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

Abstract

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 mitochondrialmore » 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.« less

Authors:

Gallaher, Sean D.  ^[1];

• Search DOE PAGES for author "Gallaher, Sean D."
• Search DOE PAGES for ORCID "0000-0002-9773-6051"

Fitz‐Gibbon, Sorel T.  ^[1];

• Search DOE PAGES for author "Fitz‐Gibbon, Sorel T."
• Search DOE PAGES for ORCID "0000-0001-7090-5719"

Strenkert, Daniela  ^[1];

• Search DOE PAGES for author "Strenkert, Daniela"
• Search DOE PAGES for ORCID "0000-0002-3420-1332"

Purvine, Samuel O.  ^[2];

• Search DOE PAGES for author "Purvine, Samuel O."
• Search DOE PAGES for ORCID "0000-0002-2257-2400"

Pellegrini, Matteo  ^[1];

• Search DOE PAGES for author "Pellegrini, Matteo"
• Search DOE PAGES for ORCID "0000-0001-9355-9564"

Merchant, Sabeeha S.  ^[1]

• Search DOE PAGES for author "Merchant, Sabeeha S."
• Search DOE PAGES for ORCID "0000-0002-2594-509X"

---

+ Show Author Affiliations

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

Publication Date:

Fri Nov 24 00:00:00 EST 2017

Research Org.:

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

Sponsoring Org.:

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

OSTI Identifier:

1922676

Alternate Identifier(s):

OSTI ID: 1416389

Grant/Contract Number:  

FC03-02ER63421; GM092473; DE‐FC03‐02ER63421

Resource Type:

Accepted Manuscript

Journal Name:

The Plant Journal

Additional Journal Information:

Journal Volume: 93; Journal Issue: 3; Journal ID: ISSN 0960-7412

Publisher:

Society for Experimental Biology

Country of Publication:

United States

Language:

English

Subject:

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