Symbiont cross-reference

Please find below a dynamically generated cross-referencing list of different marker regions. These are based on samples of which the Symbiodinium were typed using more than one marker. Please note that the resolution of markers can vary (e.g. clade-level using 18S versus subclade-level using ITS2).

ITS2 marker


B1: B1 (ITS1)
B36: B36 (ITS1)
C1: C1 (ITS1), C1a (ITS1), C3a (ITS1)
C15: C15 (ITS1), Clsu10 (LSU D1/D2), Clsu11 (LSU D1/D2)
C17: C17 (psbA)
C1c: C1c (ITS1)
C1q: C1q (ITS1)
C21: C21 (psbA), Clsu1 (LSU D1/D2)
C26: C26a (psbA)
C26a: C26a (psbA)
C3: C3 (psbA), Clsu3 (LSU D1/D2)
C31: C31 (psbA)
C33: C (18S), C33 (ITS1), C33 (LSU D1/D2), C33 (cp23S), Clsu13 (LSU D1/D2)
C33a: C (18S), C33a (ITS1), C33a (LSU D1/D2), C33a (cp23S), Clsu13 (LSU D1/D2)
C35a: C (18S), C35a (ITS1), C35a (LSU D1/D2), C35a (cp23S), C78a (ITS1), Clsu7 (LSU D1/D2)
C3h: C3h (psbA)
C3k: C3k (psbA)
C3n-t: C (18S), C3n-t (LSU D1/D2), C3n-t (cp23S), Clsu9 (LSU D1/D2)
C42: C (18S), C42 (LSU D1/D2), C42a (ITS1)
C42a: C (18S), C42a (ITS1), C42a (LSU D1/D2), C42a (cp23S)
C42ab: Clsu12 (LSU D1/D2)
C42b: C (18S), C42a (ITS1), C42b (LSU D1/D2), C42b (cp23S)
C64: C64 (ITS1)
C73: Clsu10 (LSU D1/D2), Clsu11 (LSU D1/D2)
C78a: C (18S), C35a (ITS1), C78a (ITS1), C78a (LSU D1/D2), C78a (cp23S), Clsu5 (LSU D1/D2), Clsu6 (LSU D1/D2)
C79: C (18S), C79 (ITS1), C79 (LSU D1/D2), C79 (cp23S), Clsu8 (LSU D1/D2)
C84a: C84a (ITS1)
C8a: C (18S), C8a (ITS1), C8a (LSU D1/D2), C8a (cp23S), Clsu4 (LSU D1/D2)
D(undefined): Dlsu1 (LSU D1/D2)
D1: Dlsu2 (LSU D1/D2)
D3: D3 (ITS1)

18S marker


C: C(undefined) (LSU D1/D2), C(undefined)_Al13_Loh (LSU D1/D2), C(undefined)_Al25_Loh (LSU D1/D2), C(undefined)_Al26_Loh (LSU D1/D2), C(undefined)_Al2_Loh (LSU D1/D2), C(undefined)_Al3_Loh (LSU D1/D2), C(undefined)_Al45_Loh (LSU D1/D2), C(undefined)_Al53_Loh (LSU D1/D2), C(undefined)_Al5_Loh (LSU D1/D2), C(undefined)_Al6_Loh (LSU D1/D2), C(undefined)_Loh (LSU D1/D2), C(undefined)_Sh2_Loh (LSU D1/D2), C(undefined)_Sh6_Loh (LSU D1/D2), C(undefined)_Sh8_Loh (LSU D1/D2), C33 (ITS1), C33 (ITS2), C33 (LSU D1/D2), C33 (cp23S), C33a (ITS1), C33a (ITS2), C33a (LSU D1/D2), C33a (cp23S), C35a (ITS1), C35a (ITS2), C35a (LSU D1/D2), C35a (cp23S), C3n-t (ITS2), C3n-t (LSU D1/D2), C3n-t (cp23S), C42 (ITS2), C42 (LSU D1/D2), C42a (ITS1), C42a (ITS2), C42a (LSU D1/D2), C42a (cp23S), C42b (ITS2), C42b (LSU D1/D2), C42b (cp23S), C78a (ITS1), C78a (ITS2), C78a (LSU D1/D2), C78a (cp23S), C79 (ITS1), C79 (ITS2), C79 (LSU D1/D2), C79 (cp23S), C8a (ITS1), C8a (ITS2), C8a (LSU D1/D2), C8a (cp23S)

