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1. CHLOROPLAST MRNAS ARE 30 POLYURIDYLYLATED IN THE GREEN ALGA PITHOPHORA ROETTLERI (CLADOPHORALES)

   https://doi.org/DOI:10.1111/jpy.13033-20-051  

   Meade, MJ ; Proulex, GCR ; Manoylov, KM ; Cahoon, AB ( October 2020 , Journal of phycology)

   Species within the green algal order Cladophorales have an unconventional plastome structure where individual coding regions or small numbers of genes occur as linear single-stranded DNAs folded into hairpin structures. Another group of photosynthetic organisms with an equivalently reduced chloroplast genome are the peridinin dinoflagellates of the Alveolata eukaryotic lineage whose plastomes are mini-circles carrying one or a few genes required for photosynthesis. One unusual aspect of the Alveolata is the polyuridylylation of mRNA 30 ends among peridinin dinoflagellates and the chromerid algae. This study was conducted to understand if an unconventional highly reduced plastome structure co-occurs with unconventional RNA processing. To address this, the 50 and 30 mRNA termini of the known chloroplast genes of Pithophora roettleri (order Cladophorales) were analyzed for evidence of post-transcriptional processing. Circular Reverse Transcriptase PCR (cRT-PCR) followed by deep sequencing of the amplicons was used to analyze 50 and 30 mRNA termini. Evidence of several processing events were collected, most notably the 30 termini of six of the eight genes were polyuridylylated, which has not been reported for any lineage outside of the Alveolata. Other processing events include poly(A) and heteropolymeric 30 additions, 50 primary transcript start sites, as well as the presence of circularized RNAs. Five other species representing other green algal lineages were also tested and poly(U) additions appear to be limited to the order Cladophorales. These results demonstrate that chloroplast mRNA polyuridylylation is not the sole provenance of photosynthetic alveolates and may have convergently evolved in two distinct photosynthetic lineages. 

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2. Mitochondrial mRNA Processing in the Chlorophyte Alga Pediastrum duplex and Streptophyte Alga Chara vulgaris Reveals an Evolutionary Branch in Mitochondrial mRNA Processing

   https://doi.org/10.3390/plants10030576  

   Proulex, Grayson C. ; Meade, Marcus J. ; Manoylov, Kalina M. ; Cahoon, A. Bruce ( March 2021 , Plants)

   null (Ed.)

   Mitochondria carry the remnant of an ancestral bacterial chromosome and express those genes with a system separate and distinct from the nucleus. Mitochondrial genes are transcribed as poly-cistronic primary transcripts which are post-transcriptionally processed to create individual translationally competent mRNAs. Algae post-transcriptional processing has only been explored in Chlamydomonas reinhardtii (Class: Chlorophyceae) and the mature mRNAs are different than higher plants, having no 5′ UnTranslated Regions (UTRs), much shorter and more variable 3′ UTRs and polycytidylated mature mRNAs. In this study, we analyzed transcript termini using circular RT-PCR and PacBio Iso-Seq to survey the 3′ and 5′ UTRs and termini for two green algae, Pediastrum duplex (Class: Chlorophyceae) and Chara vulgaris (Class: Charophyceae). This enabled the comparison of processing in the chlorophyte and charophyte clades of green algae to determine if the differences in mitochondrial mRNA processing pre-date the invasion of land by embryophytes. We report that the 5′ mRNA termini and non-template 3′ termini additions in P. duplex resemble those of C. reinhardtii, suggesting a conservation of mRNA processing among the chlorophyceae. We also report that C. vulgaris mRNA UTRs are much longer than chlorophytic examples, lack polycytidylation, and are polyadenylated similar to embryophytes. This demonstrates that some mitochondrial mRNA processing events diverged with the split between chlorophytic and streptophytic algae. 

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3. Improved Cladocopium goreaui Genome Assembly Reveals Features of a Facultative Coral Symbiont and the Complex Evolutionary History of Dinoflagellate Genes

   https://doi.org/10.3390/microorganisms10081662  

   Chen, Yibi ; Shah, Sarah ; Dougan, Katherine E. ; van Oppen, Madeleine J. ; Bhattacharya, Debashish ; Chan, Cheong Xin ( August 2022 , Microorganisms)

