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Abstract
BACKGROUND Repeat elements are important components of most eukaryotic genomes. Most existing tools for repeat analysis rely either on high quality reference genomes or existing repeat libraries. Thus, it is still challenging to do repeat analysis for species with highly repetitive or complex genomes which often do not have good reference genomes or annotated repeat libraries. Recently we developed a computational method called REPdenovo that constructs consensus repeat sequences directly from short sequence reads, which outperforms an existing tool called RepARK. One major issue with REPdenovo is that it doesn't perform well for repeats with relatively high divergence rates or low copy numbers. In this paper, we present an improved approach for constructing consensus repeats directly from short reads. Comparing with the original REPdenovo, the improved approach uses more repeat-related k-mers and improves repeat assembly quality using a consensus-based k-mer processing method. RESULTS We compare the performance of the new method with REPdenovo and RepARK on Human, Arabidopsis thaliana and Drosophila melanogaster short sequencing data. And the new method fully constructs more repeats in Repbase than the original REPdenovo and RepARK, especially for repeats of higher divergence rates and lower copy number. We also apply our new method on Hummingbird data which doesn't have a known repeat library, and it constructs many repeat elements that can be validated using PacBio long reads. CONCLUSION We propose an improved method for reconstructing repeat elements directly from short sequence reads. The results show that our new method can assemble more complete repeats than REPdenovo (and also RepARK). Our new approach has been implemented as part of the REPdenovo software package, which is available for download at https://github.com/Reedwarbler/REPdenovo .
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Affiliation(s)
- Chong Chu
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, 02115 MA USA
| | - Jingwen Pei
- Department of Computer Science and Engineering, University of Connecticut, 371 Fairfield Way, Unit 2155, Storrs, 06269 CT USA
| | - Yufeng Wu
- Department of Computer Science and Engineering, University of Connecticut, 371 Fairfield Way, Unit 2155, Storrs, 06269 CT USA
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McKeown DA, Schroeder JL, Stevens K, Peters AF, Sáez CA, Park J, Rothman MD, Bolton JJ, Brown MT, Schroeder DC. Phaeoviral Infections Are Present in Macrocystis, Ecklonia and Undaria (Laminariales) and Are Influenced by Wave Exposure in Ectocarpales. Viruses 2018; 10:E410. [PMID: 30081590 PMCID: PMC6116031 DOI: 10.3390/v10080410] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 08/01/2018] [Accepted: 08/02/2018] [Indexed: 01/02/2023] Open
Abstract
Two sister orders of the brown macroalgae (class Phaeophyceae), the morphologically complex Laminariales (commonly referred to as kelp) and the morphologically simple Ectocarpales are natural hosts for the dsDNA phaeoviruses (family Phycodnaviridae) that persist as proviruses in the genomes of their hosts. We have previously shown that the major capsid protein (MCP) and DNA polymerase concatenated gene phylogeny splits phaeoviruses into two subgroups, A and B (both infecting Ectocarpales), while MCP-based phylogeny suggests that the kelp phaeoviruses form a distinct third subgroup C. Here we used MCP to better understand the host range of phaeoviruses by screening a further 96 and 909 samples representing 11 and 3 species of kelp and Ectocarpales, respectively. Sporophyte kelp samples were collected from their various natural coastal habitats spanning five continents: Africa, Asia, Australia, Europe, and South America. Our phylogenetic analyses showed that while most of the kelp phaeoviruses, including one from Macrocystispyrifera, belonged to the previously designated subgroup C, new lineages of Phaeovirus in 3 kelp species, Ecklonia maxima, Ecklonia radiata, Undaria pinnatifida, grouped instead with subgroup A. In addition, we observed a prevalence of 26% and 63% in kelp and Ectocarpales, respectively. Although not common, multiple phaeoviral infections per individual were observed, with the Ectocarpales having both intra- and inter-subgroup phaeoviral infections. Only intra-subgroup phaeoviral infections were observed in kelp. Furthermore, prevalence of phaeoviral infections within the Ectocarpales is also linked to their exposure to waves. We conclude that phaeoviral infection is a widely occurring phenomenon in both lineages, and that phaeoviruses have diversified with their hosts at least since the divergence of the Laminariales and Ectocarpales.
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Affiliation(s)
- Dean A McKeown
- Marine Biological Association of the UK, Citadel Hill, Plymouth, Devon PL1 2PB, UK.
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, Devon PL4 8AA, UK.
| | - Joanna L Schroeder
- Marine Biological Association of the UK, Citadel Hill, Plymouth, Devon PL1 2PB, UK.
| | - Kim Stevens
- Marine Biological Association of the UK, Citadel Hill, Plymouth, Devon PL1 2PB, UK.
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, Devon PL4 8AA, UK.
| | - Akira F Peters
- Bezhin Rosko, 40 Rue des Pêcheurs, F-29250 Santec, France.
| | - Claudio A Sáez
- Laboratory of Aquatic Environmental Research, Centre of Advanced Studies, University of Playa Ancha, Viña del Mar 581782, Chile.
| | - Jihae Park
- Lab of Plant Growth Analysis, Ghent University Global Campus, 119, Songdomunwha-ro, Yeonsu-gu, Incheon 21985, Korea.
| | - Mark D Rothman
- Department of Agriculture, Forestry and Fisheries, Private bag X2, Vlaeberg 8018, South Africa.
- Department of Biological Sciences and Marine Research Institute, University of Cape Town, Cape Town 7701, South Africa.
| | - John J Bolton
- Department of Biological Sciences and Marine Research Institute, University of Cape Town, Cape Town 7701, South Africa.
| | - Murray T Brown
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, Devon PL4 8AA, UK.
| | - Declan C Schroeder
- Marine Biological Association of the UK, Citadel Hill, Plymouth, Devon PL1 2PB, UK.
- School of Biological Sciences, University of Reading, Reading RG6 6LA, UK.
- Veterinary Population Medicine, 225 Veterinary Medical Center, 1365 Gortner Avenue, St Paul, MN 55108, USA.
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103
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Jiang M, Chu Z. Comparative analysis of plant MKK gene family reveals novel expansion mechanism of the members and sheds new light on functional conservation. BMC Genomics 2018; 19:407. [PMID: 29843611 PMCID: PMC5975520 DOI: 10.1186/s12864-018-4793-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 05/14/2018] [Indexed: 12/15/2022] Open
Abstract
Background Mitogen-activated protein kinase (MAPK) cascades play critical functions in almost every aspect of plant growth and development, which regulates many physiological and biochemical processes. As a middle nodal point of the MAPK cascades, although evolutionary analysis of MKK from individual plant families had some reports, their evolutionary history in entire plants is still not clear. Results To better understand the evolution and function of plant MKKs, we performed systematical molecular evolutionary analysis of the MAPKK gene family and also surveyed their gene organizations, sequence features and expression patterns in different subfamilies. Phylogenetic analysis showed that plant MAPKK fall into five different groups (Group A–E). Majority orthology groups seemed to be a single or low-copy genes in all plant species analyzed in Group B, C and D, whereas group A MKKs undergo several duplication events, generating multiple gene copies. Further analysis showed that these duplication events were on account of whole genome duplications (WGDs) in plants and the duplicate genes maybe have undergone functional divergence. We also found that group E MKKs had mutation with one change of serine or theronine might lead to inactivity originated through the ancient tandem duplicates in monocots. Moreover, we also identified MKK3 integrated NTF2 domain that might have gradually lost the cytoplasmic-nuclear trafficking activity, which suggests that they may involve with the gene function more and more sophistication in the evolutionary process. Moreover, expression analyses indicated that plant MKK genes play probable roles in UV-B signaling. Conclusion In general, ancient gene and genome duplications are significantly conducive to the expansion of the plant MKK gene family. Our study reveals two distinct evolutionary patterns for plant MKK proteins and sheds new light on the functional evolution of this gene family. Electronic supplementary material The online version of this article (10.1186/s12864-018-4793-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Min Jiang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China.,Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Zhaoqing Chu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China. .,Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China.
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104
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Sun X, Wu J, Wang G, Kang Y, Ooi HS, Shen T, Wang F, Yang R, Xu N, Zhao X. Genomic analyses of unique carbohydrate and phytohormone metabolism in the macroalga Gracilariopsis lemaneiformis (Rhodophyta). BMC PLANT BIOLOGY 2018; 18:94. [PMID: 29801464 PMCID: PMC5970526 DOI: 10.1186/s12870-018-1309-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 05/10/2018] [Indexed: 05/14/2023]
Abstract
BACKGROUND Red algae are economically valuable for food and in industry. However, their genomic information is limited, and the genomic data of only a few species of red algae have been sequenced and deposited recently. In this study, we annotated a draft genome of the macroalga Gracilariopsis lemaneiformis (Gracilariales, Rhodophyta). RESULTS The entire 88.98 Mb genome of Gp. lemaneiformis 981 was generated from 13,825 scaffolds (≥500 bp) with an N50 length of 30,590 bp, accounting for approximately 91% of this algal genome. A total of 38.73 Mb of scaffold sequences were repetitive, and 9281 protein-coding genes were predicted. A phylogenomic analysis of 20 genomes revealed the relationship among the Chromalveolata, Rhodophyta, Chlorophyta and higher plants. Homology analysis indicated phylogenetic proximity between Gp. lemaneiformis and Chondrus crispus. The number of enzymes related to the metabolism of carbohydrates, including agar, glycoside hydrolases, glycosyltransferases, was abundant. In addition, signaling pathways associated with phytohormones such as auxin, salicylic acid and jasmonates are reported for the first time for this alga. CONCLUSION We sequenced and analyzed a draft genome of the red alga Gp. lemaneiformis, and revealed its carbohydrate metabolism and phytohormone signaling characteristics. This work will be helpful in research on the functional and comparative genomics of the order Gracilariales and will enrich the genomic information on marine algae.