ITS1 marker


B1: B1 (ITS2)
B36: B36 (ITS2)
C1: C1 (ITS2)
C15: C15 (ITS2)
C1a: C1 (ITS2)
C1c: C1c (ITS2)
C1q: C1q (ITS2)
C33: C (18S), C33 (ITS2), C33 (LSU D1/D2), C33 (cp23S)
C33a: C (18S), C33a (ITS2), C33a (LSU D1/D2), C33a (cp23S)
C35a: C (18S), C35a (ITS2), C35a (LSU D1/D2), C35a (cp23S), C78a (ITS2)
C3a: C1 (ITS2)
C42a: C (18S), C42 (ITS2), C42 (LSU D1/D2), C42a (ITS2), C42a (LSU D1/D2), C42a (cp23S), C42b (ITS2), C42b (LSU D1/D2), C42b (cp23S)
C64: C64 (ITS2)
C78a: C (18S), C35a (ITS2), C78a (ITS2), C78a (LSU D1/D2), C78a (cp23S)
C79: C (18S), C79 (ITS2), C79 (LSU D1/D2), C79 (cp23S)
C84a: C84a (ITS2)
C8a: C (18S), C8a (ITS2), C8a (LSU D1/D2), C8a (cp23S)
D3: D3 (ITS2)

cp23S marker


C33: C (18S), C33 (ITS1), C33 (ITS2), C33 (LSU D1/D2)
C33a: C (18S), C33a (ITS1), C33a (ITS2), C33a (LSU D1/D2)
C35a: C (18S), C35a (ITS1), C35a (ITS2), C35a (LSU D1/D2)
C3n-t: C (18S), C3n-t (ITS2), C3n-t (LSU D1/D2)
C42a: C (18S), C42a (ITS1), C42a (ITS2), C42a (LSU D1/D2)
C42b: C (18S), C42a (ITS1), C42b (ITS2), C42b (LSU D1/D2)
C78a: C (18S), C78a (ITS1), C78a (ITS2), C78a (LSU D1/D2)
C79: C (18S), C79 (ITS1), C79 (ITS2), C79 (LSU D1/D2)
C8a: C (18S), C8a (ITS1), C8a (ITS2), C8a (LSU D1/D2)

psbA marker


C17: C17 (ITS2)
C21: C21 (ITS2)
C26a: C26 (ITS2), C26a (ITS2)
C3: C3 (ITS2)
C31: C31 (ITS2)
C3h: C3h (ITS2)
C3k: C3k (ITS2)

LSU D1/D2 marker


C(undefined): C (18S)
C(undefined)_Al13_Loh: C (18S)
C(undefined)_Al25_Loh: C (18S)
C(undefined)_Al26_Loh: C (18S)
C(undefined)_Al2_Loh: C (18S)
C(undefined)_Al3_Loh: C (18S)
C(undefined)_Al45_Loh: C (18S)
C(undefined)_Al53_Loh: C (18S)
C(undefined)_Al5_Loh: C (18S)
C(undefined)_Al6_Loh: C (18S)
C(undefined)_Loh: C (18S)
C(undefined)_Sh2_Loh: C (18S)
C(undefined)_Sh6_Loh: C (18S)
C(undefined)_Sh8_Loh: C (18S)
C33: C (18S), C33 (ITS1), C33 (ITS2), C33 (cp23S)
C33a: C (18S), C33a (ITS1), C33a (ITS2), C33a (cp23S)
C35a: C (18S), C35a (ITS1), C35a (ITS2), C35a (cp23S)
C3n-t: C (18S), C3n-t (ITS2), C3n-t (cp23S)
C42: C (18S), C42 (ITS2), C42a (ITS1)
C42a: C (18S), C42a (ITS1), C42a (ITS2), C42a (cp23S)
C42b: C (18S), C42a (ITS1), C42b (ITS2), C42b (cp23S)
C78a: C (18S), C78a (ITS1), C78a (ITS2), C78a (cp23S)
C79: C (18S), C79 (ITS1), C79 (ITS2), C79 (cp23S)
C8a: C (18S), C8a (ITS1), C8a (ITS2), C8a (cp23S)
Clsu1: C21 (ITS2)
Clsu10: C15 (ITS2), C73 (ITS2)
Clsu11: C15 (ITS2), C73 (ITS2)
Clsu12: C42ab (ITS2)
Clsu13: C33 (ITS2), C33a (ITS2)
Clsu3: C3 (ITS2)
Clsu4: C8a (ITS2)
Clsu5: C78a (ITS2)
Clsu6: C78a (ITS2)
Clsu7: C35a (ITS2)
Clsu8: C79 (ITS2)
Clsu9: C3n-t (ITS2)
Dlsu1: D(undefined) (ITS2)
Dlsu2: D1 (ITS2)



Please reference as: Tonk L*, Bongaerts P*, Sampayo EM, Hoegh-Guldberg O (2013) SymbioGBR: a web-based database of
Symbiodinium associated with cnidarian hosts on the Great Barrier Reef.
BMC Ecology 13:7