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Chen H, Chu JSC, Chen J, Luo Q, Wang H, Lu R, Zhu Z, Yuan G, Yi X, Mao Y, Lu C, Wang Z, Gu D, Jin Z, Zhang C, Weng Z, Li S, Yan X, Yang R. Insights into the Ancient Adaptation to Intertidal Environments by Red Algae Based on a Genomic and Multiomics Investigation of Neoporphyra haitanensis. Mol Biol Evol 2022; 39:msab315. [PMID: 34730826 PMCID: PMC8752119 DOI: 10.1093/molbev/msab315] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Colonization of land from marine environments was a major transition for biological life on Earth, and intertidal adaptation was a key evolutionary event in the transition from marine- to land-based lifestyles. Multicellular intertidal red algae exhibit the earliest, systematic, and successful adaptation to intertidal environments, with Porphyra sensu lato (Bangiales, Rhodophyta) being a typical example. Here, a chromosome-level 49.67 Mb genome for Neoporphyra haitanensis comprising 9,496 gene loci is described based on metagenome-Hi-C-assisted whole-genome assembly, which allowed the isolation of epiphytic bacterial genome sequences from a seaweed genome for the first time. The compact, function-rich N. haitanensis genome revealed that ancestral lineages of red algae share common horizontal gene transfer events and close relationships with epiphytic bacterial populations. Specifically, the ancestor of N. haitanensis obtained unique lipoxygenase family genes from bacteria for complex chemical defense, carbonic anhydrases for survival in shell-borne conchocelis lifestyle stages, and numerous genes involved in stress tolerance. Combined proteomic, transcriptomic, and metabolomic analyses revealed complex regulation of rapid responses to intertidal dehydration/rehydration cycling within N. haitanensis. These adaptations include rapid regulation of its photosynthetic system, a readily available capacity to utilize ribosomal stores, increased methylation activity to rapidly synthesize proteins, and a strong anti-oxidation system to dissipate excess redox energy upon exposure to air. These novel insights into the unique adaptations of red algae to intertidal lifestyles inform our understanding of adaptations to intertidal ecosystems and the unique evolutionary steps required for intertidal colonization by biological life.
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Affiliation(s)
- Haimin Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Marine Drugs and Biological Products Department, Ningbo Institute of Oceanography, Ningbo, China
| | | | - Juanjuan Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
| | - Qijun Luo
- Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, Ningbo, China
| | - Huan Wang
- Wuhan Frasergen Bioinformatics Co. Ltd., Wuhan, China
| | - Rui Lu
- Wuhan Frasergen Bioinformatics Co. Ltd., Wuhan, China
| | - Zhujun Zhu
- Marine Drugs and Biological Products Department, Ningbo Institute of Oceanography, Ningbo, China
| | - Gaigai Yuan
- Wuhan Frasergen Bioinformatics Co. Ltd., Wuhan, China
| | - Xinxin Yi
- Wuhan Frasergen Bioinformatics Co. Ltd., Wuhan, China
| | - Youzhi Mao
- Wuhan Frasergen Bioinformatics Co. Ltd., Wuhan, China
| | - Caiping Lu
- Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, Ningbo, China
| | - Zekai Wang
- Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, Ningbo, China
| | - Denghui Gu
- Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, Ningbo, China
| | - Zhen Jin
- Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, Ningbo, China
| | - Caixia Zhang
- Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, Ningbo, China
| | - Ziyu Weng
- Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, Ningbo, China
| | - Shuang Li
- Ningbo Customs Technology Center, Ningbo, China
| | - Xiaojun Yan
- Marine Drugs and Biological Products Department, Ningbo Institute of Oceanography, Ningbo, China
| | - Rui Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
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Abstract
Genetic balancer systems, which allow effective capture and maintenance of lethal mutations stably, play an important role in identifying essential genes. Whole-genome sequencing (WGS) followed by bioinformatics analysis, combined with genetic mapping data analysis, allows for an efficient and economical means of identifying genomic mutations in essential genes. Using this approach, we successfully identified 104 essential genes on ChrI, ChrIII, and ChrV in C. elegans. In this report, we described a protocol that sequences the genome of prebalanced Caenorhabditis elegans (C. elegans) strains to carry lethal mutations and identifies candidate causal mutations and candidate essential genes using a robust bioinformatics procedure.
