De nova transcriptome analysis and mining extreme light environments acclimation responding genes of Antarctic seaweed Iridaea cordata (Gigartinales, Rhodophyta) and Curdiea racovitzae (Gracilariaceae, Rhodophyta)

Liu Chenlin; Wang Xiuliang; Lin Xuezheng

doi:10.3969/j.issn.0253-4193.2020.10.011

Issue 10

Dec 2020

Turn off MathJax

Article Contents

JOURNAL OF MECHANICAL ENGINEERING > 2020 > 42(10): 110-120.

Liu Chenlin，Wang Xiuliang，Lin Xuezheng. De nova transcriptome analysis and mining extreme light environments acclimation responding genes of Antarctic seaweed Iridaea cordata (Gigartinales, Rhodophyta) and Curdiea racovitzae (Gracilariaceae, Rhodophyta)[J]. Haiyang Xuebao，2020, 42(10)：110–120 doi: 10.3969/j.issn.0253-4193.2020.10.011

Citation:

Liu Chenlin，Wang Xiuliang，Lin Xuezheng. De nova transcriptome analysis and mining extreme light environments acclimation responding genes of Antarctic seaweed Iridaea cordata (Gigartinales, Rhodophyta) and Curdiea racovitzae (Gracilariaceae, Rhodophyta)[J]. Haiyang Xuebao，2020, 42(10)：110–120 doi: 10.3969/j.issn.0253-4193.2020.10.011

Citation:

PDF( 0 KB)

De nova transcriptome analysis and mining extreme light environments acclimation responding genes of Antarctic seaweed Iridaea cordata (Gigartinales, Rhodophyta) and Curdiea racovitzae (Gracilariaceae, Rhodophyta)

doi: 10.3969/j.issn.0253-4193.2020.10.011

Liu Chenlin^{1, 3
,},
Wang Xiuliang^{2, 3},
Lin Xuezheng¹

Received Date: 02 Jul 2019
Rev Recd Date: 18 Nov 2019
Publish Date: 07 Dec 2020

Abstract

Abstract

Antarctic red algae play important roles in the coastal ecosystems and industrial applications. Meanwhile, their unique physiological acclimation mechanisms to the extreme environments endow them to be ideal organisms for discovering new genes and new metabolic pathways. In this study, we sequenced the transcriptomes of Antarctic red algae Iridaea cordata (Turner) Bory and Curdiea racovitzae Hariot, and compared with their moderate temperature close relatives. The transcriptome sequences of I. cordata and C. racovitzae were assembled into 14055 and 12006 Unigenes, with an average length of 1473 bp and 1448 bp, respectively. The Lhca2, Lhca6 and Lhcb genes homologous to the green algae genes were found in I. cordata transcriptome while not in other red algae. Lhcf gene encoding fucoxanthine and Chl a/c binding protein presenting in brown algae and diatoms were identified in both I. cordata and C. racovitzae. Photolyase repairs UV-induced DNA damages. 6-4 photolyase, CPD I and CPD II genes were identified in the transcriptome of I. cordata, while only CPD II gene was found in the transcriptome of C. racovitzae. Although the functions of those specific genes in Antarctic red algae are expected further investigation, our study provides a foundation for the following researches on the acclimation mechanisms of seaweeds to the extreme light environments in Antarctica.
- Antarctic red algae,
- transcriptome,
- extreme light environmental acclimation,
- Iridaea cordata,
- Curdiea racovitzae

FullText(HTML)

References(43)

