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Table 3 rRNA sequence variations in next generation sequencing data acquisition to study Arabidopsis microbiota

From: The Arabidopsis holobiont: a (re)source of insights to understand the amazing world of plant–microbe interactions

rRNA gene target

Primer pair sequences

Publications that use it. (Declared drawbacks/biases/modifications)

V1-V2

27F/338R

[183] (1)

V1-V3

27F: 5′-AGAGTTTGATYMTGGCTCAG-3′

533R: 5′-TTACCGCGGCTGCTGGC-3′

[39]

V3-V4

314F: 5′-CCTACGGGNGGCWGCAG-3′

805R: 5′-GACTACHVGGGTATCTAATCC-3′

[111, 205] (2) [207], (3) [106],

V3-V4

338F: 5′-ACTCCTACGGGAGGCAGCA-3

806R: 5′-GGACTACHVGGGTWTCTAAT-3′

[60, 110, 112, 154, 163]

V3-V4

341F: 5′-CCTAYGGGRBGCASCAG-3′

806R: 5′-GGACTACNNGGGTATCTAAT-3′

341F: 5′-CCTACGGGAGGCAGCAG-3′

806R: 5′-GGACTACHVGGGTWTCTAAT-3′

[2] (1) [117], (2) [108], (2) [203], (2) [52, 186],

V3-V4

341F: 5′-CCTAYGGGRBGCASCAG-3′

Uni806R:5′-GGACTACNNGGGTATCTAAT-3′

[204] (4)

V3-V4

S-D-Bact-0341-b-S-17: 5′-CCTACGGGNGGCWGCAG-3′

S-D-Bact-0785-a-A-21: 5′-GACTACHVGGGTATCTAATCC-3′

[98, 174]

V3-V5

341F/907R:

[156] (1)

V3-V5

479F: 5′-CAGCMGCYGCNGTAANAC-3′ 888R: 5′-CCGYCAATTCMTTTRAGT-3′

[130]

V4

515F: 5 ‘-GTGYCAGCMGCCGCGGTAA-3′

806R:5′-GGACTACNVGGGTWTCTAAT-3′

[142] (1) [68], (1) [14], (1) [101], (1) [143], (1) [36], (1) [57], (1) [54, 155, 170, 184, 194], (1) [85], (1)

V4-V5

518F/926R

[82] (1) [46], (1)

V4-V6

518F: 5′-CCAGCAGCYGCGGTAAN-3′

1046R: 5′-CGACRRCCATGCANCACCT-3′

[124]

V5-V6

784F: 5′-RGGATTAGATACCC

1064R: 5′-CGACRRCCATGCANCACCT

[178]

V5-V7

799F2: 5´-AACMGGATTAGATACCCGG-3´

1193R: 5′-ACGCATCCCCACCTTCCTC-3′

799F: 5′-AACMGGATTAGATACCCKG-3′ 1193(2)R: 5′ACGTCATCCCCACCTTCC-3′

[30] (5), (6) [23], (7) [2, 78, 169], (1) [47, 158, 190], (1) [22, 25, 50, 81, 159], (1) [16, 40, 69, 186, 201], (1) [202], (1) [87, 126, 146], (1) [51, 52],

V5-V8

799F: 5′-AACMGGATTAGATACCCKG-3′

1392R: 5′-ACGGGCGGTGTGTRC-3′

[19]

V5-V8

803F: 5′-ATTAGATACCCTGGTAGTC-3′

1392wR: 5′-ACGGGCGGTGWGTRC-3′

[10, 33,34,35]

V5-V8

804F: 5′-ATTAGATACCCDRGTAGT-3′

926F: 5′-AAACTYAAAKGAATTGACGG-3′′

1392R: 5′-ACGGGCGGTGTGRC-3′

[115]

V6-V8

1114F: 5′-GCAACGAGCGCAACCC-3′

1392R: 5′-ACGGGCGGTGTGRC-3′

[115]

V8

1114F-1392R

[101] (1)

  1. (1) PCR primer sequences not provided in that text
  2. (2) The sequence of primer 314F has some differences from other published
  3. (3) Primer 341F corresponds to 314F
  4. (4) Modified broad 341F and Uni806R
  5. (5) 799F2 is a single nucleotide modification (bolded) of F799 to avoid amplification of 18S rRNA
  6. (6) 799F2 produced an overrepresentation of Chloroflexota sequences that was computationally removed from data analysis
  7. (7) 1193R designed by authors
  8. (8) 1392R and not 1392wR is indicated as in Carvalhais et al. [33]