Open Access Research article

De novo sequencing and analysis of the Ulva linza transcriptome to discover putative mechanisms associated with its successful colonization of coastal ecosystems

Xiaowen Zhang1, Naihao Ye1*, Chengwei Liang2, Shanli Mou1, Xiao Fan1, Jianfang Xu13, Dong Xu1 and Zhimeng Zhuang1

Author Affiliations

1 Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China

2 Qingdao University of Science > Technology, Qingdao, 266042, China

3 Key Laboratory of Marine Bioactive Substance, The First Institute of Oceanography, State Oceanic administration (SOA), Qingdao, 266061, China

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BMC Genomics 2012, 13:565  doi:10.1186/1471-2164-13-565

Published: 25 October 2012

Additional files

Additional file 1:

Table S1. Annotation of Ulva genes occurring in Chlamydomonas reinhardtii, but not in Ostreococcus tauri.

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Additional file 2:

Table S2. Eighteen Ulva special isotigs conserved in land plants.

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Additional file 3:

Table S3. a. Comparison of Ulva KEGG annotation analyzed by Reads and Isotigs respectively. b. Comparison of KEGG annotation among Ulva linza (isotigs), Chlamydomonas reinhardtii, Volvox carteri, Physcomitrella patens and Arabidopsis thaliana on three different levels.

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Additional file 4:

Figure S1. Phylogenetic analysis of Lhcb proteins in six organisms. The phylogenetic tree was constructed by the neighbor-joining algorithm of the MEGA 4.0 program. A total of 1,000 bootstrap replicates were performed. Bootstrap values (1000 replicates) >50% are indicated on the branch.

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Additional file 5:

Table S4. Putative genes encoding the enzymes required for a C4-like CCM.

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Additional file 6:

Figure S2. Phylogenetic analysis of putative ammonium transporters in U. linza. The phylogenetic tree was constructed by the neighbor-joining algorithm of the MEGA 4.0 program. A total of 1,000 bootstrap replicates were performed. The prokaryote-like ammonium transporters found in U. linza was showed in red color.

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Additional file 7:

Figure S3. Phylogenetic analysis of putative phosphate transporters in U. linza. The phylogenetic tree was constructed by the neighbor-joining algorithm of the MEGA 4.0 program. A total of 1,000 bootstrap replicates were performed.

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Additional file 8:

Figure S4. Phylogenetic analysis of putative sulfate transporters in U. linza. The phylogenetic tree was constructed by the neighbor-joining algorithm of the MEGA 4.0 program. A total of 1,000 bootstrap replicates were performed.

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Additional file 9:

Figure S5. Phylogenetic analysis of putative P450s in U. linza. The phylogenetic tree was constructed by the neighbor-joining algorithm of the MEGA 4.0 program. A total of 1,000 bootstrap replicates were performed.

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Additional file 10:

Figure S6. Phylogenetic analysis of putative Glutamate dehydrogenases (GDH) in U. linza. The phylogenetic tree was constructed by the neighbor-joining algorithm of the MEGA 4.0 program. A total of 1,000 bootstrap replicates were performed.

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Additional file 11:

Figure S7. Phylogenetic analysis of putative ascorbate peroxidase (APX) genes in U. linza. The phylogenetic tree was constructed by the neighbor-joining algorithm of the MEGA 4.0 program. A total of 1,000 bootstrap replicates were performed.

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Additional file 12:

Figure S8. Phylogenetic analysis of putative catalase (CAT) genes in U. linza. The phylogenetic tree was constructed by the neighbor-joining algorithm of the MEGA 4.0 program. A total of 1,000 bootstrap replicates were performed.

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Additional file 13:

Table S5. Putative Heat-shock proteins found in U. linza. Three genes encoding Hsp70, Hsp90 and Hsp100 that not conserved in green algae and plants were shown in yellow color.

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Additional file 14:

Figure S9. Phylogenetic analysis of putative Hsp20 proteins in U. linza. The phylogenetic tree was constructed by the neighbor-joining algorithm of the MEGA 4.0 program. A total of 1,000 bootstrap replicates were performed.

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Additional file 15:

Table S6. Comparison of Heat-shock proteins among Ulva linza, Micromonas sp. RCC299, Ostreococcus tauri, Chlorella variabilis NC64A, Chlamydomonas reinhardtii, Volvox carteri and Arabidopsis thaliana.

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Additional file 16:

Table S7. Primers used in the real-time RT-PCR analysis.

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