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1. Complete Chloroplast Genome of an Endophytic Ostreobium sp. (Ostreobiaceae) from the U.S. Virgin Islands

   https://doi.org/10.1128/mra.00272-23  

   Alesmail, Mustafa ; Becerra, Yulissa ; Betancourt, Kimberly J. ; Bracy, Shelly M. ; Castro, Anevay T. ; Cea, Cynthia ; Chavez, Justin ; Del Angel, Janet ; Diaz, Edgar ; Diaz-Guzman, Yael ; et al ( May 2023 , Microbiology Resource Announcements)

   Dennehy, John J. (Ed.)

   ABSTRACT We present the complete chloroplast genome sequence of an endophytic Ostreobium sp. isolated from a 19th-century coralline red algal specimen from St. Croix, U.S. Virgin Islands. The chloroplast genome is 84,848 bp in length, contains 114 genes, and has a high level of gene synteny to other Ostreobiaceae. 

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2. Complete Chloroplast Genome of Topotype Material of the Coast Live Oak Quercus agrifolia Née var. agrifolia (Fagaceae) from California

   https://doi.org/10.1128/mra.00004-22  

   Garcia, Adam N. ; Ramos, Jennifer Hernandez ; Mendoza, Aileen G. ; Muhrram, Asmahan ; Vidauri, Jessica M. ; Hughey, Jeffery R. ( April 2022 , Microbiology Resource Announcements)

   Stajich, Jason E. (Ed.)

   ABSTRACT Here, we present the chloroplast genome sequence of Quercus agrifolia Née, the California live oak, an ecologically important oak species along the coast of California. The genome is 161,283 bp in length, encodes 132 genes, and has a high level of gene synteny to other Fagaceae. 

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3. Multiple sgRNAs for one-step inactivation of the duplicated acetyl-coenzyme A carboxylase 2 ( ACC2 ) genes in Brassica napus

   https://doi.org/10.1093/plphys/kiac069  

   LaManna, Lisa M. ; Parulekar, Mugdha S. ; Maliga, Pal ( February 2022 , Plant Physiology)

   Efficient plastid transformation in Arabidopsis (Arabidopsis thaliana) requires genetic lines that are hypersensitive to spectinomycin due to the absence of a chloroplast acetyl-coenzyme A carboxylase (ACCase) encoded in the acetyl-coenzyme A carboxylase 2 (ACC2) nuclear gene. To obtain plastid transformation-competent oilseed rape (Brassica napus), we inactivated all nuclear encoded, chloroplast targeted ACCase copies using CRISPR–Cas9. Brassica napus (2n = 38, AACC) is a recent interspecific hybrid of Brassica rapa (2n = 20, AA) and B. oleracea (2n = 18, CC) and is expected to have at least two ACC2 copies, one from each parent. The sequenced genome has two ACC2 copies, one that is B. rapa-like and one that is B. oleracea-like. We designed single-guide RNAs (sgRNAs) that could simultaneously inactivate both nuclear ACC2 copies. We expressed Cas9 from a chimeric egg cell promoter 1.2 (EC1.2p) known to yield homozygous or biallelic mutants in Arabidopsis in the T1 generation. To maximize the probability of functionally inactivating both orthologs in a single step, each of the two vectors carried four sgRNAs. Four T0 transgenic lines were obtained by Agrobacterium tumefaciens-mediated hypocotyl transformation. Amplicon sequencing confirmed mutations in ACC2 genes in 10 T1 progeny, in seven of which no wild-type (WT) copy remained. The B. napus T2 seedlings lacking WT ACC2 gene copies exhibited a spectinomycin hypersensitive phenotype, suggesting that they will be a useful resource for chloroplast genome transformation.

    

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4. Comparative DNA sequence analyses of Pyramimonas parkeae (Prasinophyceae) chloroplast genomes

   https://doi.org/10.1111/jpy.12515  

   Satjarak, Anchittha ; Graham, Linda E. ; Wood, ed., M. ( March 2017 , Journal of Phycology)

   Prasinophytes form a paraphyletic assemblage of early diverging green algae, which have the potential to reveal the traits of the last common ancestor of the main two green lineages: (i) chlorophyte algae and (ii) streptophyte algae. Understanding the genetic composition of prasinophyte algae is fundamental to understanding the diversification and evolutionary processes that may have occurred in both green lineages. In this study, we sequenced the chloroplast genome ofPyramimonas parkeaeNIES254 and compared it with that ofP. parkeaeCCMP726, the only other fully sequencedP. parkeaechloroplast genome. The results revealed thatP. parkeaechloroplast genomes are surprisingly variable. The chloroplast genome ofNIES254 was larger than that ofCCMP726 by 3,204 bp, theNIES254 large single copy was 288 bp longer, the small single copy was 5,088 bp longer, and theIRwas 1,086 bp shorter than that ofCCMP726. Similarity values of the two strains were almost zero in four large hot spot regions. Finally, the strains differed in copy number for three protein‐coding genes:ycf20,psaC, andndhE. Phylogenetic analyses using 16S and 18SrDNAandrbcLsequences resolved a clade consisting of these twoP. parkeaestrains and a clade consisting of these plus otherPyramimonasisolates. These results are consistent with past studies indicating that prasinophyte chloroplast genomes display a higher level of variation than is commonly found among land plants. Consequently, prasinophyte chloroplast genomes may be less useful for inferring the early history of Viridiplantae than has been the case for land plant diversification.

    

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5. Fine‐Scale Geographic Variation of Cladocopium in Acropora hyacinthus Across the Palauan Archipelago

   https://doi.org/10.1002/ece3.70650  

   Armstrong, Katrina_C ; Lippert, Marilla ; Hanson, Erik ; Nestor, Victor ; Cornwell, Brendan ; Walker, Nia_S ; Golbuu, Yimnang ; Palumbi, Stephen_R ( December 2024 , Ecology and Evolution)

   Symbiont genotype plays a vital role in the ability of a coral host to tolerate rising ocean temperatures, with some members of the family Symbiodiniaceae possessing more thermal tolerance than others. While existing studies on genetic structure in symbiont populations have focused on broader scales of 10–100 s of km, there is a noticeable gap in understanding the seascape genetics of coral symbionts at finer—yet ecologically and evolutionarily relevant—scales. Here, we mapped short reads from 271 holobiont genome libraries of individualAcropora hyacinthuscolonies to protein coding genes from the chloroplast genome to identify patterns of symbiont population genetic structure. Utilizing this low‐pass method, we assayed over 13,000 bases from every individual, enabling us to discern genetic variation at a finer geographic scale than previously reported at the population level. We identified five commonCladocopiumchloroplast SNP profiles present across Palau, with symbiont structure varying between Northern, mid‐lagoon, and Southern regions, and inshore–offshore gradients. Although symbiont populations within reefs typically contained significant genetic diversity, we also observed genetic structure between some nearby reefs. To explore whether coral hosts retain their symbionts post‐transplantation, we experimentally moved 79 corals from their native reefs to transplant sites with both different and similar chloroplast SNP profiles. Over 12 months, we observed 12 instances where transplanted corals changed profiles, often transitioning to a profile present in adjacent corals. Symbiont genetic structure between reefs suggests either low dispersal of symbionts or environmental selection against dispersers, both resulting in the potential for significant adaptive differentiation across reef environments. The extent to which local corals and their symbionts are co‐adapted to environments on a reef‐by‐reef scale is currently poorly known. Chloroplast sequences offer an additional tool for monitoring symbiont genetics and coral–symbiont interactions when assisted migration is used in restoration.

    

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