禾本科主要农作物叶绿体基因组研究进展

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

摘要/Abstract

摘要：

叶绿体是植物细胞所特有的细胞器,是光合作用的主要场所。叶绿体拥有独立的核外基因组,编码与自身功能相关的部分基因,具有半自主性。叶绿体基因组（cpDNA）中含有大量功能基因,在物种鉴定及系统进化研究中的应用价值已经受到研究者们的广泛关注和逐步认可。禾本科是叶绿体基因组研究比较集中的一个科,就禾本科主要作物的叶绿体基因组特征、基因类型分布、RNA编辑以及禾本科主要作物叶绿体基因组在系统发育中的应用等方面进行了综合分析,旨为下一步解析禾本科叶绿体基因组在物种的进化、遗传、系统发育关系等方面的研究奠定基础。

关键词: 禾本科作物, 叶绿体基因组, 系统发育组学, RNA编辑

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

李裕华, 任永康, 赵兴华, 刘江, 韩斌, 王长彪, 唐朝晖. 禾本科主要农作物叶绿体基因组研究进展[J]. 生物技术通报, 2020, 36(11): 112-121.

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.

图/表 3

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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