Table 2 List of primer sets targeting the 28S rRNA gene and their coverages in 14 taxonomic groups.

From: Improved 18S and 28S rDNA primer sets for NGS-based parasite detection

Taxonomy

Representative species

DM568F/RM2Rb

DM568F/GA13Rb

DM568F/RM3Rb

RM2F/RM3Rb

RM2F/GA15Rb

GA12F/RM4Rb

D3–D4

D3–D4

D3–D5

D4–D5

D4–D5

D4–D6

284 bp

327 bp

500 bp

236 bp

369 bp

507 bp

Nematoda (659)

Roundworm, Filaria

62.1

(339/546)

42.5

(232/546)

62.1

(339/546)

94.7

(551/582)

54.8

(319/582)

92.9

(546/588)

Platyhelminthes (571)

Tapeworm, Fluke

88.2

(439/498)

84.9

(423/498)

91.4

(455/498)

95.2

(496/521)

23.2

(121/521)

97.3

(510/524)

Acanthocephala (56)

Spiny-headed worm

94.6

(53/56)

69.6

(39/56)

94.6

(53/56)

94.6

(53/56)

28.6

(16/56)

100.0

(56/56)

Coccidia (76)

Coccidium

90.4

(66/73)

91.8

(67/73)

90.4

(66/73)

91.9

(68/74)

83.8

(62/74)

93.2

(69/74)

Cryptosporida (1)

Cryptosporidium

100.0

(1/1)

100.0

(1/1)

100.0

(1/1)

100.0

(1/1)

100.0

(1/1)

100.0

(1/1)

Haemosporidia (115)

Plasmodium

100.0

(89/89)

0.0

(0/89)

95.5

(85/89)

94.9

(93/98)

87.8

(86/98)

0.0

(0/101)

Fornicata (5)

Giardia

20.0

(1/4)

0.0

(0/5)

0.0

(0/5)

0.0

(0/5)

20.0

(1/4)

40.0

(2/5)

Discicristata (35)

Trypanosoma, Leishmania

67.7

(21/31)

61.3

(19/31)

41.9

(13/31)

40.4

(13/32)

75.0

(24/32)

100.0

(33/33)

Parabasalia (20)

Trichomonas

100.0

(17/17)

94.1

(16/17)

0.0

(0/17)

0.0

(0/18)

61.1

(11/18)

5.6

(1/18)

Entamoebida (9)

Entamoeba

100.0

(5/5)

0.0

(0/5)

0.0

(0/5)

0.0

(0/8)

0.0

(0/8)

0.0

(0/8)

Longamoebia (1)

Acanthamoeba

100.0

(1/1)

100.0

(2/2)

100.0

(1/1)

100.0

(2/2)

100.0

(1/1)

100.0

(1/1)

Fungi (3671)

 

81.8

(2876/3515)

93.2

(3277/3515)

94.1

(3308/3515)

93.6

(3347/3576)

85.1

(3044/3576)

95.5

(3416/3578)

Bacteria (124805)

 

<0.1

(12/122765)

<0.1

(5/122772)

<0.1

(9/122777)

<0.1

(9/123872)

<0.1

(22/123872)

<0.1

(5/124043)

Euteleostomi (445)

Mammalc

74.7h,m

(236/316)

75.3h,m

(238/316)

77.2h,m

(244/316)

79.5h,m

(303/381)

75.3h,m

(287/381)

82.7h,m

(324/392)

RM3F/RM4R b

GA14F/RM4R b

GA18F/RM7R b

GA18F/RM8R b

GA20F/RM7R b

GA20F/RM8R b

GA20F/RM9R b

D6

D6

D8

D8

D8

D8-D9

D8-D9

333 bp

202 bp

424 bp

572 bp

348 bp

406 bp

505 bp

92.5

(564/610)

95.5

(592/620)

95.9

(626/653)

95.8

(619/646)

97.7

(638/653)

97.8

(632/646)

98.0

(632/645)

97.8

(523/535)

96.7

(526/544)

86.3

(465/539)

89.0

(471/529)

91.7

(493/539)

94.5

(500/529)

96.6

(510/528)

100.0

(56/56)

35.7

(20/56)

96.4

(54/56)

100.0

(56/56)

96.4

(54/56)

100.0

(56/56)

100.0

(56/56)

91.9

(68/74)

91.9

(68/74)

97.1

(68/70)

95.5

(64/67)

98.6

(69/70)

97.0

(65/67)

98.5

(65/66)

100.0

(1/1)

100.0

(1/1)

100.0

(1/1)

100.0

(1/1)

100.0

(1/1)

100.0

(1/1)

100.0

(1/1)

95.2

(99/104)

98.1

(104/106)

61.1

(69/113)

61.6

(69/112)

92.0

(104/113)

97.3

(109/112)

97.3

(109/112)

20.0

(1/5)

60.0

(3/5)

0.0

(0/5)

0.0

(0/5)

100.0

(5/5)

100.0

(5/5)

100.0

(5/5)

57.1

(20/35)

100.0

(35/35)

48.6

(17/35)

45.7

(16/35)

62.9

(22/35)

60.0

(21/35)

62.9

(22/35)

0.0

(0/20)

0.0

(0/20)

0.0

(0/20)

36.8

(7/19)

0.0

(0/20)

94.7

(18/19)

94.7

(18/19)

100.0

(9/9)

100.0

(9/9)

0.0

(0/9)

0.0

(0/9)

0.0

(0/9)

0.0

(0/9)

0.0

(0/9)

100.0

(1/1)

100.0

(1/1)

100.0

(2/2)

100.0

(1/1)

100.0

(1/1)

100.0

(1/1)

100.0

(1/1)

94.7

(3425/3617)

95.5

(3469/3631)

90.7

(2943/3244)

88.6

(2839/3205)

95.2

(3087/3244)

92.5

(2966/3205)

93.8

(3006/3205)

<0.1

(5/124626)

<0.1

(6/124788)

<0.1

(13/124775)

<0.1

(10/124065)

<0.1

(13/124775)

<0.1

(10/124065)

<0.1

(23/124041)

83.3h,m

(340/408)

82.3h,m

(340/413)

74.2h,m

(316/426)

75.6h,m

(304/402)

72.3h,m

(308/426)

73.6h,m

(296/402)

75.3h,m

(302/401)

  1. Primer sets were tested for matches to sequences in the SILVA database (v.132) using TestPrime under the following parameters: maximum number of mismatches of four bases and length of 0-mismatch at the 3′ end of three bases). TestPrime computes coverages for each taxonomic group by running in silico PCR on the SILVA database via sorting database sequences into “match”, “mismatch” and “nodata (sequences not covering the primer match position)”. The frequencies of “match” sequences among “match” and “mismatch” sequences are shown as percentages with the sequence numbers in parentheses.
  2. aNumbers in parentheses show the numbers of sequences available in the SILVA database. Please note these numbers are not always the denominators because of the presence of “nodata” sequences.
  3. bTarget variable regions and amplicon sizes based on the S. cerevisiae rRNA gene (NC_001144) are shown below the primer names.
  4. cPrimer match to humans and mice is indicated by superscripts h and m on the values, respectively.
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