1
|
Craig RJ, Gallaher SD, Shu S, Salomé PA, Jenkins JW, Blaby-Haas CE, Purvine SO, O’Donnell S, Barry K, Grimwood J, Strenkert D, Kropat J, Daum C, Yoshinaga Y, Goodstein DM, Vallon O, Schmutz J, Merchant SS. The Chlamydomonas Genome Project, version 6: Reference assemblies for mating-type plus and minus strains reveal extensive structural mutation in the laboratory. THE PLANT CELL 2023; 35:644-672. [PMID: 36562730 PMCID: PMC9940879 DOI: 10.1093/plcell/koac347] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 10/12/2022] [Accepted: 12/16/2022] [Indexed: 05/20/2023]
Abstract
Five versions of the Chlamydomonas reinhardtii reference genome have been produced over the last two decades. Here we present version 6, bringing significant advances in assembly quality and structural annotations. PacBio-based chromosome-level assemblies for two laboratory strains, CC-503 and CC-4532, provide resources for the plus and minus mating-type alleles. We corrected major misassemblies in previous versions and validated our assemblies via linkage analyses. Contiguity increased over ten-fold and >80% of filled gaps are within genes. We used Iso-Seq and deep RNA-seq datasets to improve structural annotations, and updated gene symbols and textual annotation of functionally characterized genes via extensive manual curation. We discovered that the cell wall-less classical reference strain CC-503 exhibits genomic instability potentially caused by deletion of the helicase RECQ3, with major structural mutations identified that affect >100 genes. We therefore present the CC-4532 assembly as the primary reference, although this strain also carries unique structural mutations and is experiencing rapid proliferation of a Gypsy retrotransposon. We expect all laboratory strains to harbor gene-disrupting mutations, which should be considered when interpreting and comparing experimental results. Collectively, the resources presented here herald a new era of Chlamydomonas genomics and will provide the foundation for continued research in this important reference organism.
Collapse
Affiliation(s)
- Rory J Craig
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sean D Gallaher
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
| | - Shengqiang Shu
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
| | - Patrice A Salomé
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
- Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, USA
| | - Jerry W Jenkins
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Crysten E Blaby-Haas
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Samuel O’Donnell
- Laboratory of Computational and Quantitative Biology, UMR 7238, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris 75005, France
| | - Kerrie Barry
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
| | - Jane Grimwood
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Daniela Strenkert
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
| | - Janette Kropat
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Chris Daum
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
| | - Yuko Yoshinaga
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
| | - David M Goodstein
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
| | - Olivier Vallon
- Unité Mixte de Recherche 7141, CNRS, Institut de Biologie Physico-Chimique, Sorbonne Université, Paris 75005, France
| | - Jeremy Schmutz
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Sabeeha S Merchant
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| |
Collapse
|
2
|
Kim SB, Karre S, Wu Q, Park M, Meyers E, Claeys H, Wisser R, Jackson D, Balint-Kurti P. Multiple insertions of COIN, a novel maize Foldback transposable element, in the Conring gene cause a spontaneous progressive cell death phenotype. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:581-595. [PMID: 32748440 DOI: 10.1111/tpj.14945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 06/11/2023]
Abstract
Similar progressive leaf lesion phenotypes, named conring for "concentric ring," were identified in 10 independently derived maize lines. Complementation and mapping experiments indicated that the phenotype had the same genetic basis in each line - a single recessive gene located in a 1.1-Mb region on chromosome 2. Among the 15 predicted genes in this interval, Zm00001d003866 (subsequently renamed Conring or Cnr) had insertions of four related 138 bp transposable element (TE) sequences at precisely the same site in exon 4 in nine of the 10 cnr alleles. The 10th cnr allele had a distinct insertion of 226 bp of in exon 3. Genetic evidence suggested that the 10 cnr alleles were independently derived, and arose during the derivation of each line. The four TEs, named COINa (for COnring INsertion) through COINd, have not been previously characterized and consist entirely of imperfect 69-bp terminal inverted repeats characteristic of the Foldback class of TEs. They belong to three clades of a family of maize TEs comprising hundreds of sequences in the genome of the B73 maize line. COIN elements preferentially insert at TNA sequences with a preference for C and G nucleotides in the immediately flanking 5' and 3' regions, respectively. They produce a three-base target site duplication and do not have homology to other characterized TEs. We propose that Cnr is an unstable gene that is mutated insertionally at high frequency, most commonly due to COIN element insertions at a specific site in the gene.
