Jonas COLLEN
Maître de Conférences SU
Research Department(s)
My principal research interests are and have been the physiology, ecophysiology and genomics of marine macroalgae, especially in relation to stress responses, photosynthesis, and reactive oxygen metabolism. The seaweeds studied include red, brown and green macroalgae from tropical to Antarctic environments. Presently, the principal interest is evolution, genomics, transcriptomics and physiology of the red algae in general focusing on Chondrus crispus. It has also included genomics of other algae and plants such as Porphyra umbilicalis, Gracilaria domingensis, Zostera marina and Ectocarpus spp.
In addition, teaching on undergraduate and graduate levels and interacting with students have always been a very rewarding and important part of my work. The courses I teach or have taught include Cell Biology, General Botany, Plant Physiology, Phycology, Algal Biology and Biotechnology, and international summer courses marine ecology, physiology and genomics.
Publications
1. Borg M, Krueger‐Hadfield SA, Destombe C, Collén J, Lipinska A & Coelho SM (2023). Red macroalgae in the genomic era. New Phytologist 240: 471-488.
2. Belcour A, Got J, Aite M, Delage L, Collén J, Frioux C, Leblanc C, Dittami SM, Blanquart S, Markov GV & Siegel A (2023) Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe. Genome Research 33: 972-987.
3. Baekelandt A, Rodrigues S, Vandasue L, Nacry P, Malyska A, Cornelissen M, Nanda A, Nair A, Rogowsky P, Pauwels L, Muller B, Collén J, Blomme J, Pribil M, Scharff LB, Davies J, Wilhelm R, Rolland N, Harbinson J, Boerjan W, Murchie E, Burgess AJ, Cohan J-P, Debaeke P, Thomine S, Inzé D, Klein Lankhorst R & Parry MAJ (2023) Paving the way towards future-proofing our crops. Food and Energy Security 12: 3, e441
4. Nakamura-Gouvea N, Alves-Lima C, Benites LF, Iha C, Maracaja-Coutinho V, Aliaga-Tobar V, Amaral M, Yokoya NS, Marinho Soriano E, Graminha MAS, Collén J, Cabral Oliveira M, Setubal JC & Colepicolo P (2022) Insights into agar and secondary metabolite pathways from the genome of the red alga Gracilaria domingensis (Rhodophyta: Gracilariales). Journal of Phycology 58: 406-423.
5. Girard J, Lanneau G, Delage L, Leroux C, Belcour A, Got J, Collén J, Boyen C, Siegel A, Dittami SM, Leblanc C & Markov GV (2021) Semi-quantitative targeted GC-MS profiling supports a late side-chain reductase cycloartenol-to-cholesterol biosynthesis pathway in brown algae. Frontiers in Plant Science 12: 740.
6. Monteiro C, Diehl N, Li H, Bischof K, Heinrich S, Collén J & Bartsch I (2021) Modulation of physiological performance by temperature and salinity in the sugar kelp Saccharina latissima. Phycological Research 69:48-57
7. Lipinska A, Collén J, Krueger‑Hadfield SA, Theo Mora T & Ficko‑Blean E (2020) To gel or not to gel: differential expression of carrageenan‑related genes between the gametophyte and tetasporophyte life cycle stages of the red alga Chondrus crispus. Scientific reports 10: 11498.
8. Belcour A, Girard J, Aite M, Delage L, Trottier C, Marteau C, Leroux C, Dittami S, Sauleau P, Corre E, Nicolas J, Boyen C, Leblanc C, Collén J, Siegel A & Markov G (2020) Inferring biochemical reactions and metabolite structures to cope with metabolic pathway drift. iScience: 100849.
