TABLE 1.
Overview of Chloroflexi co-assembled genomes (CAGsa) and single amplified genomes (SAGs) obtained from targeted cell sorting combined with single-cell genomics and metagenome assembled genomes (MAGs) from the LEA2015 sample.
| Genome | Compl. (%) | CheckM contamination Statistics* [Cont./SH/Adj-Cont.] (%) | Size (Mbp) | GC (%) | Classification | NCBI accession |
| Chloroflexi CAGs and SAGs | ||||||
| Clx_CAG1 | 89.81 | 8.7/0/8.7 | 6.97 | 53.4 | Caldilineae | JAAEJZ000000000 |
| Clx_CAG2 | 75.71 | 2.3/0/2.3 | 3.41 | 62.5 | Anaerolineae | JAAEKA000000000 |
| Clx_CAG3 | 28.74 | 0/0/0 | 1.91 | 58.9 | Caldilineae | JAAEKB000000000 |
| Clx_SAG4 | 55.17 | 1.72/0/1.72 | 2.12 | 61.3 | Anaerolineae | JAAEKC000000000 |
| Clx_SAG5 | 49.14 | 0/0/0 | 3.37 | 52.9 | Caldilineae | JAAEKE000000000 |
| Clx_SAG6 | 49.06 | 1.72/0/1.72 | 1.73 | 49.1 | Anaerolineae | JAAEKF000000000 |
| Clx_SAG7 | 45.05 | 2.41/75/0.6 | 0.63 | 36.1 | Unclassified | JAAEKG000000000 |
| Clx_SAG8 | 23.82 | 0.16/0/0.16 | 0.72 | 50.6 | Ardenticatenia | JAAEKH000000000 |
| Clx_SAG9 | 23.67 | 0/0/0 | 1.42 | 63.0 | Caldilineae | JAAEKI000000000 |
| Clx_SAG10 | 20.06 | 0.34/0/0.34 | 1.10 | 57.6 | Ardenticatenia | JAAEKJ000000000 |
| Clx_SAG11 | 19.28 | 0/0/0 | 0.51 | 60.6 | Caldilineae | JAAEKK000000000 |
| Clx_SAG12 | 18.97 | 0/0/0 | 0.72 | 50.6 | Anaerolineae | JAAEKL000000000 |
| Clx_SAG13 | 16.85 | 0/0/0 | 0.88 | 47.3 | Anaerolineae | JAAEKN000000000 |
| Clx_SAG14 | 16.14 | 1.72/0/1.72 | 0.58 | 45.4 | Anaerolineae | JAAEKO000000000 |
| Clx_SAG15 | 14.42 | 0.16/0/0.16 | 1.18 | 61.9 | Ardenticatenia | JAAEKP000000000 |
| Clx_SAG16 | 14.33 | 0/0/0 | 1.72 | 59.0 | Cand. Thermofonsia | JAAEKQ000000000 |
| Clx_SAG17 | 13.95 | 0/0/0 | 0.87 | 45.4 | Anaerolineae | JAAEKR000000000 |
| Clx_SAG18 | 10.82 | 0/0/0 | 0.54 | 60.0 | Chloroflexia | JAAEKS000000000 |
| Clx_SAG19 | 5.17 | 0/0/0 | 0.12 | 46.6 | Caldilineae | JAAEKT000000000 |
| MAGs | ||||||
| Clx_MAG1 | 92.37 | 5.83/33.33/3.89 | 5.32 | 61.4 | Ardenticatenia | JAACJX000000000 |
| Clx_MAG2 | 67.63 | 0/0/0 | 1.69 | 60.5 | Thermomicrobia | JAACJY000000000 |
| Clx_MAG3 | 75.24 | 1.33/50/0.67 | 1.64 | 55.7 | Anaerolineae | JAACJZ000000000 |
| Clx_MAG4 | 48.12 | 3.45/50/1.72 | 3.09 | 64.4 | Ardenticatenia | JAACKA000000000 |
aCAGs were co-assembled from multiple SAGs as followed when 16S rRNA gene sequences resulted from screening shared at least 99% similarity and the average nucleotide identity values (ANI) determined by the Pyani package of preliminary bins shared more than 98% over at least 10% genome coverage (component SAGs listed with corresponding CheckM completeness estimations in square brackets): Clx_CAG1 (SAG1 [42%], SAG34 [36%], SAG35 [42%], SAG37 [21%], SAG38 [46%], SAG39 [35%], SAG40 [9%]); Clx_CAG2 (SAG2 [58%], SAG28 [19%], SAG29 [27%], SAG31 [30%]); Clx_CAG3 (SAG3 [12%], SAG27 [16%], SAG32 [11%], SAG33 [10%]). * Completeness and contamination estimations were based on CheckM results (Parks et al., 2015) using universal bacterial-specific marker sets. Corresponding estimations based on Chloroflexi-specific marker sets can be found in Supplementary Table 8. The CheckM “contamination” statistics are given in the form of three values: “Cont.”, original CheckM contamination estimate, based on the number of duplicate markers; “SH”, “strain heterogeneity” indicating the fraction of duplicate markers with almost complete sequence identity not reflecting cross species contamination; “Adj.-Cont.”, “adjusted contamination” giving the fraction of duplicate marker genes with distinct sequence.