Collapse
Affiliation(s)
- Saet-Byul Kim
- Department of Entomology and Plant Pathology, NC State University, Raleigh, NC, USA
| | - Shailesh Karre
- Department of Entomology and Plant Pathology, NC State University, Raleigh, NC, USA
| | - Qingyu Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Minkyu Park
- Horticultural Sciences Department, University of Florida, 2550 Hull Rd, Gainesville, FL, 32611, USA
| | - Emily Meyers
- Department of Entomology and Plant Pathology, NC State University, Raleigh, NC, USA
| | - Hannes Claeys
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Randall Wisser
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, 19716, USA
| | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Peter Balint-Kurti
- Department of Entomology and Plant Pathology, NC State University, Raleigh, NC, USA
- Plant Science Research Unit USDA-ARS, NC State University, Raleigh, NC, USA
| |
Collapse
|
3
|
Neller KCM, Klenov A, Hudak KA. The Pokeweed Leaf mRNA Transcriptome and Its Regulation by Jasmonic Acid. FRONTIERS IN PLANT SCIENCE 2016; 7:283. [PMID: 27014307 PMCID: PMC4792876 DOI: 10.3389/fpls.2016.00283] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/22/2016] [Indexed: 05/16/2023]
Abstract
The American pokeweed plant, Phytolacca americana, is recognized for synthesizing pokeweed antiviral protein (PAP), a ribosome inactivating protein (RIP) that inhibits the replication of several plant and animal viruses. The plant is also a heavy metal accumulator with applications in soil remediation. However, little is known about pokeweed stress responses, as large-scale sequencing projects have not been performed for this species. Here, we sequenced the mRNA transcriptome of pokeweed in the presence and absence of jasmonic acid (JA), a hormone mediating plant defense. Trinity-based de novo assembly of mRNA from leaf tissue and BLASTx homology searches against public sequence databases resulted in the annotation of 59 096 transcripts. Differential expression analysis identified JA-responsive genes that may be involved in defense against pathogen infection and herbivory. We confirmed the existence of several PAP isoforms and cloned a potentially novel isoform of PAP. Expression analysis indicated that PAP isoforms are differentially responsive to JA, perhaps indicating specialized roles within the plant. Finally, we identified 52 305 natural antisense transcript pairs, four of which comprised PAP isoforms, suggesting a novel form of RIP gene regulation. This transcriptome-wide study of a Phytolaccaceae family member provides a source of new genes that may be involved in stress tolerance in this plant. The sequences generated in our study have been deposited in the SRA database under project # SRP069141.
Collapse
|
4
|
Jinkerson RE, Jonikas MC. Molecular techniques to interrogate and edit the Chlamydomonas nuclear genome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:393-412. [PMID: 25704665 DOI: 10.1111/tpj.12801] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/13/2015] [Accepted: 02/16/2015] [Indexed: 05/23/2023]
Abstract
The success of the green alga Chlamydomonas reinhardtii as a model organism is to a large extent due to the wide range of molecular techniques that are available for its characterization. Here, we review some of the techniques currently used to modify and interrogate the C. reinhardtii nuclear genome and explore several technologies under development. Nuclear mutants can be generated with ultraviolet (UV) light and chemical mutagens, or by insertional mutagenesis. Nuclear transformation methods include biolistic delivery, agitation with glass beads, and electroporation. Transforming DNA integrates into the genome at random sites, and multiple strategies exist for mapping insertion sites. A limited number of studies have demonstrated targeted modification of the nuclear genome by approaches such as zinc-finger nucleases and homologous recombination. RNA interference is widely used to knock down expression levels of nuclear genes. A wide assortment of transgenes has been successfully expressed in the Chlamydomonas nuclear genome, including transformation markers, fluorescent proteins, reporter genes, epitope tagged proteins, and even therapeutic proteins. Optimized expression constructs and strains help transgene expression. Emerging technologies such as the CRISPR/Cas9 system, high-throughput mutant identification, and a whole-genome knockout library are being developed for this organism. We discuss how these advances will propel future investigations.
