Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium

Iha, Cíntia; Dougan, Katherine E.; Varela, Javier A.; Ávila, Viridiana; Jackson, Christopher J.; Bogaert, Kenny A.; Chen, Yibi; Judd, Louise M.; Wick, Ryan R.; Holt, Kathryn E.; Pasella, Marisa M.; Ricci, Francesco; Repetti, Sonja I.; Medina, Mónica; Marcelino, Vanessa R.; Chan, Cheong Xin; Verbruggen, Heroen

doi:10.1016/j.cub.2021.01.018

Cited by 43 publications

(40 citation statements)

References 101 publications

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“…Sample underlying genome of Arctic Alaria. An interesting analogue system is the endolithic green alga Ostreobium, whose genome clearly exhibits an expansion of light-harvesting proteins and loss of photoprotective and photoreceptor genes, presumed adaptations to low and variable light environments (Iha et al 2021).…”

Section: Discussionmentioning

confidence: 99%

Whole‐genome sequencing reveals forgotten lineages and recurrent hybridizations within the kelp genus Alaria (Phaeophyceae)

Bringloe

Zaparenkov

Starko

et al. 2021

Journal of Phycology

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The genomic era continues to revolutionize our understanding of the evolution of biodiversity. In phycology, emphasis remains on assembling nuclear and organellar genomes, leaving the full potential of genomic datasets to answer long-standing questions about the evolution of biodiversity largely unexplored. Here, we used whole-genome sequencing (WGS) datasets to survey species diversity in the kelp genus Alaria, compare phylogenetic signals across organellar and nuclear genomes, and specifically test whether phylogenies behave like trees or networks. Genomes were sequenced from across the global distribution of Alaria (including Alaria crassifolia, A. praelonga, A. crispa, A. marginata, and A. esculenta), representing over 550 GB of data and over 2.2 billion paired reads. Genomic datasets retrieved 3,814 and 4,536 single-nucleotide polymorphisms (SNPs) for mitochondrial and chloroplast genomes, respectively, and upwards of 148,542 high-quality nuclear SNPs. WGS revealed an Arctic lineage of Alaria, which we hypothesize represents the synonymized taxon A. grandifolia. The SNP datasets also revealed inconsistent topologies across genomic compartments, and hybridization (i.e., phylogenetic networks) between Pacific A. praelonga, A. crispa, and putative A. grandifolia, and between some lineages of the A. marginata complex. Our analysis demonstrates the potential for WGS data to advance our understanding of evolution and biodiversity beyond amplicon sequencing, and that hybridization is potentially an important mechanism contributing to novel lineages within Alaria. We also emphasize the importance of surveying phylogenetic signals across organellar and nuclear genomes, such that models of mixed ancestry become integrated into our evolutionary and taxonomic understanding.

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Section: Discussionmentioning

confidence: 99%

Whole‐genome sequencing reveals forgotten lineages and recurrent hybridizations within the kelp genus Alaria (Phaeophyceae)

Bringloe

Zaparenkov

Starko

et al. 2021

Journal of Phycology

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“…After filtering of scaffolds, we followed the workflow described in Iha et al (2021) to predict protein-coding genes from the assembled genome sequences. Novel repeat families were identified with RepeatModeler v1.0.11 (http://www.repeatmasker.org/RepeatModeler/).…”

Section: Ab Initio Prediction Of Protein-coding Genesmentioning

confidence: 99%

“…The copyright holder for this preprint this version posted October 5, 2021. ; https://doi.org/10.1101/2021.10.04.463119 doi: bioRxiv preprint Most genomic studies in the Core Chlorophyta have investigated taxon-specific innovations that underpin their ecological success under a range of environmental pressures including high acidity (Hirooka et al, 2017), high salinity (Foflonker et al, 2015), polar conditions (Blanc et al, 2012;Zhang et al, 2020), and as symbionts (Blanc et al, 2010;Arriola et al, 2018;Iha et al, 2021). Members of the Core Chlorophyta, particularly the UTC clade, also show high morphological diversity (Table S1), including unicellular, siphonous, and multicellular forms, which appear to have arisen on multiple occasions in both the Chlorophyceae and Ulvophyceae (Featherston et al, 2017;De Clerck et al, 2018;Del Cortona et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algae

