High-throughput sequencing of the chloroplast and mitochondrion of Chlamydomonas reinhardtii to generate improved de novo assemblies, analyze expression patterns and transcript speciation, and evaluate diversity among laboratory strains and wild isolates

Gallaher, Sean D.; Fitz‐Gibbon, Sorel T.; Strenkert, Daniela; Purvine, Samuel O.; Pellegrini, Matteo; Merchant, Sabeeha S.

doi:10.1111/tpj.13788

Title: High-throughput sequencing of the chloroplast and mitochondrion of Chlamydomonas reinhardtii to generate improved de novo assemblies, analyze expression patterns and transcript speciation, and evaluate diversity among laboratory strains and wild isolates

Journal Article · Fri Nov 24 00:00:00 EST 2017 · The Plant Journal

DOI:https://doi.org/10.1111/tpj.13788· OSTI ID:1922676

^[1];

^[2];

^[1];

^[1]

Univ. of California, Los Angeles, CA (United States)
Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)

Summary Chlamydomonas reinhardtii is a unicellular chlorophyte alga that is widely studied as a reference organism for understanding photosynthesis, sensory and motile cilia, and for development of an algal‐based platform for producing biofuels and bio‐products. Its highly repetitive, ~205‐kbp circular chloroplast genome and ~15.8‐kbp linear mitochondrial genome were sequenced prior to the advent of high‐throughput sequencing technologies. Here, high coverage shotgun sequencing was used to assemble both organellar genomes de novo . These new genomes correct dozens of errors in the prior genome sequences and annotations. Genome sequencing coverage indicates that each cell contains on average 83 copies of the chloroplast genome and 130 copies of the mitochondrial genome. Using protocols and analyses optimized for organellar transcripts, RNA ‐Seq was used to quantify their relative abundances across 12 different growth conditions. Forty‐six percent of total cellular mRNA is attributable to high expression from a few dozen chloroplast genes. RNA ‐Seq data were used to guide gene annotation, to demonstrate polycistronic gene expression, and to quantify splicing of psaA and psbA introns. In contrast to a conclusion from a recent study, we found that chloroplast transcripts are not edited. Unexpectedly, cytosine‐rich polynucleotide tails were observed at the 3’‐end of all mitochondrial transcripts. A comparative genomics analysis of eight laboratory strains and 11 wild isolates of C. reinhardtii identified 2658 variants in the organellar genomes, which is 1/10th as much genetic diversity as is found in the nucleus.

View Accepted Manuscript (DOE)

View Accepted Manuscript (Publisher)

Cite

Export

Save

Research Organization:: Univ. of California, Los Angeles, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH)

Grant/Contract Number:: FC03-02ER63421; GM092473; DE‐FC03‐02ER63421

OSTI ID:: 1922676

Alternate ID(s):: OSTI ID: 1416389

Journal Information:: The Plant Journal, Vol. 93, Issue 3; ISSN 0960-7412

Publisher:: Society for Experimental BiologyCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 55 works

Citation information provided by
Web of Science

References (48)