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Affiliation(s)
- Xue Sun
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211 People’s Republic of China
| | - Jun Wu
- School of Biomedical Engineering, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240 People’s Republic of China
| | - Guangce Wang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 People’s Republic of China
| | - Yani Kang
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211 People’s Republic of China
- School of Biomedical Engineering, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240 People’s Republic of China
| | - Hong Sain Ooi
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Tingting Shen
- School of Biomedical Engineering, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240 People’s Republic of China
| | - Fangjun Wang
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211 People’s Republic of China
| | - Rui Yang
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211 People’s Republic of China
| | - Nianjun Xu
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211 People’s Republic of China
| | - Xiaodong Zhao
- School of Biomedical Engineering, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240 People’s Republic of China
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105
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Chi S, Liu T, Wang X, Wang R, Wang S, Wang G, Shan G, Liu C. Functional genomics analysis reveals the biosynthesis pathways of important cellular components (alginate and fucoidan) of Saccharina. Curr Genet 2018; 64:259-273. [PMID: 28825126 PMCID: PMC5778160 DOI: 10.1007/s00294-017-0733-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/08/2017] [Accepted: 08/08/2017] [Indexed: 11/26/2022]
Abstract
Although alginate and fucoidan are unique cellular components and have important biological significance in brown algae, and many possible involved genes are present in brown algal genomes, their functions and regulatory mechanisms have not been fully revealed. Both polysaccharides may play important roles in the evolution of multicellular brown algae, but specific and in-depth studies are still limited. In this study, a functional genomics analysis of alginate and fucoidan biosynthesis routes was conducted in Saccharina, and the key events in these pathways in brown algae were identified. First, genes from different sources, including eukaryotic hosts via endosymbiotic gene transfer and bacteria via horizontal gene transfer, were combined to build a complete pathway framework. Then, a critical event occurred to drive these pathways to have real function: one of the mannose-6-phosphate isomerase homologs that arose by gene duplication subsequently adopted the function of the mannose-1-phosphate guanylyltransferase (MGP) gene, which was absent in algal genomes. Further, downstream pathway genes proceeded with gene expansions and complex transcriptional mechanisms, which may be conducive to the synthesis of alginate and fucoidan with diverse structures and contents depending on the developmental stage, tissue structure, and environmental conditions. This study revealed the alginate and fucoidan synthesis pathways and all included genes from separate phylogenetic sources in brown algae. Enzyme assays confirmed the function of key genes and led to the determination of a substitute for the missing MPG. All gene families had constitutively expressed member(s) to maintain the basic synthesis; and the gene function differentiation, enzyme characterization and gene expression regulation differences separated brown algae from other algae lineages and were considered to be the major driving forces for sophisticated system evolution of brown algae.
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Affiliation(s)
- Shan Chi
- Ocean University of China, Qingdao, Shandong Province, People's Republic of China
- Qingdao Haida BlueTek Biotechnology Co., Ltd, Qingdao, Shandong Province, People's Republic of China
| | - Tao Liu
- Ocean University of China, Qingdao, Shandong Province, People's Republic of China.
| | - Xumin Wang
- 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, People's Republic of China
- Beijing Key Laboratory of Functional Genomics for Dao-di Herbs, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Ren Wang
- Ocean University of China, Qingdao, Shandong Province, People's Republic of China
| | - Shanshan Wang
- Ocean University of China, Qingdao, Shandong Province, People's Republic of China
| | - Guoliang Wang
- 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, People's Republic of China
- Beijing Key Laboratory of Functional Genomics for Dao-di Herbs, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Guangle Shan
- 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, People's Republic of China
- Beijing Key Laboratory of Functional Genomics for Dao-di Herbs, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Cui Liu
- Qingdao Haida BlueTek Biotechnology Co., Ltd, Qingdao, Shandong Province, People's Republic of China
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106
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Wang QZ, Downie SR, Chen ZX. Genome-wide searches and molecular analyses highlight the unique evolutionary path of flavone synthase I (FNSI) in Apiaceae. Genome 2018; 61:103-109. [DOI: 10.1139/gen-2017-0117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Flavone synthase is a key enzyme for flavone biosynthesis and is encoded by two gene families: flavone synthase I (FNSI) and flavone synthase II (FNSII). FNSII is widely distributed in plants, while FNSI has been reported in rice (Oryza sativa) and seven species of Apiaceae. FNSI has likely evolved from the duplication of flavanone 3β-hydroxylase (F3H). In this study, we used multiple bioinformatics tools to identify putative FNSI and F3H genes from 42 publicly available genome and transcriptome datasets. Results showed that rice FNSI does not share a common ancestral sequence with other known FNSI genes and that FNSI is absent from species outside of Apiaceae. Positive selection site identification analysis revealed that four sites within the FNSI tree branches of Apiaceae evolved under significant positive selection. The putative F3H genes identified in this study provide a valuable resource for further function analysis of flavone synthase.
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Affiliation(s)
- Qi-Zhi Wang
- Department of Horticulture, Huaqiao University, Xiamen 361021, Fujian, China
| | - Stephen R. Downie
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Zhen-Xi Chen
- Department of Horticulture, Huaqiao University, Xiamen 361021, Fujian, China
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107
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Alginate Oligomers and Their Use as Active Pharmaceutical Drugs. SPRINGER SERIES IN BIOMATERIALS SCIENCE AND ENGINEERING 2018. [DOI: 10.1007/978-981-10-6910-9_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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108
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Teng L, Han W, Fan X, Xu D, Zhang X, Dittami SM, Ye N. Evolution and Expansion of the Prokaryote-Like Lipoxygenase Family in the Brown Alga Saccharina japonica. FRONTIERS IN PLANT SCIENCE 2017; 8:2018. [PMID: 29234336 PMCID: PMC5712309 DOI: 10.3389/fpls.2017.02018] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 11/13/2017] [Indexed: 05/07/2023]
Abstract
Lipoxygenase (LOX) plays important roles in fatty acid oxidation and lipid mediator biosynthesis. In this study, we give first insights into brown algal LOX evolution. Whole genome searches revealed four, three, and eleven LOXs in Ectocarpus siliculosus, Cladosiphon okamuranus, and Saccharina japonica, respectively. In phylogenetic analyses, LOXs from brown algae form a robust clade with those from prokaryotes, suggesting an ancestral origin and slow evolution. Brown algal LOXs were divided into two clades, C1 and C2 in a phylogenetic tree. Compared to the two species of Ectocarpales, LOX gene expansion occurred in the kelp S. japonica through tandem duplication and segmental duplication. Selection pressure analysis showed that LOX genes in brown algae have undergone strong purifying selection, while the selective constraint in the C2 clade was more relaxed than that in the C1 clade. Furthermore, within each clade, LOXs of S. japonica evolved under more relaxed selection constraints than E. siliculosus and C. okamuranus. Structural modeling showed that unlike LOXs of plants and animals, which contain a β barrel in the N-terminal part of the protein, LOXs in brown algae fold into a single domain. Analysis of previously published transcriptomic data showed that LOXs in E. siliculosus are responsive to hyposaline, hypersaline, oxidative, and copper stresses. Moreover, clear divergence of expression patterns was observed among different life stages, as well as between duplicate gene pairs. In E. siliculosus, all four LOXs are male-biased in immature gametophytes, and mature gametophytes showed significantly higher LOX mRNA levels than immature gametophytes and sporophytes. In S. japonica, however, our RNA-Seq data showed that most LOXs are highly expressed in sporophytes. Even the most recently duplicated gene pairs showed divergent expression patterns, suggesting that functional divergence has likely occurred since LOX genes duplicated, which potentially contributes to the production of various oxylipins in brown algae.
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Affiliation(s)
- Linhong Teng
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Wentao Han
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xiao Fan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Dong Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xiaowen Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Simon M. Dittami
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Naihao Ye
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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109
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Dittami SM, Corre E. Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast. PeerJ 2017; 5:e4073. [PMID: 29158994 PMCID: PMC5695246 DOI: 10.7717/peerj.4073] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/30/2017] [Indexed: 12/03/2022] Open
Abstract
Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the post-assembly detection of contaminating sequences in the published genome of the kelp Saccharina japonica. Analyses were based on multiple blastn searches with short sequence fragments. They revealed a number of probable bacterial contaminations as well as hybrid scaffolds that contain both bacterial and algal sequences. This or similar types of analysis, in combination with manual curation, may thus constitute a useful complement to standard bioinformatics analyses prior to submission of genomic data to public repositories. Our analysis pipeline is open-source and freely available at http://sdittami.altervista.org/taxoblast and via SourceForge (https://sourceforge.net/projects/taxoblast).
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Affiliation(s)
- Simon M Dittami
- UMR8227-Sorbonne Universités CNRS UPMC, Station Biologique de Roscoff, Roscoff, Brittany, France
| | - Erwan Corre
- FR2424-Sorbonne Universités CNRS UPMC, Station Biologique de Roscoff, Roscoff, Brittany, France
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110
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Pervasive, Genome-Wide Transcription in the Organelle Genomes of Diverse Plastid-Bearing Protists. G3-GENES GENOMES GENETICS 2017; 7:3789-3796. [PMID: 28935754 PMCID: PMC5677165 DOI: 10.1534/g3.117.300290] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Organelle genomes are among the most sequenced kinds of chromosome. This is largely because they are small and widely used in molecular studies, but also because next-generation sequencing technologies made sequencing easier, faster, and cheaper. However, studies of organelle RNA have not kept pace with those of DNA, despite huge amounts of freely available eukaryotic RNA-sequencing (RNA-seq) data. Little is known about organelle transcription in nonmodel species, and most of the available eukaryotic RNA-seq data have not been mined for organelle transcripts. Here, we use publicly available RNA-seq experiments to investigate organelle transcription in 30 diverse plastid-bearing protists with varying organelle genomic architectures. Mapping RNA-seq data to organelle genomes revealed pervasive, genome-wide transcription, regardless of the taxonomic grouping, gene organization, or noncoding content. For every species analyzed, transcripts covered ≥85% of the mitochondrial and/or plastid genomes (all of which were ≤105 kb), indicating that most of the organelle DNA—coding and noncoding—is transcriptionally active. These results follow earlier studies of model species showing that organellar transcription is coupled and ubiquitous across the genome, requiring significant downstream processing of polycistronic transcripts. Our findings suggest that noncoding organelle DNA can be transcriptionally active, raising questions about the underlying function of these transcripts and underscoring the utility of publicly available RNA-seq data for recovering complete genome sequences. If pervasive transcription is also found in bigger organelle genomes (>105 kb) and across a broader range of eukaryotes, this could indicate that noncoding organelle RNAs are regulating fundamental processes within eukaryotic cells.