9. Dittami SM, Corre E, Brillet-Guéguen L, Lipinska AP, Pontoizeau N, Aite M, Komlan A, Caron C, Cho CH, Collén J, Cormier A, Delage L, Doubleau S, Frioux C, Gobet A, González-Navarrete I, Groisillier A, Hervé C, Jollivet D, KleinJan H, Leblanc C, Liu X, Marie D, Markov GV, Minoche AE, Monsoor M, Pericard P, Perrineau M-M, Peters AF, Siegel A, Siméon A, Trottier C, Yoon HS, Himmelbauer H, Boyen C & Tonon T (2020) The genome of Ectocarpus subulatus – A highly stress-tolerant brown alga. Marine Genomics: 100740.
10. Monteiro C, Heinrich S, Bartsch I, Valentin K, Corre E, Collén J, Harms L, Glöckner G & Bischof K (2019) Temperature modulates sex-biased gene expression in the gametophytes of the kelp Saccharina latissima. Frontiers Marine Science 6: 769.
11. Monteiro C, Li H, Bischof K, Bartsch I, Valentin KU, Corre E, Collén J, Harms L, Glöckner G, Heinrich S (2019) Is geographical variation driving the transcriptomic responses to multiple stressors in the kelp Saccharina latissima? BMC Plant Biology 19.1: 1-15.
12. Stiller JW, Yang C, Collén J, Kowalczyk N & Thompson BE (2018) Evolution and expression of core SWI/SNF genes in red algae. Journal of Phycology 54:879-887.
13. Tonon AP, Zaini PA, dos Reis Falcão V, Cabral Oliveira M, Collén J, Boyen C & Colepicolo P (2018) Gracilaria tenuistipitata (Rhodophyta) tolerance to cadmium and copper exposure observed through gene expression and photosynthesis analyses. Journal of Applied Phycology 30: 2129-2141.
14. Brawley SH, Blouin NA, Ficko-Blean E, Wheeler GL, Lohr M, Goodson HV, Jenkins JW, Blaby-Haas CE, Helliwell KE, Chan CX, Marriage T, Bhattacharya D, Klein A, Badis Y, Brodie B, Cao Y, Collén J, Dittami SM, Gachon C, Green BR, Karpowicz S, Kim J, Lin S, Michel G, Mittag M, Olson BJSC, Pangilinan J, Peng Y, Qiu H, Shu S-Q, Singer JT, Smith AG, Sprecher BN, Wagner V, Wang W, Wang Z, Yan J, Yarish C, Zäuner-Riek S, Zhuang YY, Zou Y, Lindquist EA, Grimwood J, Barry K, Rokhsar DS, Schmutz J, Stiller JW, Grossman AR & Prochnik SE (2017) Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta). Proceedings of the National Academy of Sciences 114: E6361-E6370.
15. Dittami SM, Heesch S, Olsen JL & Collén J (2017) Transitions between marine and freshwater environments provide new clues about the origin of multicellular plants and algae. Journal of Phycology 53: 731-745
16. Rousvoal S, Bouyer B, López-Cristoffanini C, Boyen C & Collén J (2016) Mutants swarms of a totivirus-like entity are present in the red macroalga Chondrus crispus and have been partially transferred to the nuclear genome. Journal of Phycology 52: 493-504.
17. Olsen JL, Pierre Rouzé P, Verhelst B, Lin Y-C, Bayer T, Collén J, Dattolo E, De Paoli E, Dittami S, Maumus F, Michel G, Kersting A, Lauritano C, Lohaus R, Töpel M, Tonon T, Vanneste K, Amirebrahimi M, Brakel J, Boström C, Chovatia M, Grimwood J, Jenkins JW, Jüterbock A, Mraz A, Stam WT, Tice H, Bornberg-Bauer E, Green PJ, Pearson GA, Procaccini G, Duarte CM, Schmutz J, Reusch TBH & van de Peer Y (2016) The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea. Nature 530: 331-335.
18. Collén J (2015) Win some, lose some: genome evolution in red algae. Journal of Phycology 51: 621-623.
19. Cock JM & Collén J (2015) Independent emergence of complex multicellularity in the brown and red algae. In: Evolutionary transitions to multicellular life. pp. 335-361 Editors: Ruiz-Trillo & Nedelcu Springer Netherlands.
