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Journal of Applied Phycology

, Volume 31, Issue 5, pp 3303–3316 | Cite as

Comparative transcriptome analysis of four co-occurring Ulva species for understanding the dominance of Ulva prolifera in the Yellow Sea green tides

  • Yu Wang
  • Feng LiuEmail author
  • Xingfeng Liu
  • Shitao Shi
  • Yuping BiEmail author
  • Fiona Wanjiku Moejes
Article

Abstract

The last 12 years has seen the dominance of Ulva prolifera in the green tides occurring in the Yellow Sea. To gain a better understanding of the underlying molecular clues associated with the dominance pattern of the Yellow Sea green tides, we generated and compared the transcriptomes of four co-occurring Ulva species including U. prolifera, U. linza, U. flexuosa, and U. compressa under the same conditions. Our results revealed that the transcriptomes of four Ulva species shared a set of core genes, but varied in construction of GO term categories, transcription factor (TF) styles, and metabolism pathways. Based on the KEGG database, several growth-related genes including pyruvate kinase (PK) and nitrate transporter (NRT) have been identified to be enriched in U. prolifera compared with the other three Ulva species. This study provides novel transcriptionomic data for us to understand the species dominance pattern in the Yellow Sea green tides.

Keywords

Transcriptome Ulva prolifera Chlorophyta Green tide Yellow Sea Bloom 

Notes

Funding information

This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (No. XDA23050302, XDA23050403), the Scientific and Technological Innovation Project Financially Supported by Pilot National Laboratory for Marine Science and Technology (Qingdao) (No. 2016ASKJ02), the Key Research Program of Frontier Sciences, Chinese Academy of Sciences (No. QYZDB-SSW-DQC023), the National Natural Science Foundation of China (No. 41876165), the Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology (Qingdao) (No. 2018SDKJ0504), the Youth Innovation Promotion Association, Chinese Academy of Sciences (No. 2015164), the Open Research Fund of Key Laboratory of Integrated Marine Monitoring and Applied Technologies for Harmful Algal Blooms, S.O.A. (No. MATHAB201701), and the earmarked fund for Modern Agro-industry Technology Research System in Shandong Province of China (SDAIT-26-09).

Supplementary material

10811_2019_1810_MOESM1_ESM.pptx (36 kb)
Fig S1 The number distribution of TFs in four Ulva species (PPTX 35 kb)
10811_2019_1810_MOESM2_ESM.pptx (36 kb)
Fig S2 Metabolism pathways of core expressed genes annotated by KEGG (PPTX 36 kb)
10811_2019_1810_MOESM3_ESM.pptx (94 kb)
Fig S3 Boxplots of dN/dS ratios for putative orthologs from four Ulva transcriptomes. The transverse coordinates are species pairs, and the ordinate is dN/dS. The upper and lower limit is 90%, the upper and lower edges of the box are 75%, and the horizontal line is the median (PPTX 93 kb)
10811_2019_1810_MOESM4_ESM.pptx (39 kb)
Fig S4 Venn diagram displaying the number of putative positive orthologous groups shared between the three comparison groups based on GO annotations: aU. compressa vs U. prolifera, bU. flexuosa vs U. prolifera, cU. linza vs U. prolifera (PPTX 39 kb)
10811_2019_1810_MOESM5_ESM.pptx (45 kb)
Fig S4b (PPTX 44 kb)
10811_2019_1810_MOESM6_ESM.pptx (39 kb)
Fig S4c (PPTX 39 kb)
10811_2019_1810_MOESM7_ESM.pptx (82 kb)
Fig S5 Arachidonic acid metabolism pathway. Glutathione peroxidase (GPx, K00432) was in green, secretory phospholipase A2 (sPLA2, K01047) was in blue and prostaglandin-H2 Delta-isomerase (PTGDS, K04097) was in red (PPTX 81 kb)
10811_2019_1810_MOESM8_ESM.docx (15 kb)
Table S1 (DOCX 15 kb)
10811_2019_1810_MOESM9_ESM.docx (16 kb)
Table S2 (DOCX 15 kb)
10811_2019_1810_MOESM10_ESM.docx (14 kb)
Table S3 (DOCX 14 kb)

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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.School of Life ScienceShandong UniversityJinanPeople’s Republic of China
  2. 2.CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of SciencesQingdaoPeople’s Republic of China
  3. 3.Marine Ecology and Environmental Science Laboratory, Pilot National Laboratory for Marine Science and Technology (Qingdao)QingdaoPeople’s Republic of China
  4. 4.Center for Ocean Mega-Science, Chinese Academy of SciencesQingdaoPeople’s Republic of China
  5. 5.Biotechnology Research Center, Shandong Academy of Agricultural SciencesJinanPeople’s Republic of China
  6. 6.Bantry Marine Research Station Ltd.Co. CorkIreland

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