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111
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Deniaud-Bouët E, Hardouin K, Potin P, Kloareg B, Hervé C. A review about brown algal cell walls and fucose-containing sulfated polysaccharides: Cell wall context, biomedical properties and key research challenges. Carbohydr Polym 2017; 175:395-408. [PMID: 28917882 DOI: 10.1016/j.carbpol.2017.07.082] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 07/04/2017] [Accepted: 07/28/2017] [Indexed: 12/12/2022]
Abstract
Studies on brown algal cell walls have entered a new phase with the concomitant discovery of novel polysaccharides present in cell walls and the establishment of a comprehensive generic model for cell wall architecture. Brown algal cell walls are composites of structurally complex polysaccharides. In this review we discuss the most recent progress in the structural composition of brown algal cell walls, emphasizing the significance of extraction and screening techniques, and the biological activities of the corresponding polysaccharides, with a specific focus on the fucose-containing sulfated polysaccharides. They include valuable marine molecules that exert a broad range of pharmacological properties such as antioxidant and anti-inflammatory activities, functions in the regulation of immune responses and of haemostasis, anti-infectious and anticancer actions. We identify the key remaining challenges in this research field.
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Affiliation(s)
- Estelle Deniaud-Bouët
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France.
| | - Kevin Hardouin
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France.
| | - Philippe Potin
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France.
| | - Bernard Kloareg
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France.
| | - Cécile Hervé
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France.
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112
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Raven JA, Giordano M. Acquisition and metabolism of carbon in the Ochrophyta other than diatoms. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160400. [PMID: 28717026 PMCID: PMC5516109 DOI: 10.1098/rstb.2016.0400] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2017] [Indexed: 11/12/2022] Open
Abstract
The acquisition and assimilation of inorganic C have been investigated in several of the 15 clades of the Ochrophyta other than diatoms, with biochemical, physiological and genomic data indicating significant mechanistic variation. Form ID Rubiscos in the Ochrophyta are characterized by a broad range of kinetics values. In spite of relatively high K0.5CO2 and low CO2 : O2 selectivity, diffusive entry of CO2 occurs in the Chrysophyceae and Synurophyceae. Eustigmatophyceae and Phaeophyceae, on the contrary, have CO2 concentrating mechanisms, usually involving the direct or indirect use of [Formula: see text] This variability is possibly due to the ecological contexts of the organism. In brown algae, C fixation generally takes place through a classical C3 metabolism, but there are some hints of the occurrence of C4 metabolism and low amplitude CAM in a few members of the Fucales. Genomic data show the presence of a number of potential C4 and CAM genes in Ochrophyta other than diatoms, but the other core functions of many of these genes give a very limited diagnostic value to their presence and are insufficient to conclude that C4 photosynthesis is present in these algae.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'.
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Affiliation(s)
- John A Raven
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Mario Giordano
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona 60131, Italy
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Trěboň 37901, Czech Republic
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Brodie J, Chan CX, De Clerck O, Cock JM, Coelho SM, Gachon C, Grossman AR, Mock T, Raven JA, Smith AG, Yoon HS, Bhattacharya D. The Algal Revolution. TRENDS IN PLANT SCIENCE 2017; 22:726-738. [PMID: 28610890 DOI: 10.1016/j.tplants.2017.05.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 05/04/2017] [Accepted: 05/16/2017] [Indexed: 05/28/2023]
Abstract
Algae are (mostly) photosynthetic eukaryotes that occupy multiple branches of the tree of life, and are vital for planet function and health. In this review, we highlight a transformative period in studies of the evolution and functioning of this extraordinary group of organisms and their potential for novel applications, wrought by high-throughput 'omic' and reverse genetic methods. We cover the origin and diversification of algal groups, explore advances in understanding the link between phenotype and genotype, consider algal sex determination, and review progress in understanding the roots of algal multicellularity. Experimental evolution studies to determine how algae evolve in changing environments are highlighted, as is their potential as production platforms for compounds of commercial interest, such as biofuel precursors, nutraceuticals, or therapeutics.
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Affiliation(s)
- Juliet Brodie
- Natural History Museum, Department of Life Sciences, London SW7 5BD, UK
| | - Cheong Xin Chan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Olivier De Clerck
- Research Group Phycology, Ghent University, Krijgslaan 281, S8, 9000 Ghent, Belgium
| | - J Mark Cock
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Susana M Coelho
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Claire Gachon
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, PA37 1QA, UK
| | - Arthur R Grossman
- Department of Plant Biology, The Carnegie Institution, Stanford, CA 94305, USA
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - John A Raven
- Permanent address: Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee DD2 5DA, UK; School of Plant Biology, University of Western Australia, Crawley, WA 6009, Australia
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA.
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114
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Basu S, Patil S, Mapleson D, Russo MT, Vitale L, Fevola C, Maumus F, Casotti R, Mock T, Caccamo M, Montresor M, Sanges R, Ferrante MI. Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom. THE NEW PHYTOLOGIST 2017; 215:140-156. [PMID: 28429538 PMCID: PMC5485032 DOI: 10.1111/nph.14557] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 02/25/2017] [Indexed: 05/03/2023]
Abstract
Microalgae play a major role as primary producers in aquatic ecosystems. Cell signalling regulates their interactions with the environment and other organisms, yet this process in phytoplankton is poorly defined. Using the marine planktonic diatom Pseudo-nitzschia multistriata, we investigated the cell response to cues released during sexual reproduction, an event that demands strong regulatory mechanisms and impacts on population dynamics. We sequenced the genome of P. multistriata and performed phylogenomic and transcriptomic analyses, which allowed the definition of gene gains and losses, horizontal gene transfers, conservation and evolutionary rate of sex-related genes. We also identified a small number of conserved noncoding elements. Sexual reproduction impacted on cell cycle progression and induced an asymmetric response of the opposite mating types. G protein-coupled receptors and cyclic guanosine monophosphate (cGMP) are implicated in the response to sexual cues, which overall entails a modulation of cell cycle, meiosis-related and nutrient transporter genes, suggesting a fine control of nutrient uptake even under nutrient-replete conditions. The controllable life cycle and the genome sequence of P. multistriata allow the reconstruction of changes occurring in diatoms in a key phase of their life cycle, providing hints on the evolution and putative function of their genes and empowering studies on sexual reproduction.
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Affiliation(s)
- Swaraj Basu
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | - Shrikant Patil
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | | | - Monia Teresa Russo
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | - Laura Vitale
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | - Cristina Fevola
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | | | - Raffaella Casotti
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | - Thomas Mock
- School of Environmental SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Mario Caccamo
- Earlham InstituteNorwich Research ParkNorwichNR4 7UGUK
| | - Marina Montresor
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | - Remo Sanges
- Biology and Evolution of Marine OrganismsStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
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Lipinska AP, Toda NRT, Heesch S, Peters AF, Cock JM, Coelho SM. Multiple gene movements into and out of haploid sex chromosomes. Genome Biol 2017; 18:104. [PMID: 28595587 PMCID: PMC5463336 DOI: 10.1186/s13059-017-1201-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 03/27/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Long-term evolution of sex chromosomes is a dynamic process shaped by gene gain and gene loss. Sex chromosome gene traffic has been studied in XY and ZW systems but no detailed analyses have been carried out for haploid phase UV sex chromosomes. Here, we explore sex-specific sequences of seven brown algal species to understand the dynamics of the sex-determining region (SDR) gene content across 100 million years of evolution. RESULTS A core set of sex-linked genes is conserved across all the species investigated, but we also identify modifications of both the U and the V SDRs that occurred in a lineage-specific fashion. These modifications involve gene loss, gene gain and relocation of genes from the SDR to autosomes. Evolutionary analyses suggest that the SDR genes are evolving rapidly and that this is due to relaxed purifying selection. Expression analysis indicates that genes that were acquired from the autosomes have been retained in the SDR because they confer a sex-specific role in reproduction. By examining retroposed genes in Saccharina japonica, we demonstrate that UV sex chromosomes have generated a disproportionate number of functional orphan retrogenes compared with autosomes. Movement of genes out of the UV sex chromosome could be a means to compensate for gene loss from the non-recombining region, as has been suggested for Y-derived retrogenes in XY sexual systems. CONCLUSION This study provides the first analysis of gene traffic in a haploid UV system and identifies several features of general relevance to the evolution of sex chromosomes.
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Affiliation(s)
- Agnieszka P Lipinska
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Nicholas R T Toda
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Svenja Heesch
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | | | - J Mark Cock
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Susana M Coelho
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France.
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116
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Teng L, Xu D, Zhang X, Wang B, Ye N. Sequencing of complete mitochondrial genome of brown algal Saccharina sp. ye-C. MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:163-164. [PMID: 33473753 PMCID: PMC7800431 DOI: 10.1080/23802359.2017.1298414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The complete sequence (37,609 bp) of the mitochondrial DNA (mtDNA) of the Saccharina sp. ye-C was determined using Illumina sequencing data. The genome contains 38 protein-coding genes (PCG), 3 ribosomal RNA (rRNA), 25 transfer RNA (tRNA) genes that are typical of Saccharina mtDNA. The phylogenetic analysis based on the mitochondrial genomes of brown algae showed that Saccharina sp. ye-C formed a robust clade with Saccharina coriacea, which strongly supports their close phylogenetic relationship.