References

[1]	Wiencke C, Clayton M. Antarctic seaweeds[M]//Wägele J W. Synopsis of the Antarctic Benthos. Ruggell: ARG Gantner, 2002.
[2]	Oliveira E C, Absher T M, Pellizzari F M, et al. The seaweed flora of Admiralty Bay, King George Island, Antarctic[J]. Polar Biology, 2009, 32(11): 1639−1647. doi: 10.1007/s00300-009-0663-9
[3]	Pellizzari F, Silva M C, Silva E M, et al. Diversity and spatial distribution of seaweeds in the South Shetland Islands, Antarctica: an updated database for environmental monitoring under climate change scenarios[J]. Polar Biology, 2017, 40(8): 1671−1685. doi: 10.1007/s00300-017-2092-5
[4]	Martín A, Miloslavich P, Díaz Y, et al. Intertidal benthic communities associated with the macroalgae Iridaea cordata and Adenocystis utricularis in King George Island, Antarctica[J]. Polar Biology, 2016, 39(2): 207−220. doi: 10.1007/s00300-015-1773-1
[5]	Dhargalkar V K, Verlecar X N. Southern Ocean seaweeds: a resource for exploration in food and drugs[J]. Aquaculture, 2009, 287(3/4): 229−242.
[6]	Guillemin M L, Dubrasquet H, Reyes J, et al. Comparative phylogeography of six red algae along the Antarctic Peninsula: extreme genetic depletion linked to historical bottlenecks and recent expansion[J]. Polar Biology, 2018, 41(5): 827−837. doi: 10.1007/s00300-017-2244-7
[7]	McCandless E L, Craigie J S, Hansen J E. Carrageenans of gametangial and tetrasporangial stages of Iridaea cordata (Gigartinaceae)[J]. Canadian Journal of Botany, 1975, 53(20): 2315−2318. doi: 10.1139/b75-256
[8]	Kim H J, Kim W J, Koo B W, et al. Anticancer activity of sulfated polysaccharides isolated from the Antarctic red seaweed Iridaea cordata[J]. Ocean and Polar Research, 2016, 38(2): 129−137. doi: 10.4217/OPR.2016.38.2.129
[9]	Falshaw R, Furneaux R H, Stevenson D E. Agars from nine species of red seaweed in the genus Curdiea (Gracilariaceae, Rhodophyta)[J]. Carbohydrate Research, 1998, 308(1/2): 107−115.
[10]	Wiencke C, Rahmel J, Karsten U, et al. Photosynthesis of marine Macroalgae from Antarctica: light and temperature requirements[J]. Botanica Acta, 1993, 106(1): 78−87. doi: 10.1111/j.1438-8677.1993.tb00341.x
[11]	Navarro N P, Mansilla A, Plastino E M. UVB radiation induces changes in the ultra-structure of Iridaea cordata[J]. Micron, 2010, 41(7): 899−903. doi: 10.1016/j.micron.2010.06.004
[12]	Navarro N P, Huovinen P, Gómez I. Stress tolerance of Antarctic macroalgae in the early life stages[J]. Revista Chilena de Historia Natural, 2016, 89(1): 5. doi: 10.1186/s40693-016-0051-0
[13]	McClintock J B, Karentz D. Mycosporine-like amino acids in 38 species of subtidal marine organisms from McMurdo Sound, Antarctica[J]. Antarctic Science, 1997, 9(4): 392−398. doi: 10.1017/S0954102097000503
[14]	Cormaci M, Furnari G, Scammacca B, et al. Summer biomass of a population of Iridaea cordata (Gigartinaceae, Rhodophyta) from Antarctica[J]. Hydrobiologia, 1996, 326−327(1): 267−272. doi: 10.1007/BF00047817
[15]	Wiencke C, Clayton M N, Gómez I, et al. Life strategy, ecophysiology and ecology of seaweeds in polar waters[J]. Reviews in Environmental Science and Bio/Technology, 2007, 6(1/3): 95−126.
[16]	Wulff A, Iken K, Liliana Quartino M, et al. Biodiversity, biogeography and zonation of marine benthic micro- and macroalgae in the Arctic and Antarctic[J]. Botanica Marina, 2009, 52(6): 491−507.