Repetti

Iha

Uthanumallian

et al. 2021

Preprint

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The genomic diversity underpinning high ecological and species diversity in the green algae (Chlorophyta) remains little known. Here, we aimed to track genome evolution in the Chlorophyta, focusing on loss and gain of homologous genes, and lineage-specific innovations of the Core Chlorophyta. We generated a high-quality nuclear genome for pedinophyte YPF701, a sister lineage to others in the Core Chlorophyta, and incorporated this genome in a comparative analysis with 25 other genomes from diverse Viridiplantae taxa. The nuclear genome of pedinophyte YPF701 has an intermediate size and gene number between those of most early-diverging prasinophytes and the remainder of the Core Chlorophyta. Our results suggest positive selection for genome streamlining in Pedinophyceae, independent from genome minimisation observed among prasinophyte lineages. Genome expansion was predicted along the branch leading to the UTC clade (classes Ulvophyceae, Trebouxiophyceae and Chlorophyceae) after divergence from their common ancestor with pedinophytes, with genomic novelty implicated in a range of basic biological functions. These results emphasise multiple independent signals of genome minimisation within the Chlorophyta, as well as the genomic novelty arising prior to diversification in the UTC clade, which may underpin the success of this species-rich clade in a diversity of habitats.

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“…Most genomic studies in the core Chlorophyta have investigated taxon‐specific innovations that underpin their ecological success under a range of environmental pressures including high acidity (Hirooka et al ., 2017), high salinity (Foflonker et al ., 2015), polar conditions (Blanc et al ., 2012; Zhang et al ., 2020) and as symbionts (Blanc et al ., 2010; Arriola et al ., 2018; Iha et al ., 2021). Members of the core Chlorophyta, particularly the UTC clade, also show high morphological diversity (Supporting Information Table S1), including unicellular, siphonous and multicellular forms, which appear to have arisen on multiple occasions in both the Chlorophyceae and Ulvophyceae (De Clerck et al ., 2018; Featherston et al ., 2018; Del Cortona et al ., 2020).…”

Section: Introductionmentioning

confidence: 99%

Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algae

et al. 2022

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Summary The genomic diversity underpinning high ecological and species diversity in the green algae (Chlorophyta) remains little known. Here, we aimed to track genome evolution in the Chlorophyta, focusing on loss and gain of homologous genes, and lineage‐specific innovations of the core Chlorophyta. We generated a high‐quality nuclear genome for pedinophyte YPF701, a sister lineage to others in the core Chlorophyta and incorporated this genome in a comparative analysis with 25 other genomes from diverse Viridiplantae taxa. The nuclear genome of pedinophyte YPF701 has an intermediate size and gene number between those of most prasinophytes and the remainder of the core Chlorophyta. Our results suggest positive selection for genome streamlining in the Pedinophyceae, independent from genome minimisation observed among prasinophyte lineages. Genome expansion was predicted along the branch leading to the UTC clade (classes Ulvophyceae, Trebouxiophyceae and Chlorophyceae) after divergence from their last common ancestor with pedinophytes, with genomic novelty implicated in a range of basic biological functions. Results emphasise multiple independent signals of genome minimisation within the Chlorophyta, as well as the genomic novelty arising before diversification in the UTC clade, which may underpin the success of this species‐rich clade in a diversity of habitats.

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Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium

Cited by 43 publications

References 101 publications

Whole‐genome sequencing reveals forgotten lineages and recurrent hybridizations within the kelp genus Alaria (Phaeophyceae)

Whole‐genome sequencing reveals forgotten lineages and recurrent hybridizations within the kelp genus Alaria (Phaeophyceae)

Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algae

Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algae

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