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Affiliation(s)
- Linhong Teng
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Dong Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xiaowen Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Benxin Wang
- Shandong Hongye Foods Co., Ltd, Rongcheng, China
| | - Naihao Ye
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, China
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117
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Terauchi M, Yamagishi T, Hanyuda T, Kawai H. Genome-wide computational analysis of the secretome of brown algae (Phaeophyceae). Mar Genomics 2017; 32:49-59. [PMID: 28063828 DOI: 10.1016/j.margen.2016.12.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 12/06/2016] [Accepted: 12/16/2016] [Indexed: 11/25/2022]
Abstract
Brown algae have evolved complex multicellularity in the heterokont lineage. They are phylogenetically distant to land plants, fungi and animals. Especially, the members of Laminariales (so-called kelps) have developed highly differentiated tissues. Extracellular matrix (ECM) plays pivotal roles in a number of essential processes in multicellular organisms, such as cell adhesion, cell and tissue differentiations, cell-to-cell communication, and responses to environmental stimuli. In these processes, a set of extracellular secreted proteins called the secretome operates remodeling of the physicochemical nature of ECM and signal transduction by interacting with cell surface proteins and signaling molecules. Characterization of the secretome is a critical step to clarify the contributions of ECM to the multicellularity of brown algae. However, the identity of the brown algal secretome has been poorly understood. In order to reveal the repertory of the brown algal secretome and its involvement in the evolution of Laminariales, we conducted a genome-wide analysis of the brown algal secretome utilizing the published complete genome data of Ectocarpus siliculosus and Saccharina japonica as well as newly obtained RNA-seq data of seven laminarialean species (Agarum clathratum, Alaria crassifolia, Aureophycus aleuticus, Costaria costata, Pseudochorda nagaii, Saccharina angustata and Undaria pinnatifida) largely covering the laminarialean families. We established the in silico pipeline to systematically and accurately detect the secretome by combining multiple prediction algorithms for the N-terminal signal peptide and transmembrane domain within the protein sequence. From 16,189 proteins of E. siliculosus and 18,733 proteins of S. japonica, 552 and 964 proteins respectively were predicted to be classified as the secretome. Conserved domain analysis showed that the domain repertory were very similar to each other, and that of the brown algal secretome was partially common with that of the secretome of other multicellular organisms (land plants, fungi and animals). In the laminarialean species, it was estimated that the gene abundance and the domain architecture of putative ECM remodeling-related proteins were altered compared with those of E. siliculosus, and that the alteration started from the basal group of Laminariales. These results suggested that brown algae have developed their own secretome, and its functions became more elaborated in the more derived members in Laminariales.
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Affiliation(s)
- Makoto Terauchi
- Organization for Advanced and Integrated Research, Kobe University, Kobe 657-8501, Japan.
| | | | - Takeaki Hanyuda
- Research Center for Inland Seas, Kobe University, Kobe 657-8501, Japan
| | - Hiroshi Kawai
- Research Center for Inland Seas, Kobe University, Kobe 657-8501, Japan
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Cormier A, Avia K, Sterck L, Derrien T, Wucher V, Andres G, Monsoor M, Godfroy O, Lipinska A, Perrineau MM, Van De Peer Y, Hitte C, Corre E, Coelho SM, Cock JM. Re-annotation, improved large-scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus. THE NEW PHYTOLOGIST 2017; 214:219-232. [PMID: 27870061 DOI: 10.1111/nph.14321] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 10/08/2016] [Indexed: 05/28/2023]
Abstract
The genome of the filamentous brown alga Ectocarpus was the first to be completely sequenced from within the brown algal group and has served as a key reference genome both for this lineage and for the stramenopiles. We present a complete structural and functional reannotation of the Ectocarpus genome. The large-scale assembly of the Ectocarpus genome was significantly improved and genome-wide gene re-annotation using extensive RNA-seq data improved the structure of 11 108 existing protein-coding genes and added 2030 new loci. A genome-wide analysis of splicing isoforms identified an average of 1.6 transcripts per locus. A large number of previously undescribed noncoding genes were identified and annotated, including 717 loci that produce long noncoding RNAs. Conservation of lncRNAs between Ectocarpus and another brown alga, the kelp Saccharina japonica, suggests that at least a proportion of these loci serve a function. Finally, a large collection of single nucleotide polymorphism-based markers was developed for genetic analyses. These resources are available through an updated and improved genome database. This study significantly improves the utility of the Ectocarpus genome as a high-quality reference for the study of many important aspects of brown algal biology and as a reference for genomic analyses across the stramenopiles.
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Affiliation(s)
- Alexandre Cormier
- Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Komlan Avia
- Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Lieven Sterck
- Department of Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9000, Ghent, Belgium
- Bioinformatics Institute Ghent, Technologiepark 927, 9052, Ghent, Belgium
| | | | | | - Gwendoline Andres
- Abims Platform, CNRS-UPMC, FR2424, Station Biologique de Roscoff, CS 90074, 29688, Roscoff, France
| | - Misharl Monsoor
- Abims Platform, CNRS-UPMC, FR2424, Station Biologique de Roscoff, CS 90074, 29688, Roscoff, France
| | - Olivier Godfroy
- Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Agnieszka Lipinska
- Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Marie-Mathilde Perrineau
- Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Yves Van De Peer
- Department of Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9000, Ghent, Belgium
- Bioinformatics Institute Ghent, Technologiepark 927, 9052, Ghent, Belgium
- Department of Genetics, Genomics Research Institute, University of Pretoria, 0028, Pretoria, South Africa
| | | | - Erwan Corre
- Abims Platform, CNRS-UPMC, FR2424, Station Biologique de Roscoff, CS 90074, 29688, Roscoff, France
| | - Susana M Coelho
- Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - J Mark Cock
- Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
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Avia K, Coelho SM, Montecinos GJ, Cormier A, Lerck F, Mauger S, Faugeron S, Valero M, Cock JM, Boudry P. High-density genetic map and identification of QTLs for responses to temperature and salinity stresses in the model brown alga Ectocarpus. Sci Rep 2017; 7:43241. [PMID: 28256542 PMCID: PMC5335252 DOI: 10.1038/srep43241] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 01/20/2017] [Indexed: 02/06/2023] Open
Abstract
Deciphering the genetic architecture of adaptation of brown algae to environmental stresses such as temperature and salinity is of evolutionary as well as of practical interest. The filamentous brown alga Ectocarpus sp. is a model for the brown algae and its genome has been sequenced. As sessile organisms, brown algae need to be capable of resisting the various abiotic stressors that act in the intertidal zone (e.g. osmotic pressure, temperature, salinity, UV radiation) and previous studies have shown that an important proportion of the expressed genes is regulated in response to hyposaline, hypersaline or oxidative stress conditions. Using the double digest RAD sequencing method, we constructed a dense genetic map with 3,588 SNP markers and identified 39 QTLs for growth-related traits and their plasticity under different temperature and salinity conditions (tolerance to high temperature and low salinity). GO enrichment tests within QTL intervals highlighted membrane transport processes such as ion transporters. Our study represents a significant step towards deciphering the genetic basis of adaptation of Ectocarpus sp. to stress conditions and provides a substantial resource to the increasing list of tools generated for the species.
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Affiliation(s)
- Komlan Avia
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Universités, UPMC, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
- UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
| | - Susana M. Coelho
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Universités, UPMC, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
| | - Gabriel J. Montecinos
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Universités, UPMC, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
- UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
- Centro de Conservación Marina and CeBiB, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
| | - Alexandre Cormier
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Universités, UPMC, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
| | - Fiona Lerck
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Universités, UPMC, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
| | - Stéphane Mauger
- UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
| | - Sylvain Faugeron
- UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
- Centro de Conservación Marina and CeBiB, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
| | - Myriam Valero
- UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
| | - J. Mark Cock
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Universités, UPMC, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
| | - Pierre Boudry
- Ifremer, Laboratoire des Sciences de l’Environnement Marin (UMR 6539 LEMAR, UBO, CNRS, IRD, Ifremer), Centre Bretagne – ZI de la Pointe du Diable, CS 10070, 29280 Plouzané, France
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Cock JM, Liu F, Duan D, Bourdareau S, Lipinska AP, Coelho SM, Tarver JE. Rapid Evolution of microRNA Loci in the Brown Algae. Genome Biol Evol 2017; 9:740-749. [PMID: 28338896 PMCID: PMC5381526 DOI: 10.1093/gbe/evx038] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2017] [Indexed: 02/06/2023] Open
Abstract
Stringent searches for microRNAs (miRNAs) have so far only identified these molecules in animals, land plants, chlorophyte green algae, slime molds and brown algae. The identification of miRNAs in brown algae was based on the analysis of a single species, the filamentous brown alga Ectocarpus sp. Here, we have used deep sequencing of small RNAs and a recently published genome sequence to identify miRNAs in a second brown alga, the kelp Saccharina japonica. S. japonica possesses a large number of miRNAs (117) and these miRNAs are highly diverse, falling into 98 different families. Surprisingly, none of the S. japonica miRNAs share significant sequence similarity with the Ectocarpus sp. miRNAs. However, the miRNA repertoires of the two species share a number of structural and genomic features indicating that they were generated by similar evolutionary processes and therefore probably evolved within the context of a common, ancestral miRNA system. This lack of sequence similarity suggests that miRNAs evolve rapidly in the brown algae (the two species are separated by ∼95 Myr of evolution). The sets of predicted targets of miRNAs in the two species were also very different suggesting that the divergence of the miRNAs may have had significant consequences for miRNA function.