[17]	Amsler D C, Okogbue I N, Landry D M, et al. Potential chemical defenses against diatom fouling in Antarctic macroalgae[J]. Botanica Marina, 2005, 48(4): 318−322.
[18]	Martins R M, Nedel F, Guimarães V B S, et al. Macroalgae extracts from Antarctica have antimicrobial and anticancer potential[J]. Frontiers in Microbiology, 2018, 9: 412. doi: 10.3389/fmicb.2018.00412
[19]	Maccoll R, Eisele L E, Williams E C, et al. The discovery of a novel R-phycoerythrin from an Antarctic red alga[J]. Journal of Biological Chemistry, 1996, 271(29): 17157−17160. doi: 10.1074/jbc.271.29.17157
[20]	Zacher K, Roleda M Y, Wulff A, et al. Responses of Antarctic Iridaea cordata (Rhodophyta) tetraspores exposed to ultraviolet radiation[J]. Phycological Research, 2009, 57(3): 186−193. doi: 10.1111/j.1440-1835.2009.00538.x
[21]	Carvalho E L, Maciel L F, Macedo P E, et al. De novo assembly and annotation of the Antarctic alga Prasiola crispa Transcriptome[J]. Frontiers in Molecular Biosciences, 2017, 4: 89.
[22]	Grabherr M G, Haas B J, Yassour M, et al. Full-length transcriptome assembly from RNA-seq data without a reference genome[J]. Nature Biotechnology, 2011, 29(7): 644−652. doi: 10.1038/nbt.1883
[23]	Powell S, Szklarczyk D, Trachana K, et al. eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges[J]. Nucleic Acids Research, 2012, 40(D1): D284−D289. doi: 10.1093/nar/gkr1060
[24]	Moriya Y, Itoh M, Okuda S, et al. KAAS: an automatic genome annotation and pathway reconstruction server[J]. Nucleic Acids Research, 2007, 35(S2): W182−W185.
[25]	Kumar S, Stecher G, Li M, et al. MEGA X: molecular evolutionary genetics analysis across computing platforms[J]. Molecular Biology and Evolution, 2018, 35(6): 1547−1549. doi: 10.1093/molbev/msy096
[26]	Collén J, Porcel B, Carré W, et al. Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida[J]. Proceedings of the National Academy of Sciences of the United States of America, 2013, 110(13): 5247−5252. doi: 10.1073/pnas.1221259110
[27]	Sun X, Wu J, Wang G C, et al. Genomic analyses of unique carbohydrate and phytohormone metabolism in the macroalga Gracilariopsis lemaneiformis (Rhodophyta)[J]. BMC Plant Biology, 2018, 18(1): 94. doi: 10.1186/s12870-018-1309-2
[28]	Choi S, Hwang M S, Im S, et al. Transcriptome sequencing and comparative analysis of the gametophyte thalli of Pyropia tenera under normal and high temperature conditions[J]. Journal of Applied Phycology, 2013, 25(4): 1237−1246. doi: 10.1007/s10811-012-9921-2
[29]	Im S, Choi S, Hwang M S, et al. De novo assembly of transcriptome from the gametophyte of the marine red algae Pyropia seriata and identification of abiotic stress response genes[J]. Journal of Applied Phycology, 2015, 27(3): 1343−1353. doi: 10.1007/s10811-014-0406-3
[30]	Green B R, Durnford D G. The chlorophyll-carotenoid proteins of oxygenic photosynthesis[J]. Annual Review of Plant Physiology and Plant Molecular Biology, 1996, 47: 685−714. doi: 10.1146/annurev.arplant.47.1.685
[31]	Engelken J, Brinkmann H, Adamska I. Taxonomic distribution and origins of the extended LHC (light-harvesting complex) antenna protein superfamily[J]. BMC Evolutionary Biology, 2010, 10(1): 233. doi: 10.1186/1471-2148-10-233
[32]	Durnford D G, Deane J A, Tan S, et al. A phylogenetic assessment of the eukaryotic light-harvesting antenna proteins, with implications for plastid evolution[J]. Journal of Molecular Evolution, 1999, 48(1): 59−68. doi: 10.1007/PL00006445
