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, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, ycf3
Large subunit of ribosome                       	rpl14, rpl16, rpl2, rpl20, 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, rpoC1_copy2, rpoC2
Subunit of rubisco                              	rbcL
c-type cytochrom synthesis gene             	ccsA
Envelop membrane protein                        	cemA
Maturase                                              	matK
Protease                                              	clpP
Subunit of Acetyl-CoA-carboxylase           	accD
Translational initiation factor             	infA
Conserved open reading frames             	ycf1, ycf2, ycf2_copy2, ycf4
Other genes                                           	lhbA

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                      	psbZ
Large subunit of ribosome                       	None
Small subunit of ribosome                       	None
DNA dependent RNA polymerase              	None
Subunit of rubisco                              	None
c-type cytochrom synthesis gene             	None
Envelop membrane protein                        	None
Maturase                                              	None
Protease                                              	None
Subunit of Acetyl-CoA-carboxylase           	None
Translational initiation factor             	None
Conserved open reading frames             	ycf15
Other genes                                           	None

2.
Multicopy genes with different lengths:
Genes             	Length  	Location
rpoC1             	1659    	[20614:22273](-)
rpoC1_copy2       	438     	[22981:23419](-)

3.
Common intron-contained genes:
Genes           	exons 	exon1 	exon2 	exon3
atpF               	(2/2)     	[12935:13079](-)	[11785:12194](-)	
clpP               	(3/3)     	[69924:69992](-)	[68764:69054](-)	[67977:68204](-)	
ndhA               	(2/2)     	[118288:118839](-)	[116767:117300](-)	
ndhB               	(2/2)     	[94400:95176](-)	[92965:93720](-)	
ndhB_copy2    	(2/2)     	[137485:138261](+)	[138941:139696](+)	
petB               	(2/2)     	[72874:72879](+)	[73714:74361](+)	
petD               	(2/2)     	[74550:74558](+)	[75319:75792](+)	
rpl16               	(2/2)     	[80671:80679](-)	[79240:79638](-)	
rpl2               	(2/2)     	[83473:83863](-)	[82377:82810](-)	
rpl2_copy2    	(2/2)     	[148798:149188](+)	[149851:150284](+)	
rpoC1               	(1/2)     	[20615:22273](-)	
rpoC1_copy2    	(1/2)     	[22982:23419](-)	
rps12               	(3/3)     	[67718:67831](-)	[96564:96794](-)	[95994:96020](-)	
rps12_copy2    	(3/3)     	[67718:67831](-)	[135867:136097](+)	[136641:136667](+)	
rps16               	(2/2)     	[5752:5793](-)	[4706:4933](-)	
ycf3               	(3/3)     	[43758:43886](-)	[42828:43055](-)	[41931:42083](-)	

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