Collapse
Affiliation(s)
- Robert E Jinkerson
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA, 94305, USA
| | - Martin C Jonikas
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA, 94305, USA
| |
Collapse
|
5
|
Sun X, Perera S, Haas N, Lefebvre PA, Silflow CD. Using an RSP3 reporter gene system to investigate molecular regulation of hydrogenase expression in Chlamydomonas reinhardtii. ALGAL RES 2013. [DOI: 10.1016/j.algal.2013.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
6
|
Diversification of the core RNA interference machinery in Chlamydomonas reinhardtii and the role of DCL1 in transposon silencing. Genetics 2008; 179:69-81. [PMID: 18493041 DOI: 10.1534/genetics.107.086546] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Small RNA-guided gene silencing is an evolutionarily conserved process that operates by a variety of molecular mechanisms. In multicellular eukaryotes, the core components of RNA-mediated silencing have significantly expanded and diversified, resulting in partly distinct pathways for the epigenetic control of gene expression and genomic parasites. In contrast, many unicellular organisms with small nuclear genomes seem to have lost entirely the RNA-silencing machinery or have retained only a basic set of components. We report here that Chlamydomonas reinhardtii, a unicellular eukaryote with a relatively large nuclear genome, has undergone extensive duplication of Dicer and Argonaute polypeptides after the divergence of the green algae and land plant lineages. Chlamydomonas encodes three Dicers and three Argonautes with DICER-LIKE1 (DCL1) and ARGONAUTE1 being more divergent than the other paralogs. Interestingly, DCL1 is uniquely involved in the post-transcriptional silencing of retrotransposons such as TOC1. Moreover, on the basis of the subcellular distribution of TOC1 small RNAs and target transcripts, this pathway most likely operates in the nucleus. However, Chlamydomonas also relies on a DCL1-independent, transcriptional silencing mechanism(s) for the maintenance of transposon repression. Our results suggest that multiple, partly redundant epigenetic processes are involved in preventing transposon mobilization in this green alga.
Collapse
|
7
|
Kim KS, Kustu S, Inwood W. Natural history of transposition in the green alga Chlamydomonas reinhardtii: use of the AMT4 locus as an experimental system. Genetics 2006; 173:2005-19. [PMID: 16702425 PMCID: PMC1569734 DOI: 10.1534/genetics.106.058263] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2006] [Accepted: 05/10/2006] [Indexed: 11/18/2022] Open
Abstract
The AMT4 locus of the green alga Chlamydomonas reinhardtii, which we mapped to the long arm of chromosome 8, provides a good experimental system for the study of transposition. Most mutations that confer resistance to the toxic ammonium analog methylammonium are in AMT4 and a high proportion of spontaneous mutations are caused by transposon-related events. Among the 15 such events that we have characterized at the molecular level, 9 were associated with insertions of the retrotransposon TOC1, 2 with a small Gulliver-related transposon, and 1 with the Tcr1 transposon. We found that Tcr1 is apparently a foldback transposon with terminal inverted repeats that are much longer and more complex than previously realized. A duplication of Tcr1 yielded a configuration thought to be important for chromosomal evolution. Other mutations in AMT4 were caused by two mobile elements that have not been described before. The sequence of one, which we propose to call the Bill element, indicates that it probably transposes by way of a DNA intermediate and requires functions that it does not encode. The sequence of the other and bioinformatic analysis indicates that it derives from a miniature retrotransposon or TRIM, which we propose to call MRC1 (miniature retrotransposon of Chlamydomonas).
Collapse
Affiliation(s)
- Kwang-Seo Kim
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | | | | |
Collapse
|
8
|
Sun Y, Gao X, Li Q, Zhang Q, Xu Z. Functional complementation of a nitrate reductase defective mutant of a green alga Dunaliella viridis by introducing the nitrate reductase gene. Gene 2006; 377:140-9. [PMID: 16797881 DOI: 10.1016/j.gene.2006.03.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2005] [Revised: 03/03/2006] [Accepted: 03/28/2006] [Indexed: 11/21/2022]
Abstract
Nitrate reductase (NR) catalyzes NAD (P) H dependent reduction of nitrate to nitrite. Transformation systems have been established in several species of green algae by nitrate reductase gene functional complementation. In this report, an endogenous NR cDNA (3.4 kb) and a genomic fragment (14.6 kb) containing the NR gene (DvNIA1) were isolated from the D. viridis cDNA and genomic libraries respectively. Southern blot and Northern blot analyses showed that this gene exists as a single copy in D. viridis and is induced by nitrate. To obtain a NR defective mutant as a recipient strain, D. viridis cells were treated with a chemical mutagen and then cultured on a chlorate-containing plate to enrich chlorate tolerant mutants. Southern analysis showed that one isolate, B14, had a deletion in the DvNIA1 gene region. Using electroporation conditions determined in this laboratory, plasmid pDVNR containing the intact DvNIA1 gene has been electroporated into the defective mutant B14. Strains retaining a nitrate assimilation phenotype were obtained from nitrate plates after spreading the electroporated cells. In some individual strains, transcription of the introduced gene was detected. NR activity in these strains was slightly higher than that in the defective B14 cell, but excretion of nitrite into culture media was almost as high as that of the wild-type cell. Possible episomal presence of the introduced DNA in D. viridis is discussed.
