Dynamic changes in the transcriptome and methylome of Chlamydomonas reinhardtii throughout its life cycle

Abstract

; 0000-0001-9355-9564 (M.P.).The green alga Chlamydomonas reinhardtii undergoes gametogenesis and mating upon nitrogen starvation. While the steps involved in its sexual reproductive cycle have been extensively characterized, the genome-wide transcriptional and epigenetic changes underlying different life cycle stages have yet to be fully described. Here, we performed transcriptome and methylome sequencing to quantify expression and DNA methylation from vegetative and gametic cells of each mating type and from zygotes. We identified 361 gametic genes with mating type-specific expression patterns and 627 genes that are specifically induced in zygotes; furthermore, these sex-related gene sets were enriched for secretory pathway and alga-specific genes. We also examined the C. reinhardtii nuclear methylation map with base-level resolution at different life cycle stages. Despite having low global levels of nuclear methylation, we detected 23 hypermethylated loci in gene-poor, repeat-rich regions. We observed mating type-specific differences in chloroplast DNA methylation levels in plus versus minus mating type gametes followed by chloroplast DNA hypermethylation in zygotes. Lastly, we examined the expression of candidate DNA methyltransferases and found three, DMT1a, DMT1b, and DMT4, that are differentially expressed during the life cycle and are candidate DNA methylases. The expression and methylation data we present provide insight into cell type-specific transcriptional and epigenetic programs during key stages of the C. reinhardtii life cycle.Chlamydomonas reinhardtii is a unicellular, biflagellate species of green alga found primarily in fresh water and soil (Harris et al., 2009). C. reinhardtii is an important reference organism for diverse eukaryotic cellular and metabolic processes, including photosynthetic biology (Rochaix, 2001), flagellar function and biogenesis (Silflow and Lefebvre, 2001), nutrient homeostasis (Grossman, 2000;Merchant et al., 2006;Glaesener et al., 2013), and sexual cycles (Goodenough et al., 2007). The nuclear and chloroplast genomes of C. reinhardtii have been fully sequenced, enabling genomic and epigenomic analyses (Maul et al., 2002;Merchant et al., 2007). The approximately 112-Mb haploid C. reinhardtii nuclear genome comprises 17 chromosomes. The circular chloroplast DNA (cpDNA) genome is 203 kb and present in 80 to 100 copies per cell that are organized into eight to 10 nucleoprotein complexes called nucleoids, which are distributed through the stroma.Like many unicellular eukaryotes, C. reinhardtii has a biphasic life cycle where haploid cells can reproduce vegetatively by mitotic division or, alternatively, undergo a sexual cycle. Vegetative cells can propagate indefinitely when provided with nutrients and light. Upon nitrogen starvation, however, cells stop dividing and differentiate into gametes whose mating type (plus or minus) is determined genetically by an approximately 300-kb mating type locus on chromosome 6, with two haplotypes, MT+ and MT2 (Umen, 2011; De Hoff et al.,...

Chromosome-level genome assembly and transcriptome of the green algaChromochloris zofingiensisilluminates astaxanthin production

“…Additionally, errors in gene models, especially in terminal regions, may result in inaccurate localization predictions. The predicted distribution is similar to what has been noted for C. reinhardtii (29).…”

Seaweed reproductive biology: environmental and genetic controls

“…From a molecular perspective, the factors involved in gamete formation, fusion and meiosis remain unknown for the vast majority of algal groups. Most of our knowledge is based on extensive genetic studies involving the green algal model organism Chlamydomonas , Lopez et al 2015. In the following section we draw on the knowledge of Chlamydomonas to investigate the extent to which the molecular mechanisms involved in life cycle transitions are conserved among algae in general (Figure 2).…”

Gene Regulatory Networks for the Haploid-to-Diploid Transition of Chlamydomonas reinhardtii

“…Another EZ transcriptome study by Lopez et al (2015) reported a total of 627 zygote-specific gene based on 4-fold up-regulation by RNA-seq, which is more than twice as large as our EZ-core. We found that the difference is mainly due to the inclusion of low-expressed genes (144 models with , 2 FPKM), g-lysin induced genes (60 models), and multiple models for the same gene (30 cases).…”

“…Although 203/ 253 members of the EZ-core were previously identified as zygote-specific genes by Lopez et al (2015) and 30/ 159 of the gL+EZ as g-lysin induced genes by Ning et al (2013), these earlier studies offered annotations but not detailed analyses. Therefore, we have gone on to analyze these coexpressed gene clusters, focusing on which functional systems are enriched in the EZ transcriptome and assessing the differences among EZ-core/gL+EZ/ gL-EZ gene contents.…”

“…The molecular details of the zygote differentiation program have been explored by a transcriptome analysis (Lopez et al, 2015), which reported ;600 zygote-specific genes. However, further details of the regulatory networks for the early-zygote developmental pathway, and the functional contexts of the zygote-specific genes for zygote differentiation, are largely unexplored.…”