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Table 2 Reference genome bins garnering the most metagenomic reads, organized by station and domain (top 10 Bacteria, 4 Eukarya, 2 Archaea, and 2 viruses)

From: The Amazon continuum dataset: quantitative metagenomic and metatranscriptomic inventories of the Amazon River plume, June 2010

Domain Taxon Genes L−1 Domain Taxon Genes L−1
Station 10
Bacteria Synechococcus sp. CB0205 1.46 × 1012 Eukarya Thalassiosira oceanica CCMP1005 1.26 × 1011
Bacteria SAR86 E 4.65 × 1011 Eukarya Micromonas sp. RCC299 8.27 × 1010
Bacteria SAR86 D 2.55 × 1011 Eukarya Tetrahymena thermophila SB210 2.41 × 1010
Bacteria Alphaproteobacterium HIMB5 2.32 × 1011 Eukarya Strombidinopsis sp. SopsisLIS2011 1.67 × 1010
Bacteria Cand. Pelagibacter sp. HTCC7211 2.22 × 1011    
Bacteria Cand. Pelagibacter ubique 1.54 × 1011 Archaea Nitrosopumilus maritimus SCM1 1.73 × 1010
Bacteria SAR86 C 1.39 × 1011 Archaea Cand. Nitrosopumilus koreensis AR1 1.02 × 1010
Bacteria Gammaproteobacterium HIMB55 1.33 × 1011    
Bacteria Synechococcus sp. CB0101 1.19 × 1011 Virus Synechococcus phage S-RSM4 1.74 × 1011
Bacteria Gammaproteobacterium HIMB30 1.15 × 1011 Virus Synechococcus phage S-SKS1 1.74 × 1011
Station 3
Bacteria Cand. Pelagibacter sp. HTCC7211 2.79 × 1011 Eukarya Micromonas sp. RCC299 2.28 × 1010
Bacteria Alphaproteobacterium HIMB5 2.02 × 1011 Eukarya Tetrahymena thermophila SB210 4.93 × 109
Bacteria SAR86 D 1.64 × 1011 Eukarya Alexandrium tamarense CCMP1771 3.71 × 109
Bacteria SAR86 E 1.33 × 1011 Eukarya Thalassiosira oceanica CCMP1005 3.49 × 109
Bacteria Cand. Pelagibacter ubique 1.17 × 1011    
Bacteria Alphaproteobacterium HIMB59 9.29 × 1010 Archaea Nitrosopumilus maritimus SCM1 3.01 × 109
Bacteria SAR86 C 8.58 × 1010 Archaea Cand. Nitrosoarchaeum limnia 2.31 × 109
Bacteria Synechococcus sp. WH 8109 7.33 × 1010    
Bacteria Cand. Pelagibacter ubique HTCC1062 6.37 × 1010 Virus Synechococcus phage S-RSM4 6.70 × 1010
Bacteria SAR324 JCVI-SC AAA005 5.06 × 1010 Virus Synechococcus phage S-SKS1 2.57 × 1010
Station 2
Bacteria Coraliomargarita akajimensis DSM 45221 3.31 × 1012 Eukarya Phaeocystis antarctica 1.51 × 1012
Bacteria Cand. Puniceispirillum marinum IMCC1322 7.46 × 1011 Eukarya Phytophthora sojae 1.02 × 1012
Bacteria Gammaproteobacterium HIMB55 6.13 × 1011 Eukarya Emiliania hu×leyi 9.44 × 1011
Bacteria Synechococcus sp. WH 8109 6.07 × 1011 Eukarya Aplanochytrium kerguelense 7.60 × 1011
Bacteria SAR116 HIMB100 5.95 × 1011    
Bacteria Cand. Pelagibacter sp. HTCC7211 5.09 × 1011 Archaea Cand. Nitrosopumilus salaria 1.54 × 1010
Bacteria SAR324 JCVI-SC AAA005 4.61 × 1011 Archaea Methanomassiliicoccus sp. M × 1-Issoire 5.89 × 109
Bacteria Gammaproteobacterium HTCC2207 3.91 × 1011    
Bacteria Verrucomicrobiae DG1235 3.39 × 1011 Virus Synechococcus phage S-RIP1 9.55 × 108
Bacteria Prochlorococcus marinus str. AS9601 3.16 × 1011 Virus Phaeocystis globosa virus 6.20 × 108
Station 23
Bacteria Cand. Pelagibacter sp. HTCC7211 1.36 × 1012 Eukarya Tetrahymena thermophila SB210 2.96 × 1010