[33]	Busch A, Hippler M. The structure and function of eukaryotic photosystem I[J]. Biochimica et Biophysica Acta (BBA)-Bioenergetics, 2011, 1807(8): 864−877. doi: 10.1016/j.bbabio.2010.09.009
[34]	de Martino A, Douady D, Quinet-Szely M, et al. The light-harvesting antenna of brown algae: highly homologous proteins encoded by a multigene family[J]. European Journal of Biochemistry, 2000, 267(17): 5540−5549. doi: 10.1046/j.1432-1327.2000.01616.x
[35]	Reith M. Molecular biology of Rhodophyte and Chromophyte plastids[J]. Annual Review of Plant Physiology and Plant Molecular Biology, 2014, 46: 549−575.
[36]	Ballottari M, Girardon J, Dall’Osto L, et al. Evolution and functional properties of Photosystem II light harvesting complexes in eukaryotes[J]. Biochimica et Biophysica Acta (BBA)-Bioenergetics, 2012, 1817(1): 143−157. doi: 10.1016/j.bbabio.2011.06.005
[37]	Sancar A. Structure and function of DNA photolyase and cryptochrome blue-light photoreceptors[J]. Chemical Reviews, 2003, 103(6): 2203−2237. doi: 10.1021/cr0204348
[38]	Chaves I, Pokorny R, Byrdin M, et al. The cryptochromes: blue light photoreceptors in plants and animals[J]. Annual Review of Plant Biology, 2011, 62: 335−364. doi: 10.1146/annurev-arplant-042110-103759
[39]	Selby C P, Sancar A. A cryptochrome/photolyase class of enzymes with single-stranded DNA-specific photolyase activity[J]. Proceedings of the National Academy of Sciences of the United States of America, 2006, 103(47): 17696−17700. doi: 10.1073/pnas.0607993103
[40]	Fortunato A E, Annunziata R, Jaubert M, et al. Dealing with light: the widespread and multitasking cryptochrome/photolyase family in photosynthetic organisms[J]. Journal of Plant Physiology, 2015, 172: 42−54. doi: 10.1016/j.jplph.2014.06.011
[41]	Varshney R K, Graner A, Sorrells M E. Genic microsatellite markers in plants: features and applications[J]. Trends in Biotechnology, 2005, 23(1): 48−55. doi: 10.1016/j.tibtech.2004.11.005
[42]	Allcock A L, Strugnell J M. Southern Ocean diversity: new paradigms from molecular ecology[J]. Trends in Ecology & Evolution, 2012, 27(9): 520−528.
[43]	Riesgo A, Taboada S, Avila C. Evolutionary patterns in Antarctic marine invertebrates: an update on molecular studies[J]. Marine Genomics, 2015, 23: 1−13. doi: 10.1016/j.margen.2015.07.005

Relative Articles

Supplements(0)

Cited By

Proportional views

Proportional views

Figures(6) / Tables(2)

Get Citation

PDF

XML

Article Metrics

Article views(299) PDF downloads(0)

De nova transcriptome analysis and mining extreme light environments acclimation responding genes of Antarctic seaweed Iridaea cordata (Gigartinales, Rhodophyta) and Curdiea racovitzae (Gracilariaceae, Rhodophyta)

doi: 10.3969/j.issn.0253-4193.2020.10.011

Abstract

References

Proportional views

Catalog

Article Metrics

Proportional views

Related

De nova transcriptome analysis and mining extreme light environments acclimation responding genes of Antarctic seaweed Iridaea cordata (Gigartinales, Rhodophyta) and Curdiea racovitzae (Gracilariaceae, Rhodophyta)

doi: 10.3969/j.issn.0253-4193.2020.10.011

Abstract

References

Proportional views

Catalog

Article Metrics

Proportional views

Related

Export File

Citation

Format

Content