生物技术通报 ›› 2020, Vol. 36 ›› Issue (11): 112-121.doi: 10.13560/j.cnki.biotech.bull.1985.2020-0285
李裕华1(), 任永康2, 赵兴华3, 刘江3, 韩斌3, 王长彪3(), 唐朝晖4()
收稿日期:
2020-03-16
出版日期:
2020-11-26
发布日期:
2020-11-20
作者简介:
李裕华,男,硕士研究生,研究方向:小麦遗传育种;E-mail: 基金资助:
LI Yu-hua1(), REN Yong-kang2, ZHAO Xing-hua3, LIU Jiang3, HAN bin3, WANG Chang-biao3(), TANG Zhao-hui4()
Received:
2020-03-16
Published:
2020-11-26
Online:
2020-11-20
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。
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.
Crop species | GenBank | Chloroplast genome characteristics of crops | ||||||||
---|---|---|---|---|---|---|---|---|---|---|
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 |
表1 完成测序的部分禾本科作物叶绿体基因组序列分析
Crop species | GenBank | Chloroplast genome characteristics of crops | ||||||||
---|---|---|---|---|---|---|---|---|---|---|
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 |
图1 水稻(Oryza sativa)叶绿体基因组结构图 NCBI登录号:NC_031333.1,利用在线绘制软件OGDRAW绘制因此,叶绿体基因组的大小变化在进化过程中主要受到反向重复区的长度变异所影响[20]。禾本科作物在进化过程中,其叶绿体基因组的结构发生了变化[4,19]。在禾本科作物与烟草的叶绿体基因组比对时发现,基因排列的顺序及转录方向存在差异。禾本科作物叶绿体基因组中基因的排列从trnR至trnfM、trnG至psbD以及trnT区域内出现了3次倒置[19,21]。其他物种中暂未发现此种现象,说明倒置发生在禾本科植物的共同祖先中[4,19,22]。
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 |
表2 叶绿体基因组中的基因类型分布
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 |
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