Table 4 Loss of chloroplast protein coding genes and transfer RNA genes across the Cuscuta spp

C. erosa

Grammica

ndh, psaI, psaA-C, psbA-F, psbH-L, psbN/T/Z, petA/B/D/G/L/N, rbcL

rpl23, rps15, rps16, rpo

ycf1, ycf3, ycf4, matK, ccsA, cemA, ycf15**

trnA-UGC****, trnG-UCC**, trnI-CAU, trnI-GAU**, trnI-GAU**, trnK-UUU**, trnL-UAA, trnR-ACG, trnR-ACG, trnV-UAC**

C. boldinghii

ndh, psaI, psaA-C, psbA-F, psbH-L, psbT, psbZ, petA/B/D/G/L/N, rbcL, atpF

rpl23, rpl36, rpl32, rps14, rps15, rps16, rpo

ycf1, ycf3, ycf4, matK, ccsA, ycf15**

trnA-UGC****, trnG-GCC, trnG-UCC, trnI-CAU, trnI-GAU**, trnI-GAU**, trnK-UUU**, trnL-UAG, trnR-ACG**, trnV-UAC**

C. strobilacea

ndh, psaI, psaA-C, psaJ, psbA-F, psbT, psbZ, psbH/J/K/L, petA/B/D/G/L/N, rbcL

rpl23, rpl32, rpl36, rps15, rps16, rpo

ycf1, ycf3, ycf4, matK, ccsA, ycf15**

trnA-UGC****, trnG-UCC**, trnI-CAU, trnI-GAU****, trnK-UUU**, trnL-UAA, trnR-ACG**, trnV-UAC**

C. carnosa

ndh, psaI, petN, psbM

rpl23, rpl32, rps15, rps16, rpo

ycf1, matK, ccsA, ycf15**

trnA-UGC****, trnC-GCA, trnD-GUC, trnE-UUC, trnG-UCC**, trnI-CAU, trnI-GAU****, trnK-UUU**, trnL-UAA, trnR-ACG**, trnV-GAC, trnV-UAC, trnY-GUA

C. bonafortunae

ndh, psaI, psbL

rpl23, rpl32, rpl36, rps15, rps16, rpo

ycf1, matK, ycf15**

trnA-UGC****, trnG-UCC**, trnI-CAU, trnI-GAU****, trnK-UUU**, trnL-UAA, trnR-ACG**, trnV-UAC**

C. mexicana

ndh, psaI, rbcL, psbI, psbK

rpl23, rpl32, rps15, rps16, rpo

ycf1, matK, cemA, ycf15**

trnA-UGC****, trnG-UCC**, trnI-CAU, trnI-GAU****, trnK-UUU**, trnL-UAA, trnR-ACG**, trnR-UCU, trnS-GCU, trnV-UAC**

C. chapalana

ndh, psaI

rpl23, rpl32, rps15, rps16, rpo

ycf1, matK, ycf15**

trnA-UGC****, trnG-UCC**, trnI-CAU, trnI-GAU****, trnK-UUU**, trnL-UAA, trnR-ACG**, trnV-UAC**

C. costaricensis

ndh, psaI, atpI

rpl23, rpl32, rps15, rps16, rpo

ycf1, matK, ycf15**

trnA-UGC****, trnG-UCC**, trnI-GAU****, trnK-UUU**, trnL-UAA, trnR-ACG**, trnV-UAC**

C. australis

ndh, psaI

rpl23, rpl32, rps15, rps16, rpo

ycf1, matK, ycf15**

trnA-UGC****, trnG-UCC**, trnI-GAU****, trnK-UUU**, trnL-UAA, trnR-ACG**, trnV-UAC**

C. obtusiflora

ndh, psaI

rpl23, rpl32, rps15, rps16, rpo

ycf1, matK, ycf15**

trnA-UGC****, trnG-UCC**, trnI-GAU****, trnK-UUU**, trnR-ACG**, trnV-UAC**

C. campestris

ndh, psaI

rpl23, rpl32, rps15, rps16, rps12, rpo

ycf1, matK, ycf15**

trnA-UGC****, trnG-UCC**, trnI-GAU****, trnK-UUU**, trnL-UAA, trnR-ACG**, trnV-UAC**

