1.
Annotated protein coding genes:
Group of genes                                  	Name of genes
Subunits of ATP synthase                        	atpA, atpB, atpE, atpF, atpH, atpI
Subunits of NADH-dehydrogenase            	ndhA, ndhB, ndhB_copy2, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK
Subunits of cytochrome b/f complex          	petA, petB, petD, petG, petL, petN
Subunits of photosystem I                       	psaA, psaB, psaC, psaI, psaJ
Subunits of photosystem II                      	psbA, psbB, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbT, psbZ, ycf3
Large subunit of ribosome                       	rpl14, rpl16, rpl2, rpl22, rpl23, rpl23_copy2, rpl2_copy2, rpl32, rpl33, rpl36
Small subunit of ribosome                       	rps11, rps12, rps12_copy2, rps14, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps7_copy2, rps8
DNA dependent RNA polymerase              	rpoA, rpoB, rpoC1, rpoC2
Subunit of rubisco                              	None
c-type cytochrom synthesis gene             	ccsA
Envelop membrane protein                        	cemA
Maturase                                              	matK
Protease                                              	None
Subunit of Acetyl-CoA-carboxylase           	accD
Translational initiation factor             	infA
Conserved open reading frames             	ycf1, ycf15, ycf15_copy2, ycf1_copy2, ycf2, ycf2_copy2, ycf4
Other genes                                           	clpP1, pbf1, psbc, rbcl, rps20

Possible missing protein coding genes:
Group of genes                                  	Name of genes
Subunits of ATP synthase                        	None
Subunits of NADH-dehydrogenase            	None
Subunits of cytochrome b/f complex          	None
Subunits of photosystem I                       	None
Subunits of photosystem II                      	psbC, psbN
Large subunit of ribosome                       	rpl20
Small subunit of ribosome                       	None
DNA dependent RNA polymerase              	None
Subunit of rubisco                              	rbcL
c-type cytochrom synthesis gene             	None
Envelop membrane protein                        	None
Maturase                                              	None
Protease                                              	clpP
Subunit of Acetyl-CoA-carboxylase           	None
Translational initiation factor             	None
Conserved open reading frames             	None
Other genes                                           	None

2.
Multicopy genes with different lengths:
Genes             	Length  	Location
ycf1              	5562    	[24558:30120](+)
ycf1_copy2        	1131    	[43170:44301](-)

3.
Common intron-contained genes:
Genes           	exons 	exon1 	exon2 	exon3
atpF               	(2/2)     	[81251:81394](-)	[80154:80564](-)	
ndhA               	(2/2)     	[32125:32675](+)	[33699:34239](+)	
ndhB               	(2/2)     	[11674:12450](-)	[10243:10998](-)	
ndhB_copy2    	(2/2)     	[56410:57186](+)	[57862:58617](+)	
petB               	(2/2)     	[142674:142679](+)	[143388:144029](+)	
petD               	(2/2)     	[144225:144232](+)	[144941:145415](+)	
rpl16               	(1/2)     	[148845:149204](-)	
rpl2               	(2/2)     	[1141:1539](-)	[61:495](-)	
rpl2_copy2    	(2/2)     	[67321:67719](+)	[68365:68799](+)	
rpoC1               	(2/2)     	[91570:92004](-)	[89185:90804](-)	
rps12               	(3/3)     	[137609:137722](-)	[13787:14018](-)	[13225:13250](-)	
rps12_copy2    	(3/3)     	[137609:137722](-)	[54842:55073](+)	[55610:55635](+)	
rps16               	(2/2)     	[74760:74799](-)	[73686:73912](-)	
ycf3               	(3/3)     	[112233:112358](-)	[111297:111522](-)	[110408:110562](-)	

### The exon column shows the number of (actual exons/expected exons). ###

Uncommon intron-contained genes:
clpP1               	3     	[139688:139756](-)	[138705:138993](-)	[137838:138076](-)]