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Affiliation(s)
- J. Mark Cock
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Fuli Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Delin Duan
- Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Qingdao National Laboratory for Marine Science and Technology, Lab for Marine Biology and Biotechnology, Qingdao, China
| | - Simon Bourdareau
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Agnieszka P. Lipinska
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Susana M. Coelho
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - James E. Tarver
- School of Earth Sciences, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
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Zhang J, Wang X, Yao J, Li Q, Liu F, Yotsukura N, Krupnova TN, Duan D. Effect of domestication on the genetic diversity and structure of Saccharina japonica populations in China. Sci Rep 2017; 7:42158. [PMID: 28176848 PMCID: PMC5296902 DOI: 10.1038/srep42158] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 01/09/2017] [Indexed: 11/08/2022] Open
Abstract
Saccharina japonica is a commercially and ecologically important seaweed and is an excellent system for understanding the effects of domestication on marine crops. In this study, we used 19 selected simple sequence repeat (SSR) markers to investigate the influence of domestication on the genetic diversity and structure of S. japonica populations. Wild kelp populations exhibited higher genetic diversity than cultivated populations based on total NA, HE, HO, NP and AR. Discriminant analysis of principal components (DAPC), a neighbour-joining (NJ) tree and STRUCTURE analyses indicated that S. japonica populations could be divided into two groups (a cultivated/introduced group and a wild indigenous group) with significant genetic differentiation (P < 0.0001). Divergent selection, continuous inbreeding and inter-specific hybridization have caused the divergence of these two genetically separate gene pools. The significant genetic differentiation between northern and southern cultivated populations appears to be due to inter-specific hybridization and wild germplasm introduction during the domestication process. In addition, the cultivation of S. japonica has not resulted in any serious genetic disturbance of wild introduced S. japonica populations. An understanding of the genetic diversity and genetic structure of domesticated S. japonica will be necessary for further genetic improvement and effective use of germplasm.
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Affiliation(s)
- Jie Zhang
- Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiuliang Wang
- Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Jianting Yao
- Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Qiuying Li
- Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fuli Liu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Norishige Yotsukura
- Field Science Centre for Northern Biosphere, Hokkaido University, Sapporo, 060-0809, Japan
| | - Tatiana N. Krupnova
- Pacific Research Fisheries Centre (TINRO-Centre), Vladivostok, 690600, Russia
| | - Delin Duan
- Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
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122
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Macaisne N, Liu F, Scornet D, Peters AF, Lipinska A, Perrineau MM, Henry A, Strittmatter M, Coelho SM, Cock JM. The Ectocarpus IMMEDIATE UPRIGHT gene encodes a member of a novel family of cysteine-rich proteins with an unusual distribution across the eukaryotes. Development 2017; 144:409-418. [PMID: 28049657 DOI: 10.1242/dev.141523] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 12/12/2016] [Indexed: 01/09/2023]
Abstract
The sporophyte generation of the brown alga Ectocarpus sp. exhibits an unusual pattern of development compared with the majority of brown algae. The first cell division is symmetrical and the apical-basal axis is established late in development. In the immediate upright (imm) mutant, the initial cell undergoes an asymmetric division to immediately establish the apical-basal axis. We provide evidence which suggests that this phenotype corresponds to the ancestral state of the sporophyte. The IMM gene encodes a protein of unknown function that contains a repeated motif also found in the EsV-1-7 gene of the Ectocarpus virus EsV-1. Brown algae possess large families of EsV-1-7 domain genes but these genes are rare in other stramenopiles, suggesting that the expansion of this family might have been linked with the emergence of multicellular complexity. EsV-1-7 domain genes have a patchy distribution across eukaryotic supergroups and occur in several viral genomes, suggesting possible horizontal transfer during eukaryote evolution.
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Affiliation(s)
- Nicolas Macaisne
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Fuli Liu
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Delphine Scornet
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | | | - Agnieszka Lipinska
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Marie-Mathilde Perrineau
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Antoine Henry
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Martina Strittmatter
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Susana M Coelho
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - J Mark Cock
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
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123
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Prigent S, Frioux C, Dittami SM, Thiele S, Larhlimi A, Collet G, Gutknecht F, Got J, Eveillard D, Bourdon J, Plewniak F, Tonon T, Siegel A. Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks. PLoS Comput Biol 2017; 13:e1005276. [PMID: 28129330 PMCID: PMC5302834 DOI: 10.1371/journal.pcbi.1005276] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 02/10/2017] [Accepted: 11/30/2016] [Indexed: 11/18/2022] Open
Abstract
Increasing amounts of sequence data are becoming available for a wide range of non-model organisms. Investigating and modelling the metabolic behaviour of those organisms is highly relevant to understand their biology and ecology. As sequences are often incomplete and poorly annotated, draft networks of their metabolism largely suffer from incompleteness. Appropriate gap-filling methods to identify and add missing reactions are therefore required to address this issue. However, current tools rely on phenotypic or taxonomic information, or are very sensitive to the stoichiometric balance of metabolic reactions, especially concerning the co-factors. This type of information is often not available or at least prone to errors for newly-explored organisms. Here we introduce Meneco, a tool dedicated to the topological gap-filling of genome-scale draft metabolic networks. Meneco reformulates gap-filling as a qualitative combinatorial optimization problem, omitting constraints raised by the stoichiometry of a metabolic network considered in other methods, and solves this problem using Answer Set Programming. Run on several artificial test sets gathering 10,800 degraded Escherichia coli networks Meneco was able to efficiently identify essential reactions missing in networks at high degradation rates, outperforming the stoichiometry-based tools in scalability. To demonstrate the utility of Meneco we applied it to two case studies. Its application to recent metabolic networks reconstructed for the brown algal model Ectocarpus siliculosus and an associated bacterium Candidatus Phaeomarinobacter ectocarpi revealed several candidate metabolic pathways for algal-bacterial interactions. Then Meneco was used to reconstruct, from transcriptomic and metabolomic data, the first metabolic network for the microalga Euglena mutabilis. These two case studies show that Meneco is a versatile tool to complete draft genome-scale metabolic networks produced from heterogeneous data, and to suggest relevant reactions that explain the metabolic capacity of a biological system.
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Affiliation(s)
- Sylvain Prigent
- Institute for Research in IT and Random Systems - IRISA, Université de Rennes 1, Rennes, France
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
- Irisa, CNRS, Rennes, France
- Dyliss, Inria, Rennes, France
- * E-mail: (AS); (SP)
| | - Clémence Frioux
- Institute for Research in IT and Random Systems - IRISA, Université de Rennes 1, Rennes, France
- Irisa, CNRS, Rennes, France
- Dyliss, Inria, Rennes, France
| | - Simon M. Dittami
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | | | - Abdelhalim Larhlimi
- Computer Science Laboratory of Nantes Atlantique - LINA UMR6241, Université de Nantes, Nantes, France
| | - Guillaume Collet
- Institute for Research in IT and Random Systems - IRISA, Université de Rennes 1, Rennes, France
- Irisa, CNRS, Rennes, France
- Dyliss, Inria, Rennes, France
| | - Fabien Gutknecht
- Molecular Genetics, Genomics and Microbiology - GMGM, Université de Strasbourg, Strasbourg, France
| | - Jeanne Got
- Institute for Research in IT and Random Systems - IRISA, Université de Rennes 1, Rennes, France
- Irisa, CNRS, Rennes, France
- Dyliss, Inria, Rennes, France
| | - Damien Eveillard
- Computer Science Laboratory of Nantes Atlantique - LINA UMR6241, Université de Nantes, Nantes, France
| | - Jérémie Bourdon
- Computer Science Laboratory of Nantes Atlantique - LINA UMR6241, Université de Nantes, Nantes, France
| | - Frédéric Plewniak
- Molecular Genetics, Genomics and Microbiology - GMGM, Université de Strasbourg, Strasbourg, France
- GMGM, CNRS, Strasbourg, France
| | - Thierry Tonon
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Anne Siegel
- Institute for Research in IT and Random Systems - IRISA, Université de Rennes 1, Rennes, France
- Irisa, CNRS, Rennes, France
- Dyliss, Inria, Rennes, France
- * E-mail: (AS); (SP)
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124
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Ji P, Zhang Y, Wang J, Zhao F. MetaSort untangles metagenome assembly by reducing microbial community complexity. Nat Commun 2017; 8:14306. [PMID: 28112173 PMCID: PMC5264255 DOI: 10.1038/ncomms14306] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 12/14/2016] [Indexed: 12/31/2022] Open
Abstract
Most current approaches to analyse metagenomic data rely on reference genomes. Novel microbial communities extend far beyond the coverage of reference databases and de novo metagenome assembly from complex microbial communities remains a great challenge. Here we present a novel experimental and bioinformatic framework, metaSort, for effective construction of bacterial genomes from metagenomic samples. MetaSort provides a sorted mini-metagenome approach based on flow cytometry and single-cell sequencing methodologies, and employs new computational algorithms to efficiently recover high-quality genomes from the sorted mini-metagenome by the complementary of the original metagenome. Through extensive evaluations, we demonstrated that metaSort has an excellent and unbiased performance on genome recovery and assembly. Furthermore, we applied metaSort to an unexplored microflora colonized on the surface of marine kelp and successfully recovered 75 high-quality genomes at one time. This approach will greatly improve access to microbial genomes from complex or novel communities.
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Affiliation(s)
- Peifeng Ji
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanming Zhang
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinfeng Wang
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Fangqing Zhao
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
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125
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A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity through the Eukaryotic Genomics Window. Viruses 2017; 9:v9010017. [PMID: 28117696 PMCID: PMC5294986 DOI: 10.3390/v9010017] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/13/2017] [Accepted: 01/13/2017] [Indexed: 12/16/2022] Open
Abstract
The nucleocytoplasmic large DNA viruses (NCLDV) are a group of extremely complex double-stranded DNA viruses, which are major parasites of a variety of eukaryotes. Recent studies showed that certain eukaryotes contain fragments of NCLDV DNA integrated in their genome, when surprisingly many of these organisms were not previously shown to be infected by NCLDVs. We performed an update survey of NCLDV genes hidden in eukaryotic sequences to measure the incidence of this phenomenon in common public sequence databases. A total of 66 eukaryotic genomic or transcriptomic datasets-many of which are from algae and aquatic protists-contained at least one of the five most consistently conserved NCLDV core genes. Phylogenetic study of the eukaryotic NCLDV-like sequences identified putative new members of already recognized viral families, as well as members of as yet unknown viral clades. Genomic evidence suggested that most of these sequences resulted from viral DNA integrations rather than contaminating viruses. Furthermore, the nature of the inserted viral genes helped predicting original functional capacities of the donor viruses. These insights confirm that genomic insertions of NCLDV DNA are common in eukaryotes and can be exploited to delineate the contours of NCLDV biodiversity.