20. Collén J, Cornish ML, Craigie J, Ficko-Blean E, Hervé C, Krueger-Hadfield SA, Leblanc C, Michel G, Potin P, Tonon T & Boyen C (2014) Chondrus crispus – a present and historical model organism for red seaweeds. Advances in Botanical Research 71: 53-90.
21. Collén J & Boyen B (2014) General introduction to omics. In: Outstanding marine molecules and new trends in analytical methods, pp 431-434, Editors: La Barre S & Kornprobst J-M, Wiley-Blackwell.
22. Kowalczyk N, Rousvoal S, Hervé C, Boyen C, Collén J (2014) RT-qPCR normalization genes in the red alga Chondrus crispus. PLoS one 9: e86574.
23. Collén J (2014) Antioxidant metabolism. Invited essay in: Seaweed Ecology and Physiology 2nd edition. Hurd, Harrison, Bischof & Lobban. Cambridge University Press, Cambridge, UK.
24. Kowalczyk N, Rappaport F, Boyen C, Wollman F-A, Collén J & Joliot P (2013) Photosynthesis in Chondrus crispus: the contribution of energy spill-over in the regulation of excitonic flux. Biochim Biophys Acta- Bioenergetics 1827: 834-842.
25. Janouškovec J, Liu S-L, Martone PT, Carré W, Leblanc C, Collén J & Keeling PJ (2013) Evolution of red algal plastid genomes: ancient architectures, introns, horizontal gene transfer, and taxonomic utility of plastid markers. PloS one, 8: e59001.
26. Collén J, Porcel B, Carre W, Ball S, Chaparro C, Barbeyron T, Michel G, Noel B, Valentin K, Artiguenave F, Arun A, Aury J-M, Barbosa-Neto JF, Bothwell J, Bouget F-Y, Brillet L, Cabello-Hurtado F, Capella-Gutíerrez S, Charrier B, Cladiere L, Cock JM, Coelho SM, Colleoni C, Mirjam C, Da Silva C, Delage L, Denoeud F, Deschamps P, Dittami SM, Elias M, Gabaldón T, Gachon CMM, Groisillier A, Hervé C, Jabbari K, Katinka M, Kloareg B, Kowalczyk N, Labadie K, Leblanc C, Lopez PJ, McLachlan D, Meslet-Cladiere L, Moustafa A, Nehr Z, Nyvall Collén P, Panaud O, Partensky F, Poulain J, Rensing SA, Rousvoal S, Samson G, Symeonidi A, Tonon T, Zambounis A, Wincker P & Boyen C (2013) Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida. Proceedings of the National Academy of Sciences 110: 5247-5252.
27. Cock JM, Sterck L, Ahmed S, Allen AE, Amoutzias G, Anthouard V, Artiguenave F, Arun A, Aury J-M, Badger JH, Beszteri B, Billiau K, Bonnet E, Bothwell JH, Bowler C, Boyen C, Brownlee C, Carrano CJ, Charrier B, Ga Y, Cho, Coelho SM, Collén J, Le Corguillé G, Corre E, Dartevelle L, Da Silva C, Delage L, Delaroque N, Dittami SM, Doulbeau S, Elias M, Farnham G, Gachon CMM, Godfroy O, Gschloessl B, Heesch S, Jabbari K, Jubin C, Kawai H, Kimura K, Kloareg B, Küpper FC, Lang D, Le Bail A, Luthringer R, Leblanc C, Lerouge P, Lohr M, Lopez PJ, Macaisne N, Martens C, Maumus F, Michel G, Miranda-Saavedra D, Morales J, Moreau H, Motomura T, Nagasato C, Napoli CA, Nelson DR, Nyvall-Collén P, Peters AF, Pommier C, Potin P, Poulain J, Quesneville H, Read B, Rensing SA, Ritter A, Rousvoal S, Samanta M, Samson G, Schroeder DC, Scornet D, Ségurens B, Strittmatter M, Tonon T, Tregear JW, Valentin K, Von Dassow P, Yamagishi T, Rouzé P, Van De Peer Y, Wincker P (2012) The Ectocarpus genome and brown algal genomics. Advances in Botanical Research 64: 141-184.
