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. 2024 Jul 1;20:99. doi: 10.1186/s13007-024-01227-x

Table 1.

Statistical summary and comparative read mapping of RNA-seq data used in the study

Plant Bacteria Type of pant-bacterial interaction Method Time point (hpi) Modificationa Clean readsb Plant Bacteria
Mapped genomec Mapped genome ratiod (%) Mapped genomec Mapped genome ratiod (%) Mapped CDSe Mapped
CDS
ratiof (%)
S. lycopersicum F. dauae Positive Conventional 48 B1X/C10 119,836,355 114,930,404 95.91 1,434,056 1.2 183,600 0.15
Enriched 48 B1X/C10 12,299,298 11,505,248 92.3 127,753 1.1 70,554 0.57
B3.3X/C10 18,368,732 17,565,053 95.41 353,341 1.94 182,212 0.99
B3.3X/C15 16,216,836 15,577,275 94.98 273,359 1.8 149,081 0.9
B3.3X/C20 13,658,775 13,095,302 95.47 205,142 1.55 109,220 0.8
C. annuum Xag8ra

Incompatible,

non-host resistance

 Enriched 48 B3.3X/C15 23,631,656 21,521,157 91.07 212,168 0.90 144,087 0.61
B3.3X/C20 146,198,300 131,961,491 90.59 1,475,467 0.94 1,007,895 0.64
C. annuum Xcv3 Incompatible, host resistance Enriched 24 B3.3X/C10 26,886,048 24,293,063 90.47 496,519 1.81 332,082 1.21
B3.3X/C15 23,797,803 21,503,984 90.31 507,576 2.16 347,292 1.48
B3.3X/C20 45,286,688 40,699,396 89.82 1,143,759 2.55 846,593 1.89
C. annuum Xcv3 Incompatible, host resistance Enriched 12 B3.3X/C12 26,275,757 22,468,782 85.6 194,644 0.74 103,713 0.39
24 B3.3X/C12 24,281,467 21,360,839 88.03 509,365 2.12 317,319 1.32
48 B3.3X/C12 24,790,157 18,854,536 76.17 3,781,607 15.09 2,249,053 8.92
Conventional 12 B1X/C10 30,157,170 27,458,323 91.03 159,407 0.53 99,825 0.33
24 B1X/C10 34,311,587 31,031,802 90.44 494,298 1.44 290,749 0.85
48 B1X/C10 30,267,293 24,208,517 80.01 3,152,686 10.4 1,818,018 5.99
- Xcv3 (Mock control) - Conventional 0 B0X/C10 32,050,429 - - 30,671,378 95.69 22,184,190 69.17
C. annuum (Mock control) - - Conventional 0 B1X/C10 30,610,179 27,162,689 88.7 - - - -

a B1X, 1X volume of Dynabeads; B3.3X, 3.3X volume of Dynabeads and B0X, not addition of Dynabeads; C (10, 12, 15 and 20), number of PCR cycles in PCR enrichment step

b Trimmed reads with the mean of two or three replicates

c Number of reads (mean of two or three replicates) mapped to the plant or bacterial genome

d Percentage of mapped reads (average of two or three replicates)

e Number of reads (mean of two or three replicates) mapped to the bacterial coding sequences (CDS)

f Percentage of mapped reads to the bacterial CDS (average of two or three replicates)