Phylogenomic and comparative analyses of Coffeeae alliance (Rubiaceae): deep insights into phylogenetic relationships and plastome evolution

Table 1 Plastome content of Coffeeae alliance tribes

Gene group	Gene
Subunit of acetyl-CoA	accD
Large subunit of ribosomal proteins	rpl2^+,, rpl14, rpl16^+,#, rpl20, rpl23**, rpl32, rpl33, rpl36
Small subunit of ribosomal proteins	rps2, rps3, rps4, rps7*, rps8, rps11, rps12^++,*, rps14, rps15, rps16, rps18, rps19^Ψ,#
Ribosomal RNA genes	rrn4.5, rrn5, rrn16, rrn23*
Transfer RNA genes	trnA-UGC, trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnfM-CAU, trnG-GCC, trnG-UCC, trnH-GUG, trnI-CAU, trnI-GAU, trnK-UUU, trnL-CAA**, trnL-UAA, trnL-UAG, trnM-CAU, trnN-GUU, trnP-UGG, trnQ-UUG, trnR-ACG, trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC, trnV-UAC, trnW-CCA, trnY-GUA*
DNA-dependent RNA polymerase	rpoA, rpoB, rpoC1⁺, rpoC2
Photosystem I	psaA, psaB, psaC, psaI, psaJ
Photosystem II	petA, petB⁺, petD⁺, petG, petL, petN
Cytochrome b/f complex	psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ
ATP synthase	atpA, atpB, atpE, atpF, atpH, atpI
Maturase K	matK
Envelope membrane proteins	cemA
subunit of acetyl-CoA	accD
RubisCo large subunit	rbcL
Hypothetical reading frames	ycf1^Ψ,#, ycf2, ycf3⁺⁺, ycf4*
Protease	clpP⁺⁺
NADH dehydrogenase	ndhA⁺, ndhB^+,, ndhC, ndhD, ndhE, ndhF⁺⁺, ndhG, ndhH, ndhI, ndhJ, ndhK*
c-type cytochrome	ccsA

Note: +, single intron; ++, double introns; *, gene in the IR; Ψpseudogenes; #, duplicated

ISSN: 1471-2229