28. Nyvall Collén P, Collén J, da Silva Reis M, Pedersén M, Setubal J, Varani AM, Colepicolo P & de Oliveira MC (2011) Analysis of expressed sequence tags from the agarophyte Gracilaria tenuistipitata (Rhodophyta). Journal of Applied Phycology 24: 641-647.
29. Krueger-Hadfield SA, Collén J, Daguin-Thiébaut C & Valero M (2011) Genetic population structure and mating systems in Chondrus crispus (Rhodophyta). Journal of Phycology 47: 440-450.
30. Dittami SM, Michel G, Collén J, Boyen C & Tonon T (2010) Chlorophyll-binding proteins revisited - a multigenic family of light-harvesting and stress proteins from a brown algal perspective. BMC Evolutionary Biology 10: 365.
31. Gravot A, Dittami SM, Rousvoal S, Lugan R, Eggert A, Collén J, Boyen C, Bouchereau A & Tonon T (2010) Diurnal oscillations of metabolite abundances and gene analysis provide new insights into central metabolic processes of the brown alga Ectocarpus siliculosus. New Phytologist 188: 98-110.
32. Cock JM, Sterck L, Rouzé P, Scornet D, Allen AE, Amoutzias G, Anthouard V, Artiguenave F, Aury J-M, H. Badger JH, Beszteri B, Billiau K, Bonnet E, Bothwell JHF, Bowler C, Boyen C, Brownlee C, Carrano CJ, Charrier B, Cho GY, Coelho SM, Collén J, Corre E, Da Silva C, Delage L, Delaroque N, Dittami SM, Doulbeau S, Elias M, Farnham G, Gachon CMM, Gschloessl B, Heesch S, Jabbari K, Jubin C, Kawai H, Kimura K, Kloareg B, Küpper FC, Lang D, Le Bail A, Leblanc C, Lerouge P, Lohr M, Lopez PJ, Martens C, Maumus F, Michel G, Miranda-Saavedra D, Morales J, Moreau H, Motomura T, Nagasato C, Napoli CA, Nelson DR, Nyvall-Collén P, Peters AF, Pommier C, Potin P, Poulain J, Quesneville H, Read B, Rensing SA, Ritter A, Rousvoal S, Samanta M, Samson G, Schroeder DC, Ségurens B, Strittmatter M, Tonon T, Tregear J, Valentin K, von Dassow P, Yamagishi T, Van de Peer Y & Wincker P (2010)The Ectocarpus genome and the independent evolution of multicellularity in the brown algae. Nature 465: 617-621
33. Querellou J, Allen M, Cadoret J-P & Collén J (2010) Marine Biotechnology. In: Introduction to marine genomics, pp 287-314, M Cock, V Armbrust, A Canario, M Clark, F Viard, K Tessamar-Raible, C de Vargas & C Boyen, (Eds). Springer.
34. Gantt E, Berg M, Bhattacharya D, Blouin NA, Brodie JA, Chan CX, Collén J, Cunningham FX, Gross J, Grossman AR, Karpowicz S, Kitade Y, Klein A, Levine IA, Lin S, Lu S, Lynch M, Minocha SC, Müller K, Neefus CD, de Oliveira MC, Rymarquis L, Smith A, Stiller JW, Wu W-K, Yarish C, Zhuang YY & Brawley SH (2010) Porphyra: complex life histories in a harsh environment. P. umbilicalis, an intertidal red alga for genomic analysis, pp 129-148 In: J. Seckbach and D. Chapman (eds.) Red Algae in Genomic Age. (volume 13 of Cellular Origins, Life in Extreme Habitats and Astrobiology) Springer.
