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

BMC Genomics

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

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
	Large subunit of ribosome	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
	Subunits of cytochrome b/f complex	petN
	Subunits of ATP synthase	atp A	atp B	atp E	atp F^*	atp H
	Subunits of ATP synthase	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⁾ 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

ISSN: 1471-2164