Skip to main content

Table 1 Comparison of general genome features of three Amazon Thaumarchaeota genomes and their phylogenetically closest members

From: Genome-resolved metagenomics analysis provides insights into the ecological role of Thaumarchaeota in the Amazon River and its plume

 ThauP25ThauP41ThauR71N4SAT1CN25
Genome size, bp934,7971,256,6991,047,5321,636,1251,620,1561,232,128
DNA coding region, bp878,7691,159,316970,6321,500,9291,499,2741,164,105
G + C content, mol%33.1537.8237.9942.2541.0033.16
Total RNA genes, n475030464847
tRNA genes, n444327414342
rRNA genes, n031333
Other RNA genes, n342222
Total number of genes, n145317711454195519241516
Total CDSs, n (%)1406 (96.77)1721 (97.18)1424 (97.94)1909 (97.65)1876 (97.51)1469 (96.90)
With predicted function, n (%)920 (63.32)1119 (63.18)944 (64.92)1233 (63.07)1212 (62.99)985 (64.97)
Predicted with COG database, n (%)583 (40.12)791 (44.66)660 (45.39)1006 (51.46)998 (51.87)850 (56.07)
Predicted with TIGRFAMs database, n (%)333 (22.92)402 (22.70)343 (23.59)456 (23.32)463 (24.06)413 (27.24)
Encoding signal peptides, n (%)18 (1.24)51 (2.88)36 (2.48)81 (4.14)89 (4.63)40 (2.64)
Encoding transmembrane proteins, n (%)231 (15.90)319 (18.01)255 (17.54)428 (21.89)424 (22.04)289 (19.06)
Without predicted function, n (%)486 (33.45)602 (33.99)480 (33.01)676 (34.58)644 (34.51)484 (31.93)
In internal clusters, n (%)381 (26.22)457 (25.80)234 (16.09)149 (7.62)137 (7.12)66 (4.35)
Metadata
 Isolation source, habitatSeawaterSeawaterFreshwaterGeothermal hot springWastewaterSeawater
 Atlantic OceanAtlantic OceanBrazilRussianChinaPacific Ocean
 Thaumarchaeota group1.1a1.1a1.1a1.1a1.1a1.1a
 SpeciesNitrosopelagicus sp.Nitrosotenuis sp.Nitrosotenuis sp.Nitrosotenuis uzonensisNitrosotenuis cloacaeNitrosopelagicus brevis
  1. Abbreviations: CDSs coding sequences, COG clusters of orthologous groups, rRNA ribosomal RNA, tRNA transfer RNA