35. Collén J (2009) Förstör vårt glassätande tropikernas korallrev? In: Forskarbloggen Vol 1. Eds: J Sundström & D Lundberg. ISBN 978-91-85911-95-0, pp 283-285 (Popular Science, in Swedish).
36. Collén J, Guisle-Marsollier I, Leger JJ & Boyen C (2007) Response of the transcriptome of the intertidal red seaweed Chondrus crispus to controlled and natural stresses. New Phytologist 176: 45-55.
37. Collén J, Hervé C, Guisle-Marsollier I, Leger JJ & Boyen C (2006) Expression profiling of Chondrus crispus (Rhodophyceae) after exposure to methyl jasmonate. Journal of Experimental Botany 57: 3869-3881.
38. Collén J (2006) An uncritical view of early uses of seaweeds. In: World Seaweed Resources. Eds: AT Critchley, M Ohno & DB Largo. DVD-ROM, ETI Bioinformatics, University of Amsterdam.
39. Hervé C, Tonon T, Corre E, Collén J & Boyen C (2006) NADPH oxidases in Eukaryotes: red algae provide new hints! Current Genetics 49: 190-204.
40. Collén J, Roeder V, Rousvoal S, Collin O, Kloareg B & Boyen C (2006) An expressed sequence tag analysis of thallus and regenerating protoplasts of Chondrus crispus (Gigartinales, Rhodophyceae). Journal of Phycology 42: 104-112.
41. Roeder V, Collén J, Rousvoal S, Corre E, Leblanc C & Boyen C (2005) Identification of stress genes from Laminaria digitata (Phaeophyceae) protoplast cultures by expressed sequence tag analysis. Journal of Phycology 41: 1227-1235.
42. Cock JM, Leblanc C, Colin C, Collén J, Roeder V, Hervé C, Rousvoal S, Michel G, Potin P, Boyen C & Kloareg B (2004) Genomic analysis of economically important seaweeds. Marine Biotechnology 6: S43-S47.
43. Collén J, Pinto E, Pedersén M & Colepicolo P (2003) Induction of oxidative stress in the red macroalga Gracilaria tenuistipitata by pollutant metals. Archives of Environmental Contamination and Toxicology. 45: 337-342.
44. Collén J & Davison IR (2003) Diurnal changes in photosynthesis and reactive oxygen metabolism in Gracilaria tikvahiae (Rhodophyta). In: Proceedings International Seaweed Symposium, Oxford University Press. pp 395-401. Chapman ARO, Anderson RJ, Vreeland VJ & Davison IR (Eds).
45. Collén J & Davison IR (2001) Seasonal differences and effect of cultivation conditions on reactive oxygen metabolism in Fucus vesiculosus. Journal of Phycology 37: 474-481.
46. Collén J & Davison IR (1999) Stress tolerance and reactive oxygen metabolism in the intertidal red seaweeds Mastocarpus stellatus and Chondrus crispus. Plant Cell & Environment 22: 1143-1151.
47. Collén J & Davison IR (1999) Reactive oxygen production and damage in intertidal Fucus spp. (Phaeophyceae). Journal of Phycology 35: 54-61.
48. Collén J & Davison IR (1999) Reactive oxygen metabolism in intertidal Fucus spp. (Phaeophyceae). Journal of Phycology 35: 62–69.
49. Collén J & Davison IR (1997) In vivo measurements of active oxygen production in the brown algae Fucus evanescens using 2',7' dichlorohydrofluorescein diacetate. Journal of Phycology 33: 643-648.
50. Collén J & Pedersén M (1996) Production, scavenging and toxicity of hydrogen peroxide in Ulva rigida. European Journal of Phycology 31: 265-271.