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Affiliation(s)
- Shicheng Yu
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Bioland Laboratory, Guangzhou, China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Chaoran Zheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
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Chu JSC, Peng B, Tang K, Yi X, Zhou H, Wang H, Li G, Leng J, Chen N, Feng X. Eight soybean reference genome resources from varying latitudes and agronomic traits. Sci Data 2021; 8:164. [PMID: 34210987 PMCID: PMC8249447 DOI: 10.1038/s41597-021-00947-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 04/30/2021] [Indexed: 01/18/2023] Open
Abstract
Comparative analysis of multiple reference genomes representing diverse genetic backgrounds is critical for understanding the role of key alleles important in domestication and genetic breeding of important crops such as soybean. To enrich the genetic resources for soybean, we describe the generation, technical assessment, and preliminary genomic variation analysis of eight de novo reference-grade soybean genome assemblies from wild and cultivated accessions. These resources represent soybeans cultured at different latitudes and exhibiting different agronomical traits. Of these eight soybeans, five are from new accessions that have not been sequenced before. We demonstrate the usage of these genomes to identify small and large genomic variations affecting known genes as well as screening for genic PAV regions for identifying candidates for further functional studies.
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Affiliation(s)
- Jeffrey Shih-Chieh Chu
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- Wuhan Frasergen Bioinformatics Inc., East Lake High-Tech Zone, Wuhan, China
| | - Bo Peng
- Wuhan Frasergen Bioinformatics Inc., East Lake High-Tech Zone, Wuhan, China
| | - Kuanqiang Tang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Xingxing Yi
- Wuhan Frasergen Bioinformatics Inc., East Lake High-Tech Zone, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Huangkai Zhou
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Huan Wang
- Wuhan Frasergen Bioinformatics Inc., East Lake High-Tech Zone, Wuhan, China
| | - Guang Li
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Jiantian Leng
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Nansheng Chen
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada.
| | - Xianzhong Feng
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China.
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Yu S, Zheng C, Zhou F, Baillie DL, Rose AM, Deng Z, Chu JSC. Genomic identification and functional analysis of essential genes in Caenorhabditis elegans. BMC Genomics 2018; 19:871. [PMID: 30514206 PMCID: PMC6278001 DOI: 10.1186/s12864-018-5251-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 11/14/2018] [Indexed: 11/27/2022] Open
Abstract
Background Essential genes are required for an organism’s viability and their functions can vary greatly, spreading across many pathways. Due to the importance of essential genes, large scale efforts have been undertaken to identify the complete set of essential genes and to understand their function. Studies of genome architecture and organization have found that genes are not randomly disturbed in the genome. Results Using combined genetic mapping, Illumina sequencing, and bioinformatics analyses, we successfully identified 44 essential genes with 130 lethal mutations in genomic regions of C. elegans of around 7.3 Mb from Chromosome I (left). Of the 44 essential genes, six of which were genes not characterized previously by mutant alleles, let-633/let-638 (B0261.1), let-128 (C53H9.2), let-511 (W09C3.4), let-162 (Y47G6A.18), let-510 (Y47G6A.19), and let-131 (Y71G12B.6). Examine essential genes with Hi-C data shows that essential genes tend to cluster within TAD units rather near TAD boundaries. We have also shown that essential genes in the left half of chromosome I in C. elegans function in enzyme and nucleic acid binding activities during fundamental processes, such as DNA replication, transcription, and translation. From protein-protein interaction networks, essential genes exhibit more protein connectivity than non-essential genes in the genome. Also, many of the essential genes show strong expression in embryos or early larvae stages, indicating that they are important to early development. Conclusions Our results confirmed that this work provided a more comprehensive picture of the essential gene and their functional characterization. These genetic resources will offer important tools for further heath and disease research. Electronic supplementary material The online version of this article (10.1186/s12864-018-5251-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shicheng Yu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China. .,Wuhan Frasergen Bioinformatics, Wuhan East Lake High-tech Zone, Wuhan, 430075, China.
| | - Chaoran Zheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Fan Zhou
- Wuhan Frasergen Bioinformatics, Wuhan East Lake High-tech Zone, Wuhan, 430075, China
| | - David L Baillie
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Ann M Rose
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.
