Research Progress on Chloroplast Genome of Major Gramineous Crops

doi:10.13560/j.cnki.biotech.bull.1985.2020-0285

Abstract

Abstract:

Chloroplasts are unique organelles in plant cells and the main sites of photosynthesis. The chloroplasts are semi-autonomous,possessing independent extranuclear genomes that can encode some of the genes associated with their own functions. The chloroplast genomes（cpDNA）contains a large number of functional genes,and their application values in the study of species identification and phyletic evolution have been widely accepted and gradually recognized by researchers. Gramineae is one of the most concentrated families in chloroplast genome researches. In this paper,we elaborated the studies on the characteristics of the chloroplast genome,the distribution of gene types,gene sequence analysis,RNA editing,and the application of chloroplast genomes in the phylogenetic development of major Gramineae crops,so as to lay a foundation for better analyzing the chloroplast genomes of Gramineae in terms of species evolution,genetics,and phylogenetic relationships.

Key words: gramineae crops, chloroplast genome, phylogenetics, RNA editing

LI Yu-hua, REN Yong-kang, ZHAO Xing-hua, LIU Jiang, HAN bin, WANG Chang-biao, TANG Zhao-hui. Research Progress on Chloroplast Genome of Major Gramineous Crops[J]. Biotechnology Bulletin, 2020, 36(11): 112-121.

Figures/Tables 3

References 64

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Crop species	GenBank	Chloroplast genome characteristics of crops
Crop species	GenBank	Size/b	GC/%	LSC/bp	SSC/bp	IR/bp	Gene	tRNA	rRNA
Triticum aestivum	NC_002762	134545	38.3	80349	12790	20703	140	42	4
Zea mays	NC_001666	140384	38.5	82355	12536	22748	159	39	4
Oryza sativa	NC_008155	134525	38.9	80592	12335	20799	162	40	4
Sorghum bicolor	NC_008602	140754	38.5	82688	12502	22782	142	48	4
Avena sativa	NC_027468	135890	38.5	80109	12575	21603	132	37	4
Secale cereale	NC_021761	114843	37.2	ND	ND	ND	112	30	4
Hordeum vulgare	KT962228	136462	38.1	80600	12704	21579	143	51	4
Brachypodium distachyon	NC_011032	135197	38.6	79446	12668	21540	135	41	4

Crop species	GenBank	Chloroplast genome characteristics of crops
Crop species	GenBank	Size/b	GC/%	LSC/bp	SSC/bp	IR/bp	Gene	tRNA	rRNA
Triticum aestivum	NC_002762	134545	38.3	80349	12790	20703	140	42	4
Zea mays	NC_001666	140384	38.5	82355	12536	22748	159	39	4
Oryza sativa	NC_008155	134525	38.9	80592	12335	20799	162	40	4
Sorghum bicolor	NC_008602	140754	38.5	82688	12502	22782	142	48	4
Avena sativa	NC_027468	135890	38.5	80109	12575	21603	132	37	4
Secale cereale	NC_021761	114843	37.2	ND	ND	ND	112	30	4
Hordeum vulgare	KT962228	136462	38.1	80600	12704	21579	143	51	4
Brachypodium distachyon	NC_011032	135197	38.6	79446	12668	21540	135	41	4

category for gene	Group of gene	Name of gene
Photosynthetic	photosystem I	psaA,psaB,psaC,psaI,psaJ,ycf3,ycf4
	photosystemⅡ	psbA,psbB,psbC,psbD,psbE,psbF,psbH,psbI,psaJ,psbK,psbL,psbM,psbN,psbT,psbZ
	NADH dehydrogenase	ndhA,ndhB,ndhC,ndhD,ndhE,ndhF,ndhG,ndhH,ndhI,ndhJ,ndhK
	cytochrome b/f complex	petA,petB,petD,petG,petL,petN
	ATP synthase	atpA,atpB,atpE,atpF,atpH,atpI
	Large subunit of rubisco	rbcL
Self-replication	Proteins of large ribosomal subunit	rpl12,rpl114,rpl16,rpl20,rpl22,rpl23,rpl32,rpl33,rpl36
	Proteins of small ribosomal subunit	rps2,rps3,rps4,rps7,rps8,rps11,rps12,rps14,rps15,rps16,rps18,rps19
	RNA polymerase	rpoA,rpoB,rpoC1,rpoC2
	Ribosomal RNAs	rrn4.5S,rrn5S,rrn23S,rrn16S
	Transfer RNAs	trnC-GCA,trnD-GUC,trnF-GAA,trnfM-CAU,trnG-GCC,trnH-GUG,trnI-CAU,trnK-UUU,trnL-CAA,trnL-UAA,trnL-UAG,trnM-CAU,trnN-GUU,trnP-UGG,trnQ-UUG,trnR-ACG,trnR-UCU,trnS-GCU,trnS-GGA,trnS-UGA,trnT-UGU,trnV-GAC,trnV-UAC,trnW-CCA,trnY-GUA
Biosynthesis	Maturase	matK
	Protease	clpP
	Envelope membrane protein	cemA
	Acetyl-CoA carboxylase	accD
	c-type cytochrome synthesis gene	ccsa
	Translation initiation factor	infA
Unknown function	Conserved hypothetical chloroplast Reading Frames	ycf1,ycf2,ycf15

category for gene	Group of gene	Name of gene
Photosynthetic	photosystem I	psaA,psaB,psaC,psaI,psaJ,ycf3,ycf4
	photosystemⅡ	psbA,psbB,psbC,psbD,psbE,psbF,psbH,psbI,psaJ,psbK,psbL,psbM,psbN,psbT,psbZ
	NADH dehydrogenase	ndhA,ndhB,ndhC,ndhD,ndhE,ndhF,ndhG,ndhH,ndhI,ndhJ,ndhK
	cytochrome b/f complex	petA,petB,petD,petG,petL,petN
	ATP synthase	atpA,atpB,atpE,atpF,atpH,atpI
	Large subunit of rubisco	rbcL
Self-replication	Proteins of large ribosomal subunit	rpl12,rpl114,rpl16,rpl20,rpl22,rpl23,rpl32,rpl33,rpl36
	Proteins of small ribosomal subunit	rps2,rps3,rps4,rps7,rps8,rps11,rps12,rps14,rps15,rps16,rps18,rps19
	RNA polymerase	rpoA,rpoB,rpoC1,rpoC2
	Ribosomal RNAs	rrn4.5S,rrn5S,rrn23S,rrn16S
	Transfer RNAs	trnC-GCA,trnD-GUC,trnF-GAA,trnfM-CAU,trnG-GCC,trnH-GUG,trnI-CAU,trnK-UUU,trnL-CAA,trnL-UAA,trnL-UAG,trnM-CAU,trnN-GUU,trnP-UGG,trnQ-UUG,trnR-ACG,trnR-UCU,trnS-GCU,trnS-GGA,trnS-UGA,trnT-UGU,trnV-GAC,trnV-UAC,trnW-CCA,trnY-GUA
Biosynthesis	Maturase	matK
	Protease	clpP
	Envelope membrane protein	cemA
	Acetyl-CoA carboxylase	accD
	c-type cytochrome synthesis gene	ccsa
	Translation initiation factor	infA
Unknown function	Conserved hypothetical chloroplast Reading Frames	ycf1,ycf2,ycf15