51. Sundström J, Collén J, Abrahamsson K & Pedersén M (1996) Halocarbon production and in vivo brominating activity of Eucheuma denticulatum. Phytochemistry 42: 1527-1530.
52. Mtolera MSP, Collén J, Pedersén M, Ekdahl A, Abrahamsson K & Semesi AK (1996) Stress-induced production of volatile halogenated organic compounds in Eucheuma denticulatum (Rhodophyta) caused by elevated pH and high light intensities. European Journal of Phycology 31: 89-95.
53. Mtolera MSP, Collén J, Sundström J, Semesi AK & Pedersén M (1996) Productivity of Eucheuma denticulatum and related seaweeds: HCO3- utilization and the role of water depth and circulation in minimizing light-induced stresses. pp. 162-174. In: Current trends in marine botanical research in the East African region. Björk M, Semesi AK, Pedersen M & Bergman B (Eds).
54. Pedersén M, Collén J, Abrahamsson K, Mtolera MSP, Semesi AK & Reina GG (1996) The ice-ice disease and oxidative stress of marine algae. pp. 11-24. In: Current trends in marine botanical research in the East African region. Björk M, Semesi AK, Pedersen M & Bergman B (Eds).
55. Pedersén M, Collén J, Abrahamsson K & Ekdahl A (1996) Production of halocarbons from seaweeds: An oxidative stress reaction? Scientia Marina 60: 257-263.
56. Collén J, Del Río MJ, García-Reina G & Pedersén M (1995) Photosynthetic H2O2 production by Ulva rigida. Planta 196: 225-230.
57. Abrahamsson K, Ekdahl A, Collén J & Pedersén M (1995) Marine algae- a source of trichloroethylene and perchloroethylene. Limnology and Oceanography 40: 1321-1326.
58. Abrahamsson K, Ekdahl A, Collén J & Pedersén M (1995) Formation and distribution of halogenated compounds volatile organics in sea water. In: Naturally produced organo-halogens. Grimvall A & de Leer E (Eds), Kluwer, pp 317-326.
59. Abrahamsson K, Ekdahl A, Collén J, Fahlström E & Pedersén M (1995) The natural formation of trichloroethylene and perchloroethylene in sea water. In: Naturally produced organo-halogens. Grimvall A & de Leer E (Eds), Kluwer, pp 327-332
60. Collén J, Mtolera M, Abrahamsson K, Semesi A & Pedersén M (1995) Farming and physiology of the red algae Eucheuma: species of growing commercial importance in East Africa. AMBIO 24: 497-501.
61. Mtolera MSP, Collén J, Pedersén M & Semesi AK (1995) Destructive hydrogen peroxide production in Eucheuma denticulatum (Rhodophyta) during stress caused by elevated pH, high light intensities and competition with other species. European Journal of Phycology 30: 289-297.
62. Collén J (1994) Production of hydrogen peroxide and volatile halocarbons by macroalgae. Acta Universitatis Upsaliensis. Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology: 68, Uppsala, Sweden.
63. Collén J, Abrahamsson K, Ekdahl A & Pedersén M (1994) The involvement of hydrogen peroxide on the production of volatile halogenated compounds by Meristiella gelidium (Rhodophyta). Phytochemistry 36: 1197-1202.
64. Collén J & Pedersén M (1994) Stress induced oxidative burst by Eucheuma platycladum (Rhodophyta). Physiologia Plantarum 92: 417-422.
65. Collén J, Pedersén M, Ramazanov Z, Mtolera M, Ngoile M & Semesi A (1992) Carbon assimilation of Eucheuma denticulatum. In: Proceedings of the first international workshop on sustainable seaweed resource development in Sub-Saharan Africa. pp 77-84. Mshigeni KE, Bolton J, Critchley A & Kiangi G (Eds).
66. Collén J & Pedersén M (1990) Västerhav i förvandling- en studie av alger. Bohuslän 12: 81-86 (Popular Science, in Swedish).