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126
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Teng L, Fan X, Xu D, Zhang X, Mock T, Ye N. Identification of Genes under Positive Selection Reveals Differences in Evolutionary Adaptation between Brown-Algal Species. FRONTIERS IN PLANT SCIENCE 2017; 8:1429. [PMID: 28861104 PMCID: PMC5559719 DOI: 10.3389/fpls.2017.01429] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/03/2017] [Indexed: 05/07/2023]
Abstract
Brown algae are an important taxonomic group in coastal ecosystems. The model brown algal species Ectocarpus siliculosus and Saccharina japonica are closely related lineages. Despite their close phylogenetic relationship, they vary greatly in morphology and physiology. To obtain further insights into the evolutionary forces driving divergence in brown algae, we analyzed 3,909 orthologs from both species to identify Genes Under Positive Selection (GUPS). About 12% of the orthologs in each species were considered to be under positive selection. Many GUPS are involved in membrane transport, regulation of homeostasis, and sexual reproduction in the small sporophyte of E. siliculosus, which is known to have a complex life cycle and to occupy a wide range of habitats. Genes involved in photosynthesis and cell division dominated the group of GUPS in the large kelp of S. japonica, which might explain why this alga has evolved the ability to grow very rapidly and to form some of the largest sporophytes. A significant number of molecular chaperones (e.g., heat-shock proteins) involved in stress responses were identified to be under positive selection in both species, potentially indicating their important roles for macroalgae to cope with the relatively variable environment of coastal ecosystems. Moreover, analysis of previously published microarray data of E. siliculosus showed that many GUPS in E. siliculosus were responsive to stress conditions, such as oxidative and hyposaline stress, whereas our RNA-seq data of S. japonica showed that GUPS in this species were most highly expressed in large sporophytes, which supports the suggestion that selection largely acts on different sets of genes in both marcoalgal species, potentially reflecting their adaptation to different ecological niches.
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Affiliation(s)
- Linhong Teng
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery SciencesQingdao, China
| | - Xiao Fan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery SciencesQingdao, China
| | - Dong Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery SciencesQingdao, China
| | - Xiaowen Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery SciencesQingdao, China
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research ParkNorwich, United Kingdom
| | - Naihao Ye
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery SciencesQingdao, China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China
- *Correspondence: Naihao Ye
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127
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Nishitsuji K, Arimoto A, Iwai K, Sudo Y, Hisata K, Fujie M, Arakaki N, Kushiro T, Konishi T, Shinzato C, Satoh N, Shoguchi E. A draft genome of the brown alga, Cladosiphon okamuranus, S-strain: a platform for future studies of 'mozuku' biology. DNA Res 2016; 23:561-570. [PMID: 27501718 PMCID: PMC5144679 DOI: 10.1093/dnares/dsw039] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 06/29/2016] [Indexed: 11/15/2022] Open
Abstract
The brown alga, Cladosiphon okamuranus (Okinawa mozuku), is economically one of the most important edible seaweeds, and is cultivated for market primarily in Okinawa, Japan. C. okamuranus constitutes a significant source of fucoidan, which has various physiological and biological activities. To facilitate studies of seaweed biology, we decoded the draft genome of C. okamuranus S-strain. The genome size of C. okamuranus was estimated as ∼140 Mbp, smaller than genomes of two other brown algae, Ectocarpus siliculosus and Saccharina japonica Sequencing with ∼100× coverage yielded an assembly of 541 scaffolds with N50 = 416 kbp. Together with transcriptomic data, we estimated that the C. okamuranus genome contains 13,640 protein-coding genes, approximately 94% of which have been confirmed with corresponding mRNAs. Comparisons with the E. siliculosus genome identified a set of C. okamuranus genes that encode enzymes involved in biosynthetic pathways for sulfated fucans and alginate biosynthesis. In addition, we identified C. okamuranus genes for enzymes involved in phlorotannin biosynthesis. The present decoding of the Cladosiphon okamuranus genome provides a platform for future studies of mozuku biology.
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Affiliation(s)
- Koki Nishitsuji
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Asuka Arimoto
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Kenji Iwai
- Okinawa Prefectural Fisheries Research and Extension Center, Itoman, Okinawa 901-0354, Japan
| | - Yusuke Sudo
- Okinawa Prefectural Fisheries Research and Extension Center, Itoman, Okinawa 901-0354, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Manabu Fujie
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Nana Arakaki
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Tetsuo Kushiro
- School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Teruko Konishi
- Department of Bioscience and Biotechnology, Faculty of Agriculture, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
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128
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Peng G, Ji P, Zhao F. A novel codon-based de Bruijn graph algorithm for gene construction from unassembled transcriptomes. Genome Biol 2016; 17:232. [PMID: 27855707 PMCID: PMC5114782 DOI: 10.1186/s13059-016-1094-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 10/31/2016] [Indexed: 11/10/2022] Open
Abstract
Most gene prediction methods detect coding sequences from transcriptome assemblies in the absence of closely related reference genomes. Such methods are of limited application due to high transcript fragmentation and extensive assembly errors, which may lead to redundant or false coding sequence predictions. We present inGAP-CDG, which can construct full-length and non-redundant coding sequences from unassembled transcriptomes by using a codon-based de Bruijn graph to simplify the assembly process and a machine learning-based approach to filter false positives. Compared with other methods, inGAP-CDG exhibits a significant increase in predicted coding sequence length and robustness to sequencing errors and varied read length.
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Affiliation(s)
- Gongxin Peng
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Peifeng Ji
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Fangqing Zhao
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
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129
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Torode TA, Siméon A, Marcus SE, Jam M, Le Moigne MA, Duffieux D, Knox JP, Hervé C. Dynamics of cell wall assembly during early embryogenesis in the brown alga Fucus. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:6089-6100. [PMID: 27811078 PMCID: PMC5100021 DOI: 10.1093/jxb/erw369] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Zygotes from Fucus species have been used extensively to study cell polarization and rhizoid outgrowth, and in this model system cell wall deposition aligns with the establishment of polarity. Monoclonal antibodies are essential tools for the in situ analysis of cell wall glycans, and here we report the characteristics of six monoclonal antibodies to alginates (BAM6-BAM11). The use of these, in conjunction with monoclonal antibodies to brown algal sulfated fucans, has enabled the study of the developmental dynamics of the Fucus zygote cell walls. Young zygotes are spherical and all alginate epitopes are deposited uniformly following cellulose deposition. At germination, sulfated fucans are secreted in the growing rhizoid wall. The redistribution of cell wall epitopes was investigated during treatments that cause reorientation of the growth axis (change in light direction) or disrupt rhizoid development (arabinogalactan-protein-reactive Yariv reagent). Alginate modeling was drastically impaired in the latter, and both treatments cause a redistribution of highly sulfated fucan epitopes. The dynamics of cell wall glycans in this system have been visualized in situ for the first time, leading to an enhanced understanding of the early developmental mechanisms of Fucus species. These sets of monoclonal antibodies significantly extend the available molecular tools for brown algal cell wall studies.
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Affiliation(s)
- Thomas A Torode
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Amandine Siméon
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France
| | - Susan E Marcus
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Murielle Jam
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France
| | - Marie-Anne Le Moigne
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France
| | - Delphine Duffieux
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France
| | - J Paul Knox
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Cécile Hervé
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France
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Xu L, Wang S, Fan X, Xu D, Zhang X, Miao Y, Ye N. Sequencing of complete mitochondrial genome of brown algal Saccharina sp. ye-C6. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 27:3733-4. [PMID: 26403617 DOI: 10.3109/19401736.2015.1079880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 08/02/2015] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial sequence (37 657 bp) of the Saccharina sp. ye-C6 was obtained from the assembled and annotated genome data sequenced by Illumina sequencing technology (KT271760). The circular genome contains 38 protein-coding genes (PCG), three ribosomal RNA (rRNA), and 25 transfer RNA (tRNA) genes. Base composition of genome is A (28.41%), T (36.29%), C (14.72%), and G (20.58%). Through a phylogenetic analysis based on the mitochondrial genomes of brown algae, we found that Saccharina sp. ye-C6 and Saccharina japonica are the most closely related species and strongly supports their close phylogenetic affinity.
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Affiliation(s)
- Le Xu
- a College of Fisheries and Life Science, Shanghai Ocean University , Shanghai , China and
- b Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao , China
| | - Shuai Wang
- a College of Fisheries and Life Science, Shanghai Ocean University , Shanghai , China and
- b Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao , China
| | - Xiao Fan
- b Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao , China
| | - Dong Xu
- b Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao , China
| | - Xiaowen Zhang
- b Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao , China
| | - Yu Miao
- b Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao , China
| | - Naihao Ye
- b Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao , China
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Fan X, Wang S, Xu D, Zhang X, Xu L, Miao Y, Ye N. Sequencing of complete mitochondrial genome of brown algal Saccharina sp. ye-F. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 27:3693-4. [PMID: 26358639 DOI: 10.3109/19401736.2015.1079859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 07/18/2015] [Indexed: 11/13/2022]
Abstract
The complete sequence (37 657 bp) of the mitochondrial DNA (mtDNA) of the Saccharina sp. ye-F was determined using Illumina sequencing data (Illumina Inc., San Diego, CA). The genome contains 38 protein-coding genes (PCG), three ribosomal RNA (rRNA), and 25 transfer RNA (tRNA) genes that are typical of Saccharina mtDNA. A phylogenetic analysis based on the mitochondrial genomes of brown algae indicated that Saccharina sp. ye-F and Saccharina longissima, Saccharina japonica are the most closely related species, which strongly supports their close phylogenetic affinity.