Mitochondrial DNA of Chlamydomonas reinhardtii: the structure of the ends of the linear 15.8-kb genome suggests mechanisms for DNA replication Vahrenholz, Carola; Riemen, Gudula; Pratje, Elke Current Genetics, Vol. 24, Issue 3 https://doi.org/10.1007/BF00351798	journal	September 1993
Chlamydomonas Genome Resource for Laboratory Strains Reveals a Mosaic of Sequence Variation, Identifies True Strain Histories, and Enables Strain-Specific Studies Gallaher, Sean D.; Fitz-Gibbon, Sorel T.; Glaesener, Anne G. The Plant Cell, Vol. 27, Issue 9 https://doi.org/10.1105/tpc.15.00508	journal	August 2015
Genomewide Analysis of Box C/D and Box H/ACA snoRNAs in Chlamydomonas reinhardtii Reveals an Extensive Organization Into Intronic Gene Clusters Chen, Chun-Long; Chen, Chong-Jian; Vallon, Olivier Genetics, Vol. 179, Issue 1 https://doi.org/10.1534/genetics.107.086025	journal	May 2008
A large open reading frame ( orf1995 ) in the chloroplast DNA of Chlamydomonas reinhardtii encodes an essential protein Boudreau, E.; Turmel, M.; Goldschmidt-Clermont, M. Molecular and General Genetics MGG, Vol. 253, Issue 5 https://doi.org/10.1007/s004380050368	journal	February 1997
A small chloroplast RNA may be required for trans-splicing in chlamydomonas reinhardtii Goldschmidt-Clermont, Michel; Choquet, Yves; Girard-Bascou, Jacqueline Cell, Vol. 65, Issue 1 https://doi.org/10.1016/0092-8674(91)90415-U	journal	April 1991
STAR: ultrafast universal RNA-seq aligner Dobin, Alexander; Davis, Carrie A.; Schlesinger, Felix Bioinformatics, Vol. 29, Issue 1 https://doi.org/10.1093/bioinformatics/bts635	journal	October 2012
Chloroplast ribosomal intron of Chlamydomonas reinhardtii: in vitro self-splicing, DNA endonuclease activity and in vivo mobility. Dürrenberger, F.; Rochaix, J. D. The EMBO Journal, Vol. 10, Issue 11 https://doi.org/10.1002/j.1460-2075.1991.tb04913.x	journal	November 1991
The Average Number of Generations Until Fixation of a Mutant gene in a Finite Population Kimura, Motoo; Ohta, Tomoko Genetics, Vol. 61, Issue 3 https://doi.org/10.1093/genetics/61.3.763	journal	March 1969
YCF1: A Green TIC? de Vries, Jan; Sousa, Filipa L.; Bölter, Bettina The Plant Cell, Vol. 27, Issue 7 https://doi.org/10.1105/tpc.114.135541	journal	March 2015
Structure and function of the ftsH gene in Escherichia coli Ogura, T.; Tomoyasu, T.; Yuki, T. Research in Microbiology, Vol. 142, Issue 2-3 https://doi.org/10.1016/0923-2508(91)90041-8	journal	January 1991
Chloroplast RNA Metabolism Stern, David B.; Goldschmidt-Clermont, Michel; Hanson, Maureen R. Annual Review of Plant Biology, Vol. 61, Issue 1 https://doi.org/10.1146/annurev-arplant-042809-112242	journal	June 2010
PASS: a program to align short sequences Campagna, D.; Albiero, A.; Bilardi, A. Bioinformatics, Vol. 25, Issue 7 https://doi.org/10.1093/bioinformatics/btp087	journal	February 2009
Molecular characterization at the RNA and gene levels of U3 snoRNA from a unicellular green alga, Chlamydomonas reinhardtii Antal, M. Nucleic Acids Research, Vol. 28, Issue 15 https://doi.org/10.1093/nar/28.15.2959	journal	August 2000
Chlamydomonas reinhardii gene for the 32 000 mol. wt. protein of photosystem II contains four large introns and is located entirely within the chloroplast inverted repeat Erickson, Jeanne M.; Rahire, Michèle; Rochaix, Jean-David The EMBO Journal, Vol. 3, Issue 12 https://doi.org/10.1002/j.1460-2075.1984.tb02206.x	journal	December 1984
A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii: A revised mineral nutrient supplement for Chlamydomonas Kropat, Janette; Hong-Hermesdorf, Anne; Casero, David The Plant Journal, Vol. 66, Issue 5 https://doi.org/10.1111/j.1365-313X.2011.04537.x	journal	March 2011
Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer Ha, G.; Roth, A.; Lai, D. Genome Research, Vol. 22, Issue 10 https://doi.org/10.1101/gr.137570.112	journal	May 2012
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Lowe, Todd M.; Eddy, Sean R. Nucleic Acids Research, Vol. 25, Issue 5 https://doi.org/10.1093/nar/25.5.955	journal	March 1997
Isolation and characterization of mitochondrial DNA from Chlamydomonas reinhardtii. Ryan, R.; Grant, D.; Chiang, K. S. Proceedings of the National Academy of Sciences, Vol. 75, Issue 7 https://doi.org/10.1073/pnas.75.7.3268	journal	July 1978
Structural and transcription analysis of two homologous genes for the P700 chlorophyll a -apoproteins in Chlamydomonas reinhardii : evidence for in vivo trans -splicing Kück, Ulrich; Choquet, Yves; Schneider, Michel The EMBO Journal, Vol. 6, Issue 8 https://doi.org/10.1002/j.1460-2075.1987.tb02489.x	journal	August 1987
Phylogenetic Position and Molecular Chronology of a Colonial Green Flagellate, Stephanosphaera pluvialis (Volvocales, Chlorophyceae), among Unicellular Algae Munakata, Hidehito; Nakada, Takashi; Nakahigashi, Kenji Journal of Eukaryotic Microbiology, Vol. 63, Issue 3 https://doi.org/10.1111/jeu.12283	journal	December 2015
A single nuclear locus is involved in both chloroplast RNA trans ‐splicing and 3′ end processing Hahn, Daniela; Nickelsen, Jörg; Hackert, Anke The Plant Journal, Vol. 15, Issue 4 https://doi.org/10.1046/j.1365-313X.1998.00234.x	journal	August 1998
Differential analysis of gene regulation at transcript resolution with RNA-seq Trapnell, Cole; Hendrickson, David G.; Sauvageau, Martin Nature Biotechnology, Vol. 31, Issue 1 https://doi.org/10.1038/nbt.2450	journal	December 2012
The Chloroplast atpA Gene Cluster in Chlamydomonas reinhardtii : Functional Analysis of a Polycistronic Transcription Unit Drapier, Dominique; Suzuki, Hideki; Levy, Haim Plant Physiology, Vol. 117, Issue 2 https://doi.org/10.1104/pp.117.2.629	journal	June 1998
OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets Lohse, Marc; Drechsel, Oliver; Kahlau, Sabine Nucleic Acids Research, Vol. 41, Issue W1 https://doi.org/10.1093/nar/gkt289	journal	April 2013