Bacteria Alphaproteobacterium HIMB5 9.43 × 1011 Eukarya Protocruzia adherens Boccale 2.84 × 1010
Bacteria SAR86 D 9.31 × 1011 Eukarya Strombidinopsis sp. SopsisLIS2011 2.82 × 1010
Bacteria Alphaproteobacterium HIMB59 7.03 × 1011 Eukarya Pseudo-nitzschia multiseries 1.79 × 1010
Bacteria SAR86 E 6.95 × 1011    
Bacteria Cand. Pelagibacter ubique 5.17 × 1011 Archaea Methanosarcina acetivorans C2A 1.60 × 109
Bacteria SAR86 C 4.69 × 1011 Archaea Methanosarcina barkeri str. Fusaro 1.37 × 109
Bacteria Cand. Pelagibacter ubique HTCC1062 2.74 × 1011    
Bacteria SAR324 JCVI-SC AAA005 2.33 × 1011 Virus Phaeocystis globosa virus 1.01 × 1011
Bacteria Alphaproteobacterium HIMB114 2.31 × 1011 Virus Synechococcus phage S-SM2 4.62 × 1010
Station 25
Bacteria Cand. Pelagibacter sp. HTCC7211 6.83 × 1011 Eukarya Pyraminomonas obovata CCMP722 8.58 × 109
Bacteria Alphaproteobacterium HIMB5 4.13 × 1011 Eukarya Phaeocystis antarctica 6.34 × 109
Bacteria Alphaproteobacterium HIMB59 2.35 × 1011 Eukarya Thalassiosira oceanica CCMP1005 5.67 × 109
Bacteria Cand. Pelagibacter ubique 2.07 × 1011 Eukarya Volvox carteri f. nagariensis 4.93 × 109
Bacteria Prochlorococcus marinus str. AS9601 1.87 × 1011    
Bacteria Prochlorococcus marinus str. MIT 9301 1.70 × 1011 Archaea Methanosarcina acetivorans C2A 9.95 × 108
Bacteria SAR86 E 1.67 × 1011 Archaea Methanomassiliicoccus sp. M × 1-Issoire 8.48 × 108
Bacteria SAR86 D 1.61 × 1011    
Bacteria Coraliomargarita akajimensis DSM 45221 1.45 × 1011 Virus Phaeocystis globosa virus 4.57 × 1010
Bacteria Gammaproteobacterium HTCC2207 1.29 × 1011 Virus Synechococcus phage S-SM2 2.36 × 1010
Station 27
Bacteria Prochlorococcus marinus str. AS9601 9.43 × 1012 Eukarya Phaeocystis antarctica 3.04 × 1010
Bacteria Prochlorococcus marinus str. MIT 9301 8.49 × 1012 Eukarya Tetrahymena thermophila SB210 2.25 × 1010
Bacteria Cand. Pelagibacter sp. HTCC7211 5.70 × 1012 Eukarya Ale×andrium tamarense CCMP1771 1.56 × 1010
Bacteria Prochlorococcus marinus str. MIT 9215 4.46 × 1012 Eukarya Monosiga brevicollis 1.35 × 1010
Bacteria Alphaproteobacterium HIMB5 3.96 × 1012    
Bacteria Prochlorococcus marinus str. MIT 9312 3.13 × 1012 Archaea Methanomassiliicoccus sp. M×1-Issoire 8.73 × 109
Bacteria Cand. Pelagibacter ubique 2.22 × 1012 Archaea Aciduliprofundum sp. MAR08-339 6.10 × 109
Bacteria Prochlorococcus marinus 1.75 × 1012    
Bacteria Cand. Pelagibacter ubique HTCC1062 1.31 × 1012 Virus Prochlorococcus phage P-SSM2 6.08 × 1011
Bacteria Alphaproteobacterium HIMB59 1.21 × 1012 Virus Synechococcus phage S-SM2 3.20 × 1011
  1. Bacterial, archaeal, and viral reads were annotated against the NCBI RefSeq database. Eukaryotic reads were annotated against a custom database containing marine eukaryotic genomes and transcriptomes from NCBI and 112 of the Marine Microbial Eukaryote Transcriptome Sequencing Project datasets that were public at the time of analysis (http://marinemicroeukaryotes.org).
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