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Affiliation(s)
- Xiao Fan
- a Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao , China and
| | - Shuai Wang
- a Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao , China and
- b College of Fisheries and Life Science, Shanghai Ocean University , Shanghai , China
| | - Dong Xu
- a Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao , China and
| | - Xiaowen Zhang
- a Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao , China and
| | - Le Xu
- a Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao , China and
- b College of Fisheries and Life Science, Shanghai Ocean University , Shanghai , China
| | - Yu Miao
- a Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao , China and
| | - Naihao Ye
- a Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao , China and
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132
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Wang S, Fan X, Xu D, Zhang X, Miao Y, Xu L, Ye N. Sequencing of complete mitochondrial genome of brown algal Saccharina sp. ye-W. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 27:3026-7. [PMID: 26153752 DOI: 10.3109/19401736.2015.1063051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 06/14/2015] [Indexed: 11/13/2022]
Abstract
The complete sequence (37 657 bp) of the mitochondrial DNA (mtDNA) of the Saccharina sp. ye-W was determined using Illumina sequencing data. The genome contains 38 protein-coding genes (PCG), three ribosomal RNA (rRNA), 25 transfer RNA (tRNA) genes that are typical of Saccharina mtDNA. Phylogenetic analysis based on the mitochondrial genomes of brown algae indicated that Saccharina sp. ye-W and Saccharina longissima, Saccharina japonica are the most closely related species, which strongly supports their close phylogenetic affinity.
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Affiliation(s)
- Shuai Wang
- a Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao , China and
- b College of Fisheries and Life Science, Shanghai Ocean University , Shanghai , China
| | - Xiao Fan
- a Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao , China and
| | - Dong Xu
- a Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao , China and
| | - Xiaowen Zhang
- a Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao , China and
| | - Yu Miao
- a Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao , China and
| | - Le Xu
- b College of Fisheries and Life Science, Shanghai Ocean University , Shanghai , China
| | - Naihao Ye
- a Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao , China and
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Inoue A, Satoh A, Morishita M, Tokunaga Y, Miyakawa T, Tanokura M, Ojima T. Functional heterologous expression and characterization of mannuronan C5-epimerase from the brown alga Saccharina japonica. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.03.030] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Zhang P, Shao Z, Jin W, Duan D. Comparative characterization of two GDP-mannose dehydrogenase genes from Saccharina japonica (Laminariales, Phaeophyceae). BMC PLANT BIOLOGY 2016; 16:62. [PMID: 26956020 PMCID: PMC4782291 DOI: 10.1186/s12870-016-0750-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/27/2016] [Indexed: 05/26/2023]
Abstract
BACKGROUND Saccharina japonica is an important commercial brown seaweed, its main product is alginate, which is used in food, textile and by the cosmetic and pharmaceutical industries. GDP-mannose dehydrogenase (GMD) is the key enzyme involved in the synthesis of alginate. However, little is known about GMD in S. japonica. Here we report comparative biochemical analysis of two GMD genes in S. japonica. RESULTS Two GMD genes from S. japonica (Sjgmd1, Sjgmd2) were cloned. The open reading frame lengths of Sjgmd1, Sjgmd2 are 963 bp and 948 bp, respectively. Alignment analysis showed that the two SjGMD sequences shared 79.38 % identity. Both proteins possess the GGxCLPKDV and GxGxVG sequence motifs characteristic of the short-chain dehydrogenase/reductase superfamily. The optimum temperatures for SjGMDs were 30 °C (SjGMD1) and 20 °C (SjGMD2), and the optimum pH values were 8.0 (SjGMD1) and 8.25 (SjGMD2). Kinetic analysis demonstrated the Km values for the substrate GDP-mannose were 289 μM (SjGMD1) and 177 μM (SjGMD2), and the Km values for the cofactor NAD(+) were 139 μM (SjGMD1) and 195 μM (SjGMD2). The metal iron Zn(2+) is a potent inhibitor of SjGMD1 and SjGMD2. Real-time PCR analysis showed that heat and desiccation treatments resulted in a significant increase in Sjgmd1 and Sjgmd2 transcript abundance, suggesting that the SjGMDs are directly involved in the acclimitisation of S. japonica to abiotic stresses. CONCLUSION Our work identified two novel genes encoding GMD in S. japonica, comparatively characterized their structural characteristics and enzyme kinetics, and revealed the function of GMD in the stress adaptability of S. japonica. The knowledge obtained here enriched our understanding of the alginate synthesis mechanism in S. japonica, and may promote further research on functional differences between GMD genes.
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Affiliation(s)
- Pengyan Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Zhanru Shao
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
| | - Weihua Jin
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
| | - Delin Duan
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
- State Key Laboratory of Seaweed Bioactive Substances, Qingdao, 266400, China.
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Qiao ZY, Lin YX, Lai WJ, Hou CY, Wang Y, Qiao SL, Zhang D, Fang QJ, Wang H. A General Strategy for Facile Synthesis and In Situ Screening of Self-Assembled Polymer-Peptide Nanomaterials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:1859-1867. [PMID: 26698326 DOI: 10.1002/adma.201504564] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 11/18/2015] [Indexed: 06/05/2023]
Abstract
A universal strategy for efficient, mild, and purification-free synthesis and in situ screening of functional polymer-peptide nanomaterials is described. More than 1000 polymer-peptide conjugates (PPCs) with various chemical structures, compositions, and therapeutic efficacy are created. According to this strategy, the structure-function relationship of the PPCs is revealed, and the antitumor efficacies of the top performing PPCs are evaluated in vivo.
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Affiliation(s)
- Zeng-Ying Qiao
- Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Yao-Xin Lin
- Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Wen-Jia Lai
- Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Chun-Yuan Hou
- Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Yi Wang
- Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Sheng-Lin Qiao
- Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Di Zhang
- Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Qiao-Jun Fang
- Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Hao Wang
- Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
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136
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Li X, Zhang Z, Qu S, Liang G, Sun J, Zhao N, Cui C, Cao Z, Li Y, Pan J, Yu S, Wang Q, Li X, Luo S, Song S, Guo L, Yang G. Improving seedless kelp (Saccharina japonica) during its domestication by hybridizing gametophytes and seedling-raising from sporophytes. Sci Rep 2016; 6:21255. [PMID: 26887644 PMCID: PMC4757934 DOI: 10.1038/srep21255] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 01/20/2016] [Indexed: 11/09/2022] Open
Abstract
Dongfang no.7 (Saccharina japonica) was bred and maintained by hybridizing gametophytes, self-crossing the best individuals, selecting the best self-crossing line and seedling-raising from yearly reconstructed sporophytes. It increased the air dry yield by 43.2% in average over 2 widely farmed controls. Dongfang no.7 was seedling-raised from bulked sporophytes reconstructed from its representative gametophyte clones. Such strategy ensured it against variety contamination due to possible cross fertilization and occasional mixing and inbred depletion due to self-crossing number-limited sporophytes year after year. It derived from an intraspecific hybrid through 4 rounds of self-crossing and selection and retained a certain degree of genetic heterozygosity, thus being immune to inbred depletion due to purification of unknown detrimental alleles. Most importantly, it can be farmed in currently available system as the seedlings for large scale culture can be raised from reconstructed Dongfang no.7 sporophytes. Breeding and maintaining Dongfang no.7 provided a model that other varieties of kelp (S. japonica) and brown algae may follow during their domestication.
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Affiliation(s)
- Xiaojie Li
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Yantai, Shandong 264003, PR China
- Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Yantai, Shandong 264003, PR China
- Shandong Oriental Ocean Sci-tech Co., Ltd., Yantai, Shandong 264003, PR China
| | - Zhuangzhi Zhang
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Yantai, Shandong 264003, PR China
- Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Yantai, Shandong 264003, PR China
- Shandong Oriental Ocean Sci-tech Co., Ltd., Yantai, Shandong 264003, PR China
| | - Shancun Qu
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Yantai, Shandong 264003, PR China
- Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Yantai, Shandong 264003, PR China
- Shandong Oriental Ocean Sci-tech Co., Ltd., Yantai, Shandong 264003, PR China
| | - Guangjin Liang
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Yantai, Shandong 264003, PR China
- Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Yantai, Shandong 264003, PR China
- Shandong Oriental Ocean Sci-tech Co., Ltd., Yantai, Shandong 264003, PR China
| | - Juan Sun
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Yantai, Shandong 264003, PR China
- Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Yantai, Shandong 264003, PR China
- Shandong Oriental Ocean Sci-tech Co., Ltd., Yantai, Shandong 264003, PR China
| | - Nan Zhao
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Yantai, Shandong 264003, PR China
- Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Yantai, Shandong 264003, PR China
- Shandong Oriental Ocean Sci-tech Co., Ltd., Yantai, Shandong 264003, PR China
| | - Cuiju Cui
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Yantai, Shandong 264003, PR China
- Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Yantai, Shandong 264003, PR China
- Shandong Oriental Ocean Sci-tech Co., Ltd., Yantai, Shandong 264003, PR China
| | - Zengmei Cao
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Yantai, Shandong 264003, PR China
- Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Yantai, Shandong 264003, PR China
- Shandong Oriental Ocean Sci-tech Co., Ltd., Yantai, Shandong 264003, PR China
| | - Yan Li
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Yantai, Shandong 264003, PR China
- Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Yantai, Shandong 264003, PR China
- Shandong Oriental Ocean Sci-tech Co., Ltd., Yantai, Shandong 264003, PR China
| | - Jinhua Pan
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Yantai, Shandong 264003, PR China
- Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Yantai, Shandong 264003, PR China
- Shandong Oriental Ocean Sci-tech Co., Ltd., Yantai, Shandong 264003, PR China
| | - Shenhui Yu
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Yantai, Shandong 264003, PR China
- Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Yantai, Shandong 264003, PR China
- Shandong Oriental Ocean Sci-tech Co., Ltd., Yantai, Shandong 264003, PR China
| | - Qingyan Wang
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Yantai, Shandong 264003, PR China
- Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Yantai, Shandong 264003, PR China
- Shandong Oriental Ocean Sci-tech Co., Ltd., Yantai, Shandong 264003, PR China
| | - Xia Li
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Yantai, Shandong 264003, PR China
- Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Yantai, Shandong 264003, PR China
- Shandong Oriental Ocean Sci-tech Co., Ltd., Yantai, Shandong 264003, PR China
| | - Shiju Luo
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Yantai, Shandong 264003, PR China
- Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Yantai, Shandong 264003, PR China
- Shandong Oriental Ocean Sci-tech Co., Ltd., Yantai, Shandong 264003, PR China
| | - Shaofeng Song
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Yantai, Shandong 264003, PR China
- Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Yantai, Shandong 264003, PR China
- Shandong Oriental Ocean Sci-tech Co., Ltd., Yantai, Shandong 264003, PR China
| | - Li Guo
- Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266003, PR China
- Institutes of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Guanpin Yang
- Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266003, PR China
- Institutes of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
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137
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Fan X, Wang S, Xu L, Xu D, Zhang X, Ye N. Sequencing of complete mitochondrial genome of brown algal Saccharina sp. ye-C5. Mitochondrial DNA B Resour 2016; 1:14-15. [PMID: 33473390 PMCID: PMC7800857 DOI: 10.1080/23802359.2015.1137799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 12/22/2015] [Accepted: 12/30/2015] [Indexed: 11/26/2022] Open
Abstract
The complete genome (37 635 bp) mitochondrial DNA (mtDNA) of the Saccharina sp. ye-C5 was determined, which contains 38 protein-coding genes (PCG), three ribosomal RNA (rRNA) and 25 transfer RNA (tRNA) genes that are consistent in Saccharina genus. The phylogenetic tree that was established based on the mitochondrial genomes of brown algae, which indicated that Saccharina sp. ye-C5 and Saccharina longissima are the most closely related species.