Nuclear suppressors define three factors that participate in both 5′ and 3′ end processing of mRNAs in Chlamydomonas chloroplasts Rymarquis, Linda A.; Higgs, David C.; Stern, David B. The Plant Journal, Vol. 46, Issue 3 https://doi.org/10.1111/j.1365-313X.2006.02711.x	journal	May 2006
Full transcription of the chloroplast genome in photosynthetic eukaryotes Shi, Chao; Wang, Shuo; Xia, En-Hua Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep30135	journal	July 2016
Chlamydomonas as a model for biofuels and bio‐products production Scranton, Melissa A.; Ostrand, Joseph T.; Fields, Francis J. The Plant Journal, Vol. 82, Issue 3 https://doi.org/10.1111/tpj.12780	journal	February 2015
Comparison of prokaryotic diversity at offshore oceanic locations reveals a different microbiota in the Mediterranean Sea: Offshore prokaryotic diversity Zaballos, Milagros; LÃ³pez-LÃ³pez, Arantxa; Ovreas, Lise FEMS Microbiology Ecology, Vol. 56, Issue 3 https://doi.org/10.1111/j.1574-6941.2006.00060.x	journal	June 2006
Two copies of a DNA element, ?Wendy?, in the chloroplast chromosome of Chlamydomonas reinhardtii between rearranged gene clusters Fan, Wen-Hua; Woelfle, Mark A.; Mosig, Gisela Plant Molecular Biology, Vol. 29, Issue 1 https://doi.org/10.1007/BF00019119	journal	October 1995
Organization and Expression of Algal (Chlamydomonas reinhardtii) Mitochondrial DNA Gray, M. W.; Boer, P. H. Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 319, Issue 1193 https://doi.org/10.1098/rstb.1988.0038	journal	May 1988
The catalytic group-I introns of the psbA gene of Chlamydomonas reinhardtii : core structures, ORFs and evolutionary implications Holloway, Stephen P.; Deshpande, Nita N.; Herrin, David L. Current Genetics, Vol. 36, Issue 1-2 https://doi.org/10.1007/s002940050474	journal	August 1999
Isolation and phenotypic characterization ofChlamydomonas reinhardtii mutants defective in chloroplast DNA segregation Misumi, O.; Suzuki, L.; Nishimura, Y. Protoplasma, Vol. 209, Issue 3-4 https://doi.org/10.1007/BF01453455	journal	September 1999
The Chlamydomonas reinhardtii Plastid Chromosome : Islands of Genes in a Sea of Repeats Maul, Jude E.; Lilly, Jason W.; Cui, Liying The Plant Cell, Vol. 14, Issue 11 https://doi.org/10.1105/tpc.006155	journal	October 2002
The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions Merchant, S. S.; Prochnik, S. E.; Vallon, O. Science, Vol. 318, Issue 5848, p. 245-250 https://doi.org/10.1126/science.1143609	journal	October 2007
Polyadenylation of three classes of chloroplast RNA in Chlamydomonas reinhardtii Komine, Yutaka; Kwong, Linda; Anguera, Montserrat C. RNA, Vol. 6, Issue 4 https://doi.org/10.1017/S1355838200992252	journal	April 2000
Nucleotide diversity of the Chlamydomonas reinhardtii plastid genome: addressing the mutational-hazard hypothesis Smith, David Roy; Lee, Robert W. BMC Evolutionary Biology, Vol. 9, Issue 1 https://doi.org/10.1186/1471-2148-9-120	journal	January 2009
The GreenCut2 Resource, a Phylogenomically Derived Inventory of Proteins Specific to the Plant Lineage Karpowicz, Steven J.; Prochnik, Simon E.; Grossman, Arthur R. Journal of Biological Chemistry, Vol. 286, Issue 24 https://doi.org/10.1074/jbc.M111.233734	journal	April 2011
Whole-Genome Resequencing Reveals Extensive Natural Variation in the Model Green Alga Chlamydomonas reinhardtii Flowers, Jonathan M.; Hazzouri, Khaled M.; Pham, Gina M. The Plant Cell, Vol. 27, Issue 9 https://doi.org/10.1105/tpc.15.00492	journal	September 2015
Summarizing and correcting the GC content bias in high-throughput sequencing Benjamini, Yuval; Speed, Terence P. Nucleic Acids Research, Vol. 40, Issue 10 https://doi.org/10.1093/nar/gks001	journal	February 2012
Inhibition of chloroplast DNA recombination and repair by dominant negative mutants of Escherichia coli RecA. Cerutti, H.; Johnson, A. M.; Boynton, J. E. Molecular and Cellular Biology, Vol. 15, Issue 6 https://doi.org/10.1128/MCB.15.6.3003	journal	June 1995
Transcription Factor–Dependent Chromatin Remodeling at Heat Shock and Copper-Responsive Promoters in Chlamydomonas reinhardtii Strenkert, Daniela; Schmollinger, Stefan; Sommer, Frederik The Plant Cell, Vol. 23, Issue 6 https://doi.org/10.1105/tpc.111.085266	journal	June 2011
Systems and Trans -System Level Analysis Identifies Conserved Iron Deficiency Responses in the Plant Lineage Urzica, Eugen I.; Casero, David; Yamasaki, Hiroaki The Plant Cell, Vol. 24, Issue 10 https://doi.org/10.1105/tpc.112.102491	journal	October 2012
Polyadenylation in Arabidopsis and Chlamydomonas organelles: the input of nucleotidyltransferases, poly(A) polymerases and polynucleotide phosphorylase Zimmer, Sarah L.; Schein, Aleks; Zipor, Gadi The Plant Journal, Vol. 59, Issue 1 https://doi.org/10.1111/j.1365-313X.2009.03853.x	journal	July 2009
Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data Lopez, David; Casero, David; Cokus, Shawn J. BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-282	journal	January 2011
Chlamydomonas reinhardtii as a viable platform for the production of recombinant proteins: current status and perspectives Rosales-Mendoza, Sergio; Paz-Maldonado, Luz María Teresita; Soria-Guerra, Ruth Elena Plant Cell Reports, Vol. 31, Issue 3 https://doi.org/10.1007/s00299-011-1186-8	journal	November 2011
Epigenetic silencing of a foreign gene in nuclear transformants of Chlamydomonas. Cerutti, H.; Johnson, A. M.; Gillham, N. W. The Plant Cell, Vol. 9, Issue 6 https://doi.org/10.1105/tpc.9.6.925	journal	June 1997
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Love, Michael I.; Huber, Wolfgang; Anders, Simon Genome Biology, Vol. 15, Issue 12 https://doi.org/10.1186/s13059-014-0550-8	journal	December 2014
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w Cingolani, Pablo; Platts, Adrian; Wang, Le Lily Fly, Vol. 6, Issue 2 https://doi.org/10.4161/fly.19695	journal	April 2012

