhang1, Kaiqiang Liu1, Mengqi Zhang1, Yong Zhao1, Chang Li1, Jiao Guo1, Xinyu Guo1, Jiahao Wang1, Meiqi Lv1, Haoyang Gao1, Yujie Liu1, Yue Song1, Shengjun Wang1, Yang Deng1, Binjie Ouyang1, Jinzhong Lin1, Yingjia Yu1, lynn Fink4, Xianwei Yang1, Xun Xu1,2,3, Xin Liu1,2,3. 1 BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong Province, 266555, China. 2 BGI-Shenzhen, Shenzhen, 518083, China. 3 China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China. 4BGI-Australia, QLD 4006 Australia. Correspondence should be addressed to Xin Liu ([email protected]) and Guangyi Fan ([email protected]). Key words: marine microorganisms, marine fungi, algae, marine plants, marine invertebrates, marine vertebrates, genome, metagenome. © 2018 by the author(s). Distributed under a Creative Commons CC BY license. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 12 December 2018 doi:10.20944/preprints201812.0156.v1 Preface With the continuing development of sequencing technology, genomics has been applied in a variety of biological research areas. In particular, the application of genomics to marine species, which boast a high diversity, promises great scientific and industrial potential. Significant progress has been made in marine genomics especially over the past few years. Consequently, BGI, leveraging its prominent contributions in genomics research, established BGI-Qingdao, an institute specifically aimed at exploring marine genomics. In order to accelerate marine genomics research and related applications, BGI-Qingdao initiated the International Conference on Genomics of the Ocean (ICG- Ocean) to develop international collaborations and establish a focused and coherent global research plan. Last year, the first ICG-Ocean conference was held in Qingdao, China, during which 47 scientists in marine genomics from all over the world reported on their research progress to an audience of about 300 attendees. This year, we would like to build on that success, drafting a report on marine genomics to draw global attention to marine genomics. We summarized the recent progress, proposed future directions, and we would like to enable additional profound insights on marine genomics. Similar to the annual report on plant and fungal research by Kew Gardens, and the White Paper of ethical issues on experimental animals, we hope our first report on marine genomics can provide some useful insights for researchers, funding agencies as well as industry, and that future versions will expand upon the foundation established here in both breadth and depth of knowledge. This report summarizes the recent progress in marine genomics in six parts including: marine microorganisms, marine fungi, marine algae and plants, marine invertebrates, marine vertebrates and genomics-based applications. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 12 December 2018 doi:10.20944/preprints201812.0156.v1 Content Reports of marine life genomic research ................................................................... 1 Preface ........................................................................................................................... 1 1 Overview .............................................................................................................. 5 1.1 Current status of marine genomics ......................................................................... 5 1.2 Summary of marine organism genomes ................................................................. 7 1.3 Sequencing technology ............................................................................................. 9 1.4 Large-scale genome projects ................................................................................. 10 2 Genomics of marine microorganisms ............................................................. 12 2.1 Genomes of bacteria and archaea ......................................................................... 12 2.2 Marine metagenomics ............................................................................................ 16 2.3 Genomics of marine viruses .................................................................................. 22 3 Genomics of marine fungi ................................................................................ 24 3.1 Basic introduction of marine fungi ....................................................................... 24 3.2 High-throughput sequencing for marine fungi .................................................... 26 4 Genomics of marine algae and plants ............................................................. 30 4.1 Algae genome .......................................................................................................... 30 4.2 Genomics of marine plants .................................................................................... 34 5 Marine Invertebrates ....................................................................................... 36 5.1 Global diversity and phylogeny ............................................................................ 36 5.2 Genomics of marine invertebrates ........................................................................ 37 6 Fish genomes ..................................................................................................... 44 6.1 Brief introduction of fish ....................................................................................... 44 6.2 Research focuses of fish genomics ......................................................................... 46 6.2.1 Viviparity in teleost ........................................................................................ 46 6.2.2 Water-to-land transition .................................................................................. 47 6.2.3 Adaptation to extreme cold ............................................................................ 47 6.2.4 Convergent evolution toward adaptation to darkness .................................... 48 6.2.5 Fish disease and immunity ............................................................................. 48 6.2.6 Sex determination .......................................................................................... 49 6.2.7 Metamorphosis ............................................................................................... 50 7 Genomics of marine tetrapods......................................................................... 52 7.1 Brief introduction and genomes ............................................................................ 52 7.2 Current status of marine tetrapod genomes ........................................................ 52 7.3 Conservation of marine tetrapods using genomics ............................................. 54 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 12 December 2018 doi:10.20944/preprints201812.0156.v1 8 Applications of genomic data ........................................................................... 57 8.1 Genetic engineering ................................................................................................ 57 8.2 Marine natural products ....................................................................................... 60 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 12 December 2018 doi:10.20944/preprints201812.0156.v1 1 Overview 1.1 Current status of marine genomics The ocean, comprising the majority of our planet’s hydrosphere, is the cradle of life. After evolving for billions of years, more than two million species inhabit the ocean, of which only 230,000 species are documented. The high biodiversity in the ocean provides unprecedented opportunity to explore various scientific questions, including the origin and evolution of life, adaptation to different environments, chemo- and photosynthesis, ecology, etc. Marine life can also serve as a crucial food resource for the future development of human society, providing sustainable protein, peptides and metabolites. Despite the importance and potential of marine life exploration and research, current biological research is relatively limited, especially compared to exploration of ocean resources, the development of marine equipment, and biological research of land plants and animals (for example, humans - ourselves). Thanks to the development of biotechnology, research in marine biology has made great progress in the past decade, especially with the recent developments in sequencing technology and genomics. Even marine life without a clear evolutionary background can be studied in more efficiently. Subsequently, marine genomics, which uses cutting-edge sequencing technologies to produce genomic data supported by bioinformatics analysis of the data, has significantly facilitated improvements in marine biology and industrial applications in recent years (Fig. 1.1). Subsequent to the publication of the first fish genome (Fugu rubripes) in 2002 (see a list of first genomes from different clades of marine species in Table 1.1), 453 marine species now have a published reference
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