C. pentagona

ndh, psaI, atpE

rpl23, rpl32, rps15, rps16, rpo

matK, ycf15**

trnA-UGC****, trnG-UCC**, trnI-GAU****, trnK-UUU**, trnL-UAA, trnR-ACG**, trnV-UAC**

C. gronovii

ndh, psaI

rpl23, rpl32, rps15, rps16, rpo

ycf1, matK, ycf15**

trnA-UGC****, trnG-UCC**, trnI-GAU****, trnK-UUU**, trnL-UAA, trnR-ACG**, trnV-UAC**

C. gronovii (this study)

ndh, psaI

rpl23, rpl32, rps15, rps16, rpo

ycf1, matK, ycf15**

trnA-UGC****, trnG-UCC**, trnI-GAU****, trnK-UUU**, trnL-UAA, trnR-ACG**, trnV-UAC**

C. chinensis

ndh, psaI

rpl23, rpl32, rps15, rps16, rpo

matK, ycf15**

trnA-UGC****, trnG-UCC**, trnI-GAU****, trnK-UUU**, trnL-UAA**, trnR-ACG**, trnT-GGU, trnV-UAC**

C. chinensis (this study)

ndh, psaI

rpl23, rpl32, rps15, rps16, rpo

matK, ycf15**

trnA-UGC****, trnG-UCC**, trnI-GAU****, trnK-UUU**, trnL-UAA**, trnR-ACG**, trnT-GGU, trnV-UAC**

C. epithymum (this study)

Cuscuta

ndh

rpl23, rps7, rps12, rps15

ycf1, ycf2, ycf15**

trnA-UGC^***, trnG-UCC^**, trnI-GAU^***, trnK-UUU^**, trnL-CAA, trnL-CAA, trnV-GUU, trnR-ACG, trnV-GAC^**

C. europaea (this study)

ndh, psaA

rpl16, rpl2, rpl23, rps12, rps15, rps4, rps7

ycf1, ycf2, ycf15**, matK, ccsA

trnA-UGC^***, trnG-UCC^**, trnI-CAU, trnI-GAU^**, trnK-UUU^**, trnL-CAA, trnL-UAA, trnN-GUU, trnR-ACG, trnV-GAC, trnV-UAC

C. pedicellata

ndh

rpl23, rps15, rps16, rps7, rps12, rpoC2

ycf1, ycf2, ycf15**

trnA-UGC***, trnG-UCC**, trnI-CAU, trnI-GAU***, trnK-UUU**, trnL-CAA, trnL-UAA, trnN-GUU, trnR-ACG, trnV-GAC, trnV-UAC**

C. approximata

ndh

rpl23, rps15, rps16, rps7, rps12, rpoC2

ycf1, ycf2, ycf15**

trnA-UGC***, trnG-UCC**, trnI-CAU, trnI-GAU**, trnK-UUU**, trnL-CAA, trnL-UAA, trnN-GUU, trnR-ACG, trnV-GAC, trnV-UAC**

C. africana

Pachystigma

ndh, psbZ

rpl23, rps15, rps16, rpo

ycf1, ycf15**, clpP

trnA-UGC****, trnG-UCC**, trnI-GAU****, trnK-UUU**, trnL-UAA, trnV-UAC**

C. nitida

ndh

rpl23, rps15, rps16

ycf1, ycf15**

trnA-UGC****, trnG-UCC**, trnI-GAU****, trnK-UUU**, trnL-UAA, trnV-UAC**

C. japonica

Monogynella

ndh

rpl23, rps15, rps16

ycf1, ycf2, ycf15**

trnA-UGC**, trnG-UCC**, trnI-CAU, trnI-GAU**, trnK-UUU**, trnL-UAA, trnV-UAC**

C. japonica (this study)

ndh

rpl23, rps15, rps16

ycf1, ycf2, ycf15**

trnA-UGC**, trnG-UCC**, trnI-CAU, trnI-GAU**, trnK-UUU**, trnL-UAA, trnV-UAC**

C. reflexa

ndh

rpl23, rps15, rps16

ycf1, ycf2, ycf15**

trnA-UGC**, trnG-UCC, trnI-CAU, trnI-GAU**, trnK-UUU**, trnL-UAA, trnV-GAC**

C. exaltata

ndh

rpl23, rps15, rps16

ycf1, ycf2, ycf15**

trnA-UGC**, trnG-UCC, trnI-CAU, trnI-GAU**, trnK-UUU**, trnL-UAA, trnV-UAC