Cited By (1)

A streamlined and predominantly diploid genome in the tiny marine green alga Chloropicon primus Lemieux, Claude; Turmel, Monique; Otis, Christian Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-12014-x	journal	September 2019

Similar Records

High-throughput sequencing of the chloroplast and mitochondrion of Chlamydomonas reinhardtii to generate improved de novo assemblies, analyze expression patterns and transcript speciation, and evaluate diversity among laboratory strains and wild isolates

Journal Article · Sun Jan 07 00:00:00 EST 2018 · The Plant Journal · OSTI ID:1922676

Gallaher, Sean D.; Fitz-Gibbon, Sorel T.; Strenkert, Daniela; +3 more

The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization

Journal Article · Tue Nov 21 00:00:00 EST 2017 · The Plant Journal · OSTI ID:1922676

McCormick, Ryan F.; Truong, Sandra K.; Sreedasyam, Avinash; +12 more

The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data

Journal Article · Sun Apr 22 00:00:00 EDT 2018 · The Plant Journal · OSTI ID:1922676

Perroud, Pierre‐François; Haas, Fabian B.; Hiss, Manuel; +29 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
plastid
organelles
RNA-Seq
transcript editing
trans-splicing
rpoC1
rps2
Wendy transposon
ftsH
ycf1

Title: High-throughput sequencing of the chloroplast and mitochondrion of Chlamydomonas reinhardtii to generate improved de novo assemblies, analyze expression patterns and transcript speciation, and evaluate diversity among laboratory strains and wild isolates

Citation Formats

References (48)

Cited By (1)

Similar Records

Related Subjects