The genomes of polyextremophilic cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions

Rossoni, Alessandro W.; Price, Dana C.; Seger, Mark; Lyska, Dagmar; Lammers, Peter J.; Bhattacharya, Debashish; Weber, Andreas P.M.

doi:10.7554/elife.45017

Cited by 62 publications

(61 citation statements)

References 137 publications

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“…table 1) 45 . Additionally, 28 genomes from Chlorophytes, Rhodophytes 46 and one Glaucophyte were downloaded either from the Refseq, GenBank or the JGI Genome Portal 47 (Suppl. table 1).…”

Section: Methodsmentioning

confidence: 99%

Major changes in plastid protein import and the origin of the Chloroplastida

Knopp

Garg

Handrich

et al. 2019

Preprint

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10While core components of plastid protein import (Toc and Tic) and the principle of using N-11 terminal targeting sequences (NTS) are conserved, lineage-specific differences are known. 12Rhodophytes and glaucophytes carry a conserved NTS motif, which was lost in the green 13 lineage that also added novel proteins to Toc and Tic. Here we compare the components of 14 plastid protein import and generated RNA-Seq, pigment profile and trans-electron microscopy 15data based on high-light stress from representatives of the three archaeplastidal groups. In light 16 of plastid protein targeting, we compare the response to high-light stress of archaeplastidal 17representatives based on RNA-Seq, pigment profile and trans-electron microscopy data. Like 18 land plants, the chlorophyte Chlamydomonas reinhardtii displays a broad respond to high-light 19 stress, not observed to the same degree in the glaucophyte Cyanophora paradoxa or the 20 rhodophyte Porphyridium purpureum. We find that only the green lineage encodes a conserved 21 duplicate of the outer plastid membrane protein channel Oep80, namely Toc75 and suggest that 22 the ability to respond to high-light stress entailed evolutionary changes in protein import, 23including the departure from phenylalanine-based targeting and the introduction of a green-24 specific Toc75 next to other import components unique to Chloroplastida. One consequence of 25 relaxed NTS specificity was the origin of dual-targeting of plastid derived proteins to 26 mitochondria and vice versa, using a single ambiguous NTS. Changes in the plastid protein 27 import enabled the green lineage to import proteins at a more efficient rate, including those 28 required for high-light stress response, a prerequisite for the colonization of land. 29 30

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“…table 1) 45 . Additionally, 28 genomes from Chlorophytes, Rhodophytes 46 and one Glaucophyte were downloaded either from the Refseq, GenBank or the JGI Genome Portal 47 (Suppl. table 1).…”

Section: Methodsmentioning

confidence: 99%

Major changes in plastid protein import and the origin of the Chloroplastida

Knopp

Garg

Handrich

et al. 2019

Preprint

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“…Indeed, there is evidence for loss of FDBRs during evolution of rhodophyte and cryptophyte algae: polyextremophilic Cyanidioschyzon spp. contain only PCYA (Rockwell & Lagarias, ; Rossoni et al , ), whereas many other rhodophytes instead contain PEBA and PEBB (Rockwell & Lagarias, ). Cryptophytes have rhodophyte‐derived secondary plastids (Fig.…”

Section: Deletion: Life Without Phytochromementioning

confidence: 99%

Phytochrome evolution in 3D: deletion, duplication, and diversification

Rockwell

Lagarias

2019

New Phytologist

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Summary Canonical plant phytochromes are master regulators of photomorphogenesis and the shade avoidance response. They are also part of a widespread superfamily of photoreceptors with diverse spectral and biochemical properties. Plant phytochromes belong to a clade including other phytochromes from glaucophyte, prasinophyte, and streptophyte algae (all members of the Archaeplastida) and those from cryptophyte algae. This is consistent with recent analyses supporting the existence of an AC (Archaeplastida + Cryptista) clade. AC phytochromes have been proposed to arise from ancestral cyanobacterial genes via endosymbiotic gene transfer (EGT), but most recent studies instead support multiple horizontal gene transfer (HGT) events to generate extant eukaryotic phytochromes. In principle, this scenario would be compared to the emerging understanding of early events in eukaryotic evolution to generate a coherent picture. Unfortunately, there is currently a major discrepancy between the evolution of phytochromes and the evolution of eukaryotes; phytochrome evolution is thus not a solved problem. We therefore examine phytochrome evolution in a broader context. Within this context, we can identify three important themes in phytochrome evolution: deletion, duplication, and diversification. These themes drive phytochrome evolution as organisms evolve in response to environmental challenges.

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“…table 1). Additionally, 28 genomes from Chlorophytes, Rhodophytes (Rossoni et al, 2019) and one Glaucophyte were downloaded either from the Refseq, GenBank or the JGI Genome Portal (Grigoriev et al, 2012) (Suppl. table 1).…”

Section: Phylogenomic Analysismentioning

confidence: 99%