Table 2 Functional classification of Gracilaria firma chloroplast genes

 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

 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 synthase

atpA, atpB, atpD, atpE, atpF, atpG, atpH, atpI

 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

cemA, secA, secG, secY, tatC, sufB, sufC, ycf38, ycf63

 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

 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