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Affiliation(s)
- Xiao Fan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Shuai Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Le Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Dong Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xiaowen Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Naihao Ye
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for for Marine Science and Technology, China
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138
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Fan X, Xu L, Wang S, Xu D, Zhang X, Ye N. Sequencing of complete mitochondrial genome of brown algal Saccharina sp. ye-C2. MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:16-17. [PMID: 33473391 PMCID: PMC7800502 DOI: 10.1080/23802359.2015.1137800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The complete sequence (37 657 bp) of the mitochondrial DNA (mtDNA) of the Saccharina sp. ye-C2 was determined. About 38 protein-coding genes (PCG), 3 ribosomal RNAs (rRNA) and 25 transfer RNA (tRNA) genes were annotated in the genome. The phylogenetic analysis strongly supports the close phylogenetic affinity of Saccharina sp. ye-C2 and Saccharina japonica based on the mitochondrial genomes of other brown algae.
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Affiliation(s)
- Xiao Fan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Le Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Shuai Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Dong Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xiaowen Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Naihao Ye
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for for Marine Science and Technology, China
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139
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Xu D, Fan X, Wang S, Xu L, Zhang X, Ye N, Zhuang Z. Sequencing of complete mitochondrial genome of brown algal Saccharina sp. ye- C12. MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:62-63. [PMID: 33473408 PMCID: PMC7800219 DOI: 10.1080/23802359.2015.1137824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The complete sequence (37 654 bp) of the mitochondrial DNA (mtDNA) of the Saccharina sp. ye-C12 was determined using Illumina sequencing data. The genome contains 38 protein-coding genes (PCG), three ribosomal RNA (rRNA), 25 transfer RNA (tRNA) genes and the phylogenetic analysis based on the mitochondrial genomes of brown algae indicated that Saccharina sp. ye-C12 and Saccharina japonica are the most closely related species, which strongly supports their close phylogenetic affinity.
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Affiliation(s)
- Dong Xu
- Fisheries College, Ocean University of China, Qingdao, China.,Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xiao Fan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Shuai Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Le Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xiaowen Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Naihao Ye
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for for Marine Science and Technology, China
| | - Zhimeng Zhuang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
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141
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Shan T, Pang S, Li J, Li X, Su L. Construction of a high-density genetic map and mapping of a sex-linked locus for the brown alga Undaria pinnatifida (Phaeophyceae) based on large scale marker development by specific length amplified fragment (SLAF) sequencing. BMC Genomics 2015; 16:902. [PMID: 26541547 PMCID: PMC4635539 DOI: 10.1186/s12864-015-2184-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/03/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Undaria pinnatifida is an important economic brown alga in East Asian countries. However, its genetic and genomic information is very scarce, which hinders further research in this species. A high-density genetic map is a basic tool for fundamental and applied research such as discovery of functional genes and mapping of quantitative trait loci (QTL). In this study the recently developed specific length amplified fragment sequencing (SLAF-seq) technology was employed to construct a high-density genetic linkage map and locate a sex determining locus for U. pinnatifida. RESULTS A total of 28.06 Gb data including 140.31 M pair-end reads was obtained. After linkage analysis 4626 SLAF markers were mapped onto the genetic map. After adding the sex linked simple sequence repeat (SSR) marker [GenBank:AY738602.1], the final genetic map was 1816.28 cM long, consisting of 30 linkage groups with an average distance of 0.39 cM between adjacent markers. The length of LGs ranged from 20.12 to 106.95 cM. A major sex associated QTL was mapped to LG22 within a window starting at 29.01 cM and ending at 68.81 cM with a total of 68 SLAF markers. The SSR marker and five SLAF markers (Marker6556, 19020, 43089, 60771 and 26359) were identified as tightly sex-linked markers, as indicated by the absence of recombination between them and the sex phenotype. These markers were located at the position of 59.50 cM, which was supposed to be the sex determining region. CONCLUSIONS A high-density genetic linkage map was constructed using SLAF-seq technique and F1 gametophyte population for the first time in the economically important brown alga U. pinnatifida. For the first time, a major sex associated QTL suggesting a sex determining region was mapped to a single LG. This map will facilitate the further fundamental and applied research such as QTL mapping and map-based gene clone in U. pinnatifida and provide a reference for studies in other kelp species.
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Affiliation(s)
- Tifeng Shan
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, PR China.
| | - Shaojun Pang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, PR China.
| | - Jing Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, PR China.
- Graduate University of Chinese Academy of Science, Beijing, 100049, PR China.
| | - Xia Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, PR China.
- Graduate University of Chinese Academy of Science, Beijing, 100049, PR China.
| | - Li Su
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, PR China.
- Graduate University of Chinese Academy of Science, Beijing, 100049, PR China.
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142
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Luthringer R, Lipinska AP, Roze D, Cormier A, Macaisne N, Peters AF, Cock JM, Coelho SM. The Pseudoautosomal Regions of the U/V Sex Chromosomes of the Brown Alga Ectocarpus Exhibit Unusual Features. Mol Biol Evol 2015; 32:2973-85. [PMID: 26248564 PMCID: PMC4610043 DOI: 10.1093/molbev/msv173] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The recombining regions of sex chromosomes (pseudoautosomal regions, PARs) are predicted to exhibit unusual features due to their being genetically linked to the nonrecombining, sex-determining region. This phenomenon is expected to occur in both diploid (XY, ZW) and haploid (UV) sexual systems, with slightly different consequences for UV sexual systems because of the absence of masking during the haploid phase (when sex is expressed) and because there is no homozygous sex in these systems. Despite a considerable amount of theoretical work on PAR genetics and evolution, these genomic regions have remained poorly characterized empirically. We show here that although the PARs of the U/V sex chromosomes of the brown alga Ectocarpus recombine at a similar rate to autosomal regions of the genome, they exhibit many genomic features typical of nonrecombining regions. The PARs were enriched in clusters of genes that are preferentially, and often exclusively, expressed during the sporophyte generation of the life cycle, and many of these genes appear to have evolved since the Ectocarpales diverged from other brown algal lineages. A modeling-based approach was used to investigate possible evolutionary mechanisms underlying this enrichment in sporophyte-biased genes. Our results are consistent with the evolution of the PAR in haploid systems being influenced by differential selection pressures in males and females acting on alleles that are advantageous during the sporophyte generation of the life cycle.
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Affiliation(s)
- Rémy Luthringer
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Agnieszka P Lipinska
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Denis Roze
- UMI 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, PUCCh, UACH, Station Biologique de Roscoff, Roscoff, France
| | - Alexandre Cormier
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Nicolas Macaisne
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | | | - J Mark Cock
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Susana M Coelho
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
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143
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Xiang J. Recent Major Advances of Biotechnology and Sustainable Aquaculture in China. ACTA ACUST UNITED AC 2015; 4:296-310. [PMID: 28553577 PMCID: PMC5436491 DOI: 10.2174/2211550105666151105190012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 11/05/2015] [Accepted: 11/05/2015] [Indexed: 11/22/2022]
Abstract
Background: Global aquaculture production has increased continuously over the last five decades, and particularly in China. Its aquaculture has become the fastest growing and most efficient agri-sector, with production accounting for more than 70% of the world’s aquaculture output. In the new century, with serious challenges regarding population, resources and the environment, China has been working to develop high-quality, effective, healthy, and sustainable blue agriculture through the application of modern biotechnology. Sound knowledge related to the biology and ecology of aquatic organisms has laid a solid foundation and provided the innovation and technology for rapid development of the aquaculture industry. Marine biotechnology, which is enabling solutions for ocean productivity and sustainability, has been promoted since the last decades of the 20th Century in China. Objective: In this article, priority areas of research, mainly genetic breeding, omics studies, novel production systems, biosecurity, bioprocesses and biorefinery, as well as the major progress of marine biotechnology R&D in China are reviewed. Conclusion: Current innovative achievements in China are not enough and the level and frequency of academic advancements must be improved. International cooperation and assistance remain crucial for the success of marine biotechnology.
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Affiliation(s)
- Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
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