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Chu JSC, Chua SY, Wong K, Davison AM, Johnsen R, Baillie DL, Rose AM. High-throughput capturing and characterization of mutations in essential genes of Caenorhabditis elegans. BMC Genomics 2014; 15:361. [PMID: 24884423 PMCID: PMC4039747 DOI: 10.1186/1471-2164-15-361] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 05/06/2014] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Essential genes are critical for the development of all organisms and are associated with many human diseases. These genes have been a difficult category to study prior to the availability of balanced lethal strains. Despite the power of targeted mutagenesis, there are limitations in identifying mutations in essential genes. In this paper, we describe the identification of coding regions for essential genes mutated using forward genetic screens in Caenorhabditis elegans. The lethal mutations described here were isolated and maintained by a wild-type allele on a rescuing duplication. RESULTS We applied whole genome sequencing to identify the causative molecular lesion resulting in lethality in existing C. elegans mutant strains. These strains are balanced and can be easily maintained for subsequent characterization. Our method can be effectively used to analyze mutations in a large number of essential genes. We describe here the identification of 64 essential genes in a region of chromosome I covered by the duplication sDp2. Of these, 42 are nonsense mutations, six are splice signal mutations, one deletion, and 15 are non-synonymous mutations. Many of the essential genes in this region function in cell cycle, transcriptional regulation, and RNA processing. CONCLUSIONS The essential genes identified here are represented by mutant strains, many of which have more than one mutant allele. The genetic resource can be utilized to further our understanding of essential gene function and will be applicable to the study of C. elegans development, conserved cellular function, and ultimately lead to improved human health.
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Affiliation(s)
| | - Shu-Yi Chua
- />Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Kathy Wong
- />Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Ann Marie Davison
- />Department of Biology, Kwantlen Polytechnic University, Surrey, Canada
| | - Robert Johnsen
- />Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - David L Baillie
- />Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Ann M Rose
- />Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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Aftab S, Semenec L, Chu JSC, Chen N. Identification and characterization of novel human tissue-specific RFX transcription factors. BMC Evol Biol 2008; 8:226. [PMID: 18673564 PMCID: PMC2533330 DOI: 10.1186/1471-2148-8-226] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Accepted: 08/01/2008] [Indexed: 02/06/2023] Open
Abstract
Background Five regulatory factor X (RFX) transcription factors (TFs)–RFX1-5–have been previously characterized in the human genome, which have been demonstrated to be critical for development and are associated with an expanding list of serious human disease conditions including major histocompatibility (MHC) class II deficiency and ciliaophathies. Results In this study, we have identified two additional RFX genes–RFX6 and RFX7–in the current human genome sequences. Both RFX6 and RFX7 are demonstrated to be winged-helix TFs and have well conserved RFX DNA binding domains (DBDs), which are also found in winged-helix TFs RFX1-5. Phylogenetic analysis suggests that the RFX family in the human genome has undergone at least three gene duplications in evolution and the seven human RFX genes can be clearly categorized into three subgroups: (1) RFX1-3, (2) RFX4 and RFX6, and (3) RFX5 and RFX7. Our functional genomics analysis suggests that RFX6 and RFX7 have distinct expression profiles. RFX6 is expressed almost exclusively in the pancreatic islets, while RFX7 has high ubiquitous expression in nearly all tissues examined, particularly in various brain tissues. Conclusion The identification and further characterization of these two novel RFX genes hold promise for gaining critical insight into development and many disease conditions in mammals, potentially leading to identification of disease genes and biomarkers.
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Affiliation(s)
- Syed Aftab
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
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