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When Less is More: Red Algae as Models for Studying Gene Loss and Genome Evolution in Eukaryotes

Published on Jan 2, 2018in Critical Reviews in Plant Sciences 4.19
· DOI :10.1080/07352689.2018.1482364
Debashish Bhattacharya64
Estimated H-index: 64
(RU: Rutgers University),
Huan Qiu18
Estimated H-index: 18
(RU: Rutgers University)
+ 3 AuthorsDana C. Price19
Estimated H-index: 19
(RU: Rutgers University)
AbstractGenome evolution is usually viewed through the lens of growth in size and complexity over time, exemplified by plants and animals. In contrast, genome reduction is associated with a narrowing of ecological potential, such as in parasites and endosymbionts. But, can nuclear genome reduction also occur in, and potentially underpin a major radiation of free-living eukaryotes? An intriguing example of this phenomenon is provided by the red algae (Rhodophyta) that have lost many conserved pathways such as for flagellar motility, macroautophagy regulation, and phytochrome based light sensing. This anciently diverged, species-rich, and ecologically important algal lineage has undergone at least two rounds of large-scale genome reduction during its >1 billion-year evolutionary history. Here, using recent analyses of genome data, we review knowledge about the evolutionary trajectory of red algal nuclear and organelle gene inventories and plastid encoded autocatalytic introns. We compare and contrast Rhodop...
  • References (119)
  • Citations (5)
Published on Dec 1, 2018in BMC Evolutionary Biology 3.04
Huan Qiu18
Estimated H-index: 18
(RU: Rutgers University),
Alessandro W. Rossoni2
Estimated H-index: 2
(HHU: University of Düsseldorf)
+ 2 AuthorsDebashish Bhattacharya64
Estimated H-index: 64
(RU: Rutgers University)
Background Genome reduction in intracellular pathogens and endosymbionts is usually compensated by reliance on the host for energy and nutrients. Free-living taxa with reduced genomes must however evolve strategies for generating functional diversity to support their independent lifestyles. An emerging model for the latter case is the Rhodophyta (red algae) that comprises an ecologically widely distributed, species-rich phylum. Red algae have undergone multiple phases of significant genome reduc...
3 Citations Source Cite
Published on Aug 1, 2018in Molecular Biology and Evolution 14.80
JunMo Lee6
Estimated H-index: 6
(SKKU: Sungkyunkwan University),
Jun Mo Lee3
Estimated H-index: 3
(SKKU: Sungkyunkwan University)
+ 16 AuthorsAndreas P. M. Weber58
Estimated H-index: 58
(HHU: University of Düsseldorf)
Red algae (Rhodophyta) underwent two phases of large-scale genome reduction during their early evolution. The red seaweeds did not attain genome sizes or gene inventories typical of other multicellular eukaryotes. We generated a high quality 92.1 Mbp draft genome assembly from the red seaweed Gracilariopsis chorda, including methylation and small (s)RNA data. We analyzed these and other Archaeplastida genomes to address three questions: 1) what is the role of repeats and transposable elements (T...
10 Citations Source Cite
Published on Mar 1, 2018in Cell 36.22
Cindy J. Castelle18
Estimated H-index: 18
(University of California, Berkeley),
Jillian F. Banfield104
Estimated H-index: 104
The recent recovery of genomes for organisms from phyla with no isolated representative (candidate phyla) via cultivation-independent genomics enabled delineation of major new microbial lineages, namely the bacterial candidate phyla radiation (CPR), DPANN archaea, and Asgard archaea. CPR and DPANN organisms are inferred to be mostly symbionts, and some are episymbionts of other microbial community members. Asgard genomes encode typically eukaryotic systems, and their inclusion in phylogenetic an...
58 Citations Source Cite
Published on Dec 1, 2017in Biology Direct 3.01
Julian Vosseberg2
Estimated H-index: 2
(UU: Utrecht University),
Berend Snel51
Estimated H-index: 51
(UU: Utrecht University)
ᅟ The spliceosome is a eukaryote-specific complex that is essential for the removal of introns from pre-mRNA. It consists of five small nuclear RNAs (snRNAs) and over a hundred proteins, making it one of the most complex molecular machineries. Most of this complexity has emerged during eukaryogenesis, a period that is characterised by a drastic increase in cellular and genomic complexity. Although not fully resolved, recent findings have started to shed some light on how and why the spliceosome ...
2 Citations Source Cite
Susan H. Brawley33
Estimated H-index: 33
(UMaine: University of Maine),
Nicolas A. Blouin12
Estimated H-index: 12
(UMaine: University of Maine)
+ 47 AuthorsCheong Xin Chan19
Estimated H-index: 19
(UQ: University of Queensland)
Porphyra umbilicalis (laver) belongs to an ancient group of red algae (Bangiophyceae), is harvested for human food, and thrives in the harsh conditions of the upper intertidal zone. Here we present the 87.7-Mbp haploid Porphyra genome (65.8% G + C content, 13,125 gene loci) and elucidate traits that inform our understanding of the biology of red algae as one of the few multicellular eukaryotic lineages. Novel features of the Porphyra genome shared by other red algae relate to the cytoskeleton, c...