Collapse
Affiliation(s)
- Yu Sun
- Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, The Chinese Academy of Science, Shanghai, People's Republic of China
| | | | | | | | | |
Collapse
|
9
|
Grossman AR, Harris EE, Hauser C, Lefebvre PA, Martinez D, Rokhsar D, Shrager J, Silflow CD, Stern D, Vallon O, Zhang Z. Chlamydomonas reinhardtii at the crossroads of genomics. EUKARYOTIC CELL 2004; 2:1137-50. [PMID: 14665449 PMCID: PMC326643 DOI: 10.1128/ec.2.6.1137-1150.2003] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Arthur R Grossman
- The Carnegie Institution of Washington, Department of Plant Biology, Stanford, California 94305. Biology Department, Duke University, Durham, North Carolina 27708, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Li JB, Lin S, Jia H, Wu H, Roe BA, Kulp D, Stormo GD, Dutcher SK. Analysis of Chlamydomonas reinhardtii genome structure using large-scale sequencing of regions on linkage groups I and III. J Eukaryot Microbiol 2003; 50:145-55. [PMID: 12836870 DOI: 10.1111/j.1550-7408.2003.tb00109.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Chlamydomonas reinhardtii is a unicellular green alga that has been used as a model organism for the study of flagella and basal bodies as well as photosynthesis. This report analyzes finished genomic DNA sequence for 0.5% of the nuclear genome. We have used three gene prediction programs as well as EST and protein homology data to estimate the total number of genes in Chlamydomonas to be between 12,000 and 16,400. Chlamydomonas appears to have many more genes than any other unicellular organism sequenced to date. Twenty-seven percent of the predicted genes have significant identity to both ESTs and to known proteins in other organisms, 32% of the predicted genes have significant identity to ESTs alone, and 14% have significant similarity to known proteins in other organisms. For gene prediction in Chlamydomonas, GreenGenie appeared to have the highest sensitivity and specificity at the exon level, scoring 71% and 82%. respectively. Two new alternative splicing events were predicted by aligning Chlamydomonas ESTs to the genomic sequence. Finally recombination differs between the two sequenced contigs. The 350-Kb of the Linkage group III contig is devoid of recombination, while the Linkage group I contig is 30 map units long over 33-kb.
Collapse
Affiliation(s)
- Jin Billy Li
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | | | | | | | | | | | | | | |
Collapse
|
11
|
Dent RM, Han M, Niyogi KK. Functional genomics of plant photosynthesis in the fast lane using Chlamydomonas reinhardtii. TRENDS IN PLANT SCIENCE 2001; 6:364-371. [PMID: 11495790 DOI: 10.1016/s1360-1385(01)02018-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Oxygenic photosynthesis by algae and plants supports much of life on Earth. Several model organisms are used to study this vital process, but the unicellular green alga Chlamydomonas reinhardtii offers significant advantages for the genetic dissection of photosynthesis. Recent experiments with Chlamydomonas have substantially advanced our understanding of several aspects of photosynthesis, including chloroplast biogenesis, structure-function relationships in photosynthetic complexes, and environmental regulation. Chlamydomonas is therefore the organism of choice for elucidating detailed functions of the hundreds of genes involved in plant photosynthesis.
Collapse
Affiliation(s)
- R M Dent
- Dept of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
| | | | | |
Collapse
|
12
|
Harris EH. CHLAMYDOMONAS AS A MODEL ORGANISM. ANNUAL REVIEW OF PLANT PHYSIOLOGY AND PLANT MOLECULAR BIOLOGY 2001; 52:363-406. [PMID: 11337403 DOI: 10.1146/annurev.arplant.52.1.363] [Citation(s) in RCA: 430] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The unicellular green alga Chlamydomonas offers a simple life cycle, easy isolation of mutants, and a growing array of tools and techniques for molecular genetic studies. Among the principal areas of current investigation using this model system are flagellar structure and function, genetics of basal bodies (centrioles), chloroplast biogenesis, photosynthesis, light perception, cell-cell recognition, and cell cycle control. A genome project has begun with compilation of expressed sequence tag data and gene expression studies and will lead to a complete genome sequence. Resources available to the research community include wild-type and mutant strains, plasmid constructs for transformation studies, and a comprehensive on-line database.
Collapse
Affiliation(s)
- Elizabeth H Harris
- Developmental, Cell and Molecular Biology Group, Biology Department, Duke University, Durham, North Carolina 27708-1000; e-mail:
| |
Collapse
|
13
|
Abstract
Chlamydomonas reinhardtii has been the subject of genetic, biochemical, cytological, and molecular analyses for over 50 years. It is an ideal model system for the study of flagella and basal bodies as well as the study of photosynthesis and chloroplast biogenesis, cell-cell recognition and fusion, phototaxis, and secretion. It is clear that many of the genes identified in Chlamydomonas have homologs in land plants as well as animals. Thus, a genomic approach in Chlamydomonas will provide another important avenue for the understanding of important biological processes.
Collapse
Affiliation(s)
- S K Dutcher
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA.
| |
Collapse
|