Table 2.

Functional classification of Gracilaria firma chloroplast genes

Classification	Genes
Genetic system
Maintenance	dnaB, rne, rnz, mat
RNA polymerase	rpoA, rpoB, rpoC1, rpoC2, rpoZ
Transcription factors	ompR, rbcR, tctD, ntcA
Translation	infB, infC, tsf, tufA
Ribosomal proteins	rpl1, rpl2, rpl3, rpl4, rpl5, rpl6, rpl9, rpl11, rpl12, rpl13, rpl14, rpl16, rpl18, rpl19, rpl20, rpl21, rpl22, rpl23, rpl24, rpl27, rpl28, rpl29, rpl31, rpl32, rpl33, rpl34, rpl35, rpl36, rps1, rps2, rps3, rps4, rps5, rps6, rps7, rps8, rps9, rps10, rps11, rps12, rps13, rps14, rps16, rps17, rps18, rps19, rps20
tRNA processing	tilS,
Protein quality control	clpC, dnaK, ftsH, groEL
Photosystems
Phycobilisomes	apcA, apcB, apcD, apcE, apcF, cpcA, cpcB, cpcG, cpeA, cpeB, nblA, ycf58
Photosystem I	psaA, psaB, psaC, psaD, psaE, psaF, psaI, psaJ, psaK, psaL, psaM, ycf3, ycf4
Photosystem II	psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbN, psbT, psbV, psbW, psbX, psbY, psbZ, ycf12
Cytochrome complex	petA, petB, petD, petF, petG, petJ, petL, petM, petN, ccsA, ccs1
Redox system	acsF, bas1, ftrB, dsbD, trxA
ATP synthesis
ATP synthase	atpA, atpB, atpD, atpE, atpF, atpG, atpH, atpI
Metabolism
Carbohydrates	odpA, odpB, rbcL, rbcS, cbbX, pgmA
Lipids	accA, accB, accD, acpP, fabH
Nucleotides	carA, upp
Amino acids	argB, gltB, syh, ilvB, ilvH, trpA, trpG, syfB
Cofactors	chlI, moeB, preA, thiG
Transport
Transport	cemA, secA, secG, secY, tatC, sufB, sufC, ycf38, ycf63
Unknown
Conserved ORFs	dfr, ycf17, ycf19, ycf20, ycf21, ycf22, ycf23, ycf33, ycf34, ycf35, ycf36, ycf37, ycf39, ycf40, ycf45, ycf46, ycf52, ycf53, ycf54, ycf55, ycf60, ycf65, ycf80
Unique ORFs	Gfir_ORF1, Gfir_ORF2, Gfir_ORF3, …, Gfir_ORF23
RNA genes
rRNAs	rrf, rrs, rrl
tRNAs	trnA, trnC, trnD, trnE, trnF, trnG, trnG, trnH, trnI, trnK, trnL, trnL, trnL, trnM, trnM, trnM, trnN, trnP, trnQ, trnR, trnR, trnR, trnS, trnS, trnT, trnT, trnV, trnV, trnW, trnY
Miscellaneous RNAs	ssrA, rnpB