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Table 2 List of genes present of complete chloroplast genomes 12 subg. Amygdalus species

From: The chloroplast genome of Amygdalus L. (Rosaceae) reveals the phylogenetic relationship and divergence time

Category of Genes Group of Gene Name of Gene Name of Gene Name of Gene Name of Gene Name of Gene
Self-replication Ribosomal RNA genes rrn4.5(× 2) rrn5(× 2) rrn16(× 2) rrn23(× 2)  
Transfer RNA genes trnA-UGC*,(× 2) trnC-GCA trnD-GUC trnE-UUC trnF-GAA
trnfM-CAU trnG-GCC* trnG-UCC trnH-GUG trnI-CAU(×2)
trnI-GAU*,(× 2) trnK-UUU* trnL-CAA(× 2) trnL-UAA* trnL-UAG
trnM-CAU trnN-GUU(× 2) trnP-UGG trnQ-UUG trnR-ACG(×2)
trnR-UCU trnS-GCU trnS-GGA trnS-UGA trnT-GGU
trnT-UGU trnV-GAC(× 2) trnV-UAC* trnW-CCA trnY-GUA
Small subunit of ribosome rps2 rps3 rps4(a,b,d,h,l) rps7(×2) rps8
rps11 rps12**,(×2) rps14 rps15 rps16*
rps18 rps191)    
Large subunit of ribosome rpl2*,(×2) rpl14 rpl16* rpl20 rpl22
rpl23(×2) rpl32 rpl33 rpl36  
DNA-dependent RNA polymerase rpoA rpoB rpoC1* rpoC2  
Genes for photosynthesis Subunits of NADH-dehydrogenase ndhA* ndhB*,(×2) ndhC ndhD ndhE
ndhF ndhG ndhH ndhI ndhJ
ndhK     
Subunits of photosystem I psaA psaB psaC psaI psaJ
Subunits of photosystem II psbA psbB psbC psbD psbE
psbF psbH psbI psbJ psbK
psbL psbM psbN psbT psbZ
Subunits of cytochrome b/f complex petA petB* petD* petG petL
petN     
Subunits of ATP synthase atp A atp B atp E atp F* atp H
atpI     
Subunits of rubisco rbcL     
Other genes Maturase matK     
Protease clpP**     
Envelope membrane protein cemA     
Subunit of acetyl-CoA carboxylase accD     
C-type cytochrome synthesis gene ccsA     
Genes of unknown function Conserved open reading frames ycf1(×2) ycf2(×2) ycf3**(c) ycf4 ycf15(×2)(e,f,g,i,j,k)
  1. 1) genes are two in P. davidiana var. potaninii Rehd., P. kansuensis, P. persica, P. dulcis, P. davidiana and P. mongolica and only one in P. ferganensis, P. mira, P. tenella, P. pedunculata, P. tangutica, P. triloba; a that does not have this gene in P. ferganensis; b that does not have this gene in P. mira; d that does not have this gene in P. tangutica; e that does not have this gene in P. davidiana var. potaninii Rehd.; f that does not have this gene in P. kansuensis; g that does not have this gene in P. persica; h that does not have this gene in p. pedunculata; i that does not have this gene in P. dulcis; j that does not have this gene in P. davidiana; k that does not have this gene in P. mongolica; l that does not have this gene in P. triloba; * Gene contains one intron; ** gene contains two introns; (× 2) indicates that the number of the repeat unit is 2