The mitochondrial and chloroplast genomes of the haptophyte Chrysochromulina tobin contain unique repeat structures and gene profiles

Hovde, Blake T.; Starkenburg, Shawn R.; Hunsperger, Heather M.; Mercer, Laina D.; Deodato, Chloe R.; Jha, Ramesh K.; Chertkov, Olga; Monnat, Raymond J.; Cattolico, Rose Ann

doi:10.1186/1471-2164-15-604

Cited by 34 publications

(29 citation statements)

References 103 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In contrast to the above findings, other plastid phylogenies find cryptophytes and haptophytes more closely related to one another than they are to stramenopiles (e.g., [ 79 - 81 ]). Importantly, a shared, horizontally transferred rpl36 gene encoded in the chloroplasts of only cryptophytes and haptophytes strongly indicates a sister relationship between these two taxa [ 82 , 83 ]. If haptophyte and cryptophyte plastids are indeed more closely related to one another than to stramenopile plastids, the xenologous por genes would have to have been transferred from stramenopiles to haptophytes via HGT early in the evolution of the haptophytes.…”

Section: Resultsmentioning

confidence: 99%

Extensive horizontal gene transfer, duplication, and loss of chlorophyll synthesis genes in the algae

2015

Self Cite

View full text Add to dashboard Cite

BackgroundTwo non-homologous, isofunctional enzymes catalyze the penultimate step of chlorophyll a synthesis in oxygenic photosynthetic organisms such as cyanobacteria, eukaryotic algae and land plants: the light-independent (LIPOR) and light-dependent (POR) protochlorophyllide oxidoreductases. Whereas the distribution of these enzymes in cyanobacteria and land plants is well understood, the presence, loss, duplication, and replacement of these genes have not been surveyed in the polyphyletic and remarkably diverse eukaryotic algal lineages.ResultsA phylogenetic reconstruction of the history of the POR enzyme (encoded by the por gene in nuclei) in eukaryotic algae reveals replacement and supplementation of ancestral por genes in several taxa with horizontally transferred por genes from other eukaryotic algae. For example, stramenopiles and haptophytes share por gene duplicates of prasinophytic origin, although their plastid ancestry predicts a rhodophytic por signal. Phylogenetically, stramenopile pors appear ancestral to those found in haptophytes, suggesting transfer from stramenopiles to haptophytes by either horizontal or endosymbiotic gene transfer. In dinoflagellates whose plastids have been replaced by those of a haptophyte or diatom, the ancestral por genes seem to have been lost whereas those of the new symbiotic partner are present. Furthermore, many chlorarachniophytes and peridinin-containing dinoflagellates possess por gene duplicates.In contrast to the retention, gain, and frequent duplication of algal por genes, the LIPOR gene complement (chloroplast-encoded chlL, chlN, and chlB genes) is often absent. LIPOR genes have been lost from haptophytes and potentially from the euglenid and chlorarachniophyte lineages. Within the chlorophytes, rhodophytes, cryptophytes, heterokonts, and chromerids, some taxa possess both POR and LIPOR genes while others lack LIPOR. The gradual process of LIPOR gene loss is evidenced in taxa possessing pseudogenes or partial LIPOR gene compliments. No horizontal transfer of LIPOR genes was detected.ConclusionsWe document a pattern of por gene acquisition and expansion as well as loss of LIPOR genes from many algal taxa, paralleling the presence of multiple por genes and lack of LIPOR genes in the angiosperms. These studies present an opportunity to compare the regulation and function of por gene families that have been acquired and expanded in patterns unique to each of various algal taxa.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0286-4) contains supplementary material, which is available to authorized users.

show abstract

Section: Resultsmentioning

confidence: 99%

Extensive horizontal gene transfer, duplication, and loss of chlorophyll synthesis genes in the algae

2015

Self Cite

View full text Add to dashboard Cite

show abstract

“…tobin nuclear and chloroplast genomes. For example, a duplicated nuclear-encoded por gene that is indispensable for chlorophyll synthesis has a chlorophytic algal origin [ 29 ] while the ribosomal subunit rpl36 [ 30 ], xanthorhodopsin and RuBisCO activase (presented in this work) appear to be of bacterial origin [ 31 ].…”