   Dinoflagellates of the family Symbiodiniaceae are crucial photosymbionts in corals and other marine organisms. Of these, Cladocopium goreaui is one of the most dominant symbiont species in the Indo-Pacific. Here, we present an improved genome assembly of C. goreaui combining new long-read sequence data with previously generated short-read data. Incorporating new full-length transcripts to guide gene prediction, the C. goreaui genome (1.2 Gb) exhibits a high extent of completeness (82.4% based on BUSCO protein recovery) and better resolution of repetitive sequence regions; 45,322 gene models were predicted, and 327 putative, topologically associated domains of the chromosomes were identified. Comparison with other Symbiodiniaceae genomes revealed a prevalence of repeats and duplicated genes in C. goreaui, and lineage-specific genes indicating functional innovation. Incorporating 2,841,408 protein sequences from 96 taxonomically diverse eukaryotes and representative prokaryotes in a phylogenomic approach, we assessed the evolutionary history of C. goreaui genes. Of the 5246 phylogenetic trees inferred from homologous protein sets containing two or more phyla, 35–36% have putatively originated via horizontal gene transfer (HGT), predominantly (19–23%) via an ancestral Archaeplastida lineage implicated in the endosymbiotic origin of plastids: 10–11% are of green algal origin, including genes encoding photosynthetic functions. Our results demonstrate the utility of long-read sequence data in resolving structural features of a dinoflagellate genome, and highlight how genetic transfer has shaped genome evolution of a facultative symbiont, and more broadly of dinoflagellates. 

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4. Chloroplast genome evolution and phylogeny of the early‐diverging charophycean green algae with a focus on the Klebsormidiophyceae and Streptofilum

   https://doi.org/10.1111/jpy.13359  

   Glass, Sarah E. ; McCourt, Richard M. ; Gottschalk, Stephen D. ; Lewis, Louise A. ; Karol, Kenneth G. ( August 2023 , Journal of Phycology)

   The Klebsormidiophyceae are a class of green microalgae observed globally in both freshwater and terrestrial habitats. Morphology‐based classification schemes of this class have been shown to be inadequate due to the simple morphology of these algae, the tendency of morphology to vary in culture versus field conditions, and rampant morphological homoplasy. Molecular studies revealing cryptic diversity have renewed interest in this group. We sequenced the complete chloroplast genomes of a broad series of taxa spanning the known taxonomic breadth of this class. We also sequenced the chloroplast genomes of three strains ofStreptofilum, a recently discovered green algal lineage with close affinity to the Klebsormidiophyceae. Our results affirm the previously hypothesized polyphyly of the genusKlebsormidiumas well as the polyphyly of the nominal species in this genus,K. flaccidum. Furthermore, plastome sequences strongly support the status ofStreptofilumas a distinct, early‐diverging lineage of charophytic algae sister to a clade comprising Klebsormidiophyceae plus Phragmoplastophyta. We also uncovered major structural alterations in the chloroplast genomes of species inKlebsormidiumthat have broad implications regarding the underlying mechanisms of chloroplast genome evolution.

    

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5. Iron Availability Modulates the Response of Endosymbiotic Dinoflagellates to Heat Stress

   https://doi.org/10.1111/jpy.13078  

   Reich, Hannah G. ; Tu, Wan‐Chen ; Rodriguez, Irene B. ; Chou, Yalan ; Keister, Elise F. ; Kemp, Dustin W. ; LaJeunesse, Todd C. ; Ho, Tung‐Yuan ( December 2020 , Journal of Phycology)

   Warming and nutrient limitation are stressors known to weaken the health of microalgae. In situations of stress, access to energy reserves can minimize physiological damage. Because of its widespread requirements in biochemical processes, iron is an important trace metal, especially for photosynthetic organisms. Lowered iron availability in oceans experiencing rising temperatures may contribute to the thermal sensitivity of reef‐building corals, which rely on mutualisms with dinoflagellates to survive. To test the influence of iron concentration on thermal sensitivity, the physiological responses of cultured symbiotic dinoflagellates (genusBreviolum; family Symbiodiniaceae) were evaluated when exposed to increasing temperatures (26 to 30°C) and iron concentrations ranging from replete (500 pM Fe’) to limiting (50 pM Fe’) under a diurnal light cycle with saturating radiance. Declines in photosynthetic efficiency at elevated temperatures indicated sensitivity to heat stress. Furthermore, five times the amount of iron was needed to reach exponential growth during heat stress (50 pM Fe′ at 26–28°C vs. 250 pM Fe′ at 30°C). In treatments where exponential growth was reached,Breviolum psygmophilumgrew faster thanB.minutum, possibly due to greater cellular contents of iron and other trace metals. The metal composition ofB.psygmophilumshifted only at the highest temperature (30°C), whereas changes inB.minutumwere observed at lower temperatures (28°C). The influence of iron availability in modulating each alga’s response to thermal stress suggests the importance of trace metals to the health of coral‐algal mutualisms. Ultimately, a greater ability to acquire scarce metals may improve the tolerance of corals to physiological stressors and contribute to the differences in performance associated with hosting one symbiont species over another.

    

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