32 Citations Source Cite
Published on Aug 1, 2017in Trends in Plant Science 14.01
Juliet Brodie23
Estimated H-index: 23
(AMNH: American Museum of Natural History),
Cheong Xin Chan19
Estimated H-index: 19
(UQ: University of Queensland)
+ 9 AuthorsAlison G. Smith50
Estimated H-index: 50
(University of Cambridge)
Algae are (mostly) photosynthetic eukaryotes that occupy multiple branches of the tree of life, and are vital for planet function and health. In this review, we highlight a transformative period in studies of the evolution and functioning of this extraordinary group of organisms and their potential for novel applications, wrought by high-throughput ‘omic’ and reverse genetic methods. We cover the origin and diversification of algal groups, explore advances in understanding the link between pheno...
11 Citations Source Cite
Published on Jun 1, 2017in Nature microbiology 14.30
David A. Hutchins59
Estimated H-index: 59
Fei-Xue Fu25
Estimated H-index: 25
This Review Article examines how microorganisms that have key roles in the ocean carbon and nitrogen cycles may respond to anthropogenic changes in the Earth's marine ecosystems.
38 Citations Source Cite
Published on Jun 1, 2017in Genome Research 9.94
Tristan Lefébure21
Estimated H-index: 21
(UCBL: Claude Bernard University Lyon 1),
Claire Morvan2
Estimated H-index: 2
(UCBL: Claude Bernard University Lyon 1)
+ 14 AuthorsClio Der Sarkissian16
Estimated H-index: 16
(UCPH: University of Copenhagen)
The evolutionary origin of the striking genome size variations found in eukaryotes remains enigmatic. The effective size of populations, by controlling selection efficacy, is expected to be a key parameter underlying genome size evolution. However, this hypothesis has proved difficult to investigate using empirical datasets. Here, we tested this hypothesis using twenty-two de novo transcriptomes and low-coverage genomes of asellid isopods, which represent eleven independent habitat shifts from s...
16 Citations Source Cite
Published on Jun 1, 2017in Journal of Phycology 2.83
Huan Qiu18
Estimated H-index: 18
(RU: Rutgers University),
Jun Mo Lee3
Estimated H-index: 3
(SKKU: Sungkyunkwan University)
+ 1 AuthorsDebashish Bhattacharya64
Estimated H-index: 64
(RU: Rutgers University)
Red algae (Rhodophyta) putatively diverged from the eukaryote tree of life >1.2 billion years ago and are the source of plastids in the ecologically important diatoms, haptophytes, and dinoflagellates. In general, red algae contain the largest plastid gene inventory among all such organelles derived from primary, secondary, or additional rounds of endosymbiosis. In contrast, their nuclear gene inventory is reduced when compared to their putative sister lineage, the Viridiplantae, and other photo...
5 Citations Source Cite
Published on Jun 1, 2017in Current Biology 9.19
Sergio A. Muñoz-Gómez7
Estimated H-index: 7
(Dal: Dalhousie University),
Fabian G. Mejía-Franco1
Estimated H-index: 1
+ 4 AuthorsClaudio H. Slamovits26
Estimated H-index: 26
(CIFAR: Canadian Institute for Advanced Research)
Summary Red algal plastid genomes are often considered ancestral and evolutionarily stable, and thus more closely resembling the last common ancestral plastid genome of all photosynthetic eukaryotes [1, 2]. However, sampling of red algal diversity is still quite limited (e.g., [2–5]). We aimed to remedy this problem. To this end, we sequenced six new plastid genomes from four undersampled and phylogenetically disparate red algal classes (Porphyridiophyceae, Stylonematophyceae, Compsopogonophycea...
30 Citations Source Cite
Cited By5
Published on May 28, 2019in New Phytologist 7.30
R I Ponce-Toledo (Université Paris-Saclay), Purificación López-García46
Estimated H-index: 46
(Université Paris-Saclay),
David Moreira54
Estimated H-index: 54
(Université Paris-Saclay)
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Published on Feb 1, 2019in Plant Physiology 6.30
Guo Wei1
Estimated H-index: 1
(UT: University of Tennessee),
Qidong Jia6
Estimated H-index: 6
(UT: University of Tennessee)
+ 5 AuthorsFeng Chen30
Estimated H-index: 30
(UT: University of Tennessee)
Red algae (Rhodophyta) and land plants belong to the monophyletic clade Archaeplastida, and taxa of both groups are rich producers of terpene secondary metabolites. The terpene carbon skeletons of land plants are made by two types of terpene synthases: typical plant terpene synthases and microbial-type terpene synthases (MTPSLs); however, terpene biosynthesis in red algae is poorly understood. By systematic sequence analysis of seven genomes and 34 transcriptomes of red algae, MTPSL homologs wer...
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