Section: Resultsmentioning

confidence: 99%

“…Complete C . tobin mitochondrial and chloroplast genomes are presented in detail elsewhere [ 30 ]. Briefly, the 34,288 kb mitochondrial genome encodes 48 genes.…”

Section: Resultsmentioning

confidence: 99%

Genome Sequence and Transcriptome Analyses of Chrysochromulina tobin: Metabolic Tools for Enhanced Algal Fitness in the Prominent Order Prymnesiales (Haptophyceae)

et al. 2015

Self Cite

View full text Add to dashboard Cite

Haptophytes are recognized as seminal players in aquatic ecosystem function. These algae are important in global carbon sequestration, form destructive harmful blooms, and given their rich fatty acid content, serve as a highly nutritive food source to a broad range of eco-cohorts. Haptophyte dominance in both fresh and marine waters is supported by the mixotrophic nature of many taxa. Despite their importance the nuclear genome sequence of only one haptophyte, Emiliania huxleyi (Isochrysidales), is available. Here we report the draft genome sequence of Chrysochromulina tobin (Prymnesiales), and transcriptome data collected at seven time points over a 24-hour light/dark cycle. The nuclear genome of C. tobin is small (59 Mb), compact (∼40% of the genome is protein coding) and encodes approximately 16,777 genes. Genes important to fatty acid synthesis, modification, and catabolism show distinct patterns of expression when monitored over the circadian photoperiod. The C. tobin genome harbors the first hybrid polyketide synthase/non-ribosomal peptide synthase gene complex reported for an algal species, and encodes potential anti-microbial peptides and proteins involved in multidrug and toxic compound extrusion. A new haptophyte xanthorhodopsin was also identified, together with two “red” RuBisCO activases that are shared across many algal lineages. The Chrysochromulina tobin genome sequence provides new information on the evolutionary history, ecology and economic importance of haptophytes.

show abstract

“…Simultaneously, the NAABB team used genomic and RNAseq transcriptome data produced by the U.S. Department of Energy Joint Genome Institute to analyze the production of hydrocarbons by B. braunii. Although annotation and comparative genomics analyses of the data continue, the sequence data developed by NAABB have thus far allowed us to conduct a pangenomic comparison of the chloroplast and mitochondrial genomes of Nannochloropsis and Chrysochromulina with other algal taxa [30,31]. Many of the organellar gene modifications observed in these algae are novel and deviate from conserved orthologs found across the tree of life; moreover, many such modifications have been aquired via lateral gene transfer.…”

Section: Genome Sequencingmentioning

confidence: 98%

Review of the algal biology program within the National Alliance for Advanced Biofuels and Bioproducts

et al. 2017

Self Cite

View full text Add to dashboard Cite

In 2010, when the National Alliance for Advanced Biofuels and Bioproducts (NAABB) consortium began, little was known about the molecular basis of algal biomass or oil production. Very few algal genome sequences were available and efforts to identify the best-producing wild species through bioprospecting approaches had largely stalled after the U.S. Department of Energy's Aquatic Species Program. This lack of knowledge included how reduced carbon was partitioned into storage products like triglycerides or starch and the role played by metabolite remodeling in the accumulation of energy-dense storage products. Furthermore, genetic transformation and metabolic engineering approaches to improve algal biomass and oil yields were in their infancy. Genome sequencing and transcriptional profiling were becoming less expensive, however; and the tools to annotate gene expression profiles under various growth and engineered conditions were just starting to be developed for algae. It was in this context that an integrated algal biology program was introduced in the NAABB to address the greatest constraints limiting algal biomass yield. This review describes the NAABB algal biology program, including hypotheses, research objectives, and strategies to move algal biology research into the twenty-first century and to realize the greatest potential of algae biomass systems to produce biofuels.

show abstract

The mitochondrial and chloroplast genomes of the haptophyte Chrysochromulina tobin contain unique repeat structures and gene profiles

Cited by 34 publications

References 103 publications

Extensive horizontal gene transfer, duplication, and loss of chlorophyll synthesis genes in the algae

Extensive horizontal gene transfer, duplication, and loss of chlorophyll synthesis genes in the algae

Genome Sequence and Transcriptome Analyses of Chrysochromulina tobin: Metabolic Tools for Enhanced Algal Fitness in the Prominent Order Prymnesiales (Haptophyceae)

Review of the algal biology program within the National Alliance for Advanced Biofuels and Bioproducts

Contact Info

Product

Resources

About