Porphyra (Bangiophyceae) transcriptomes provide insights into red algal development and metabolism

Chan, Cheong Xin, Blouin, Nicolas A., Zhuang, Yunyun, Zaeuner, Simone, Prochnik, Simon E., Lindquist, Erika, Lin, Senjie, Benning, Christoph, Lohr, Martin, Yarish, Charles, Gantt, Elisabeth, Grossman, Arthur R., Lu, Shan, Mueller, Kirsten, Stiller, John W., Brawley, Susan H. and Bhattacharya, Debashish (2012) Porphyra (Bangiophyceae) transcriptomes provide insights into red algal development and metabolism. Journal of Phycology, 48 6: 1328-1342. doi:10.1111/j.1529-8817.2012.01229.x


Author Chan, Cheong Xin
Blouin, Nicolas A.
Zhuang, Yunyun
Zaeuner, Simone
Prochnik, Simon E.
Lindquist, Erika
Lin, Senjie
Benning, Christoph
Lohr, Martin
Yarish, Charles
Gantt, Elisabeth
Grossman, Arthur R.
Lu, Shan
Mueller, Kirsten
Stiller, John W.
Brawley, Susan H.
Bhattacharya, Debashish
Title Porphyra (Bangiophyceae) transcriptomes provide insights into red algal development and metabolism
Formatted title
Porphyra (Bangiophyceae) transcriptomes provide insights into red algal development and metabolism
Journal name Journal of Phycology   Check publisher's open access policy
ISSN 0022-3646
1529-8817
Publication date 2012-12-01
Sub-type Article (original research)
DOI 10.1111/j.1529-8817.2012.01229.x
Open Access Status DOI
Volume 48
Issue 6
Start page 1328
End page 1342
Total pages 15
Place of publication Hoboken, NJ, United States
Publisher Wiley-Blackwell
Language eng
Abstract 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, calcium signaling, the cell cycle, and stress-tolerance mechanisms including photoprotection. Cytoskeletal motor proteins in Porphyra are restricted to a small set of kinesins that appear to be the only universal cytoskeletal motors within the red algae. Dynein motors are absent, and most red algae, including Porphyra, lack myosin. This surprisingly minimal cytoskeleton offers a potential explanation for why red algal cells and multicellular structures are more limited in size than in most multicellular lineages. Additional discoveries further relating to the stress tolerance of bangiophytes include ancestral enzymes for sulfation of the hydrophilic galactan-rich cell wall, evidence for mannan synthesis that originated before the divergence of green and red algae, and a high capacity for nutrient uptake. Our analyses provide a comprehensive understanding of the red algae, which are both commercially important and have played a major role in the evolution of other algal groups through secondary endosymbioses.
Formatted abstract
The red seaweed Porphyra (Bangiophyceae) and related Bangiales have global economic importance. Here, we report the analysis of a comprehensive transcriptome comprising ca. 4.7 million expressed sequence tag (EST) reads from P. umbilicalis (L.) J. Agardh and P. purpurea (Roth) C. Agardh (ca. 980 Mbp of data generated using 454 FLX pyrosequencing). These ESTs were isolated from the haploid gametophyte (blades from both species) and diploid conchocelis stage (from P. purpurea). In a bioinformatic analysis, only 20% of the contigs were found to encode proteins of known biological function. Comparative analysis of predicted protein functions in mesophilic (including Porphyra) and extremophilic red algae suggest that the former has more putative functions related to signaling, membrane transport processes, and establishment of protein complexes. These enhanced functions may reflect general mesophilic adaptations. A near-complete repertoire of genes encoding histones and ribosomal proteins was identified, with some differentially regulated between the blade and conchocelis stage in P. purpurea. This finding may reflect specific regulatory processes associated with these distinct phases of the life history. Fatty acid desaturation patterns, in combination with gene expression profiles, demonstrate differences from seed plants with respect to the transport of fatty acid/lipid among subcellular compartments and the molecular machinery of lipid assembly. We also recovered a near-complete gene repertoire for enzymes involved in the formation of sterols and carotenoids, including candidate genes for the biosynthesis of lutein. Our findings provide key insights into the evolution, development, and biology of Porphyra, an important lineage of red algae.
Keyword Bangiales
Cellulose synthase
Extremophile
Fatty acid synthesis
Q-Index Code C1
Q-Index Status Confirmed Code
Grant ID P20 GM103418
P20 GM103638
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2013 Collection
Institute for Molecular Bioscience - Publications
 
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