The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants

Li, Linzhou; Wang, Sibo; Wang, Hongli; Sahu, Sunil Kumar; Marin, Birger; Li, Haoyuan; Xu, Yan; Liang, Hongping; Zhen, Li; Cheng, Shifeng; Reder, Tanja; Çebi, Zehra; Wittek, Sebastian; Petersen, Morten; Melkonian, Barbara; Du, Hongli; Yang, Huanming; Wang, Jian; Wong, Gane Ka‐Shu; Xu, Xun; Liu, Xin; Peer, Yves Van de; Melkonian, Michael; Liu, Huan

doi:10.1038/s41559-020-1221-7

Cited by 97 publications

(137 citation statements)

References 91 publications

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“…The asterisk represents the number of kinase‐associated domains except transposon/virus‐related domains. The plant phylogeny is based on previous studies (Sanchez‐Baracaldo et al ., 2017; Gitzendanner et al ., 2018; One Thousand Plant Transcriptomes Initiative, 2019; Li et al ., 2020). (b) Relationship among domain repertoires of glaucophyte, chlorophyte, charophyte, and land plant RLKs.…”

Section: Resultsmentioning

confidence: 99%

Flourishing in water: the early evolution and diversification of plant receptor‐like kinases

Gong

Han

2021

The Plant Journal

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SUMMARY Receptor‐like kinases (RLKs) play significant roles in mediating innate immunity and development of plants. The evolution of plant RLKs has been characterized by extensive variation in copy numbers and domain configurations. However, much remains unknown about the origin, evolution, and early diversification of plant RLKs. Here, we perform phylogenomic analyses of RLKs across plants (Archaeplastida), including embryophytes, charophytes, chlorophytes, prasinodermophytes, glaucophytes, and rhodophytes. We identify the presence of RLKs in all the streptophytes (land plants and charophytes), nine out of 18 chlorophytes, one prasinodermophyte, and one glaucophyte, but not in rhodophytes. Interestingly, the copy number of RLKs increased drastically in streptophytes after the split of the clade of Mesostigmatophyceae and Chlorokybophyceae and other streptophytes. Moreover, phylogenetic analyses suggest RLKs from charophytes form diverse distinct clusters, and are dispersed along the diversity of land plant RLKs, indicating that RLKs have extensively diversified in charophytes and charophyte RLKs seeded the major diversity of land plant RLKs. We identify at least 81 and 76 different kinase‐associated domains for charophyte and land plant RLKs, 23 of which are shared, suggesting that RLKs might have evolved in a modular fashion through frequent domain gains or losses. We also detect signatures of positive selection for many charophyte RLK groups, indicating potential functions in host–microbe interaction. Taken together, our findings provide significant insights into the early evolution and diversification of plant RLKs and the ancient evolution of plant–microbe symbiosis.

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Section: Resultsmentioning

confidence: 99%

Flourishing in water: the early evolution and diversification of plant receptor‐like kinases

Gong

Han

2021

The Plant Journal

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“…However, crucial steps in green plant terrestrialization have not been fully understood. Viridiplantae comprise two major clades: Streptophyta, which contains streptophyte algae and land plants (embryophytes), and Chlorophyta, which includes all remaining green algae (with exception of Prasinodermophyta, which split before the divergence of Streptophyta and Chlorophyta) 24 (Fig. 1 ).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide analyses across Viridiplantae reveal the origin and diversification of small RNA pathway-related genes

Wang

Liang

et al. 2021

Commun Biol

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Small RNAs play a major role in the post-transcriptional regulation of gene expression in eukaryotes. Despite the evolutionary importance of streptophyte algae, knowledge on small RNAs in this group of green algae is almost non-existent. We used genome and transcriptome data of 34 algal and plant species, and performed genome-wide analyses of small RNA (miRNA & siRNA) biosynthetic and degradation pathways. The results suggest that Viridiplantae started to evolve plant-like miRNA biogenesis and degradation after the divergence of the Mesostigmatophyceae in the streptophyte algae. We identified two major evolutionary transitions in small RNA metabolism in streptophyte algae; during the first transition, the origin of DCL-New, DCL1, AGO1/5/10 and AGO4/6/9 in the last common ancestor of Klebsormidiophyceae and all other streptophytes could be linked to abiotic stress responses and evolution of multicellularity in streptophytes. During the second transition, the evolution of DCL 2,3,4, and AGO 2,3,7 as well as DRB1 in the last common ancestor of Zygnematophyceae and embryophytes, suggests their possible contribution to pathogen defense and antibacterial immunity. Overall, the origin and diversification of DICER and AGO along with several other small RNA pathway-related genes among streptophyte algae suggested progressive adaptations of streptophyte algae during evolution to a subaerial environment.

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“…They are called Archaeplastida ( Adl et al, 2005 ) and radiated into three major lineages, the Glaucophyta, the Rhodophyceae or red algae, and the Chloroplastida ( Adl et al, 2005 ), also known as Viridiplantae ( Cavalier-Smith, 1981 ). Recently, Li et al (2020) described the new phylum/division Prasinodermophyta and demonstrated that Prasinodermophyta belongs to Viridiplantae ( Li et al, 2020 ).…”

Section: Evolution and Plastid Architecture In Stramenopilesmentioning

confidence: 99%

Lipid Droplets in Unicellular Photosynthetic Stramenopiles

et al. 2021

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The Heterokonta or Stramenopile phylum comprises clades of unicellular photosynthetic species, which are promising for a broad range of biotechnological applications, based on their capacity to capture atmospheric CO2 via photosynthesis and produce biomolecules of interest. These molecules include triacylglycerol (TAG) loaded inside specific cytosolic bodies, called the lipid droplets (LDs). Understanding TAG production and LD biogenesis and function in photosynthetic stramenopiles is therefore essential, and is mostly based on the study of a few emerging models, such as the pennate diatom Phaeodactylum tricornutum and eustigmatophytes, such as Nannochloropsis and Microchloropsis species. The biogenesis of cytosolic LD usually occurs at the level of the endoplasmic reticulum. However, stramenopile cells contain a complex plastid deriving from a secondary endosymbiosis, limited by four membranes, the outermost one being connected to the endomembrane system. Recent cell imaging and proteomic studies suggest that at least some cytosolic LDs might be associated to the surface of the complex plastid, via still uncharacterized contact sites. The carbon length and number of double bonds of the acyl groups contained in the TAG molecules depend on their origin. De novo synthesis produces long-chain saturated or monounsaturated fatty acids (SFA, MUFA), whereas subsequent maturation processes lead to very long-chain polyunsaturated FA (VLC-PUFA). TAG composition in SFA, MUFA, and VLC-PUFA reflects therefore the metabolic context that gave rise to the formation of the LD, either via an early partitioning of carbon following FA de novo synthesis and/or a recycling of FA from membrane lipids, e.g., plastid galactolipids or endomembrane phosphor- or betaine lipids. In this review, we address the relationship between cytosolic LDs and the complex membrane compartmentalization within stramenopile cells, the metabolic routes leading to TAG accumulation, and the physiological conditions that trigger LD production, in response to various environmental factors.

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The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants

Cited by 97 publications

References 91 publications

Flourishing in water: the early evolution and diversification of plant receptor‐like kinases

Flourishing in water: the early evolution and diversification of plant receptor‐like kinases

Genome-wide analyses across Viridiplantae reveal the origin and diversification of small RNA pathway-related genes

Lipid Droplets in Unicellular Photosynthetic Stramenopiles

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