生物多样性 ›› 2019, Vol. 27 ›› Issue (4): 366-372. DOI: 10.17520/biods.2018332
陈志祥1,姚雪莹1,Stephen R.Downie2,王奇志1,*()
收稿日期:
2018-12-18
接受日期:
2019-01-09
出版日期:
2019-04-20
发布日期:
2019-06-05
通讯作者:
王奇志
基金资助:
Chen Zhixiang1,Yao Xueying1,Stephen R. Downie2,Wang Qizhi1,*()
Received:
2018-12-18
Accepted:
2019-01-09
Online:
2019-04-20
Published:
2019-06-05
Contact:
Wang Qizhi
摘要:
直刺变豆菜(Sanicula orthacantha)是中国广泛分布的多年生草本植物, 也是一味著名的民族药。本文通过二代高通量测序平台Illumina HiSeq PE150对直刺变豆菜叶绿体全基因组进行测序, 并通过生物信息学方法对其结构特征进行分析。结果表明: 直刺变豆菜叶绿体全基因组大小为157,163 bp, 包括大单拷贝区(large single copy, LSC)、小单拷贝区(small single copy, SSC)和2个反向重复序列(inverted repeat sequence, IRa和IRb), 长度分别为87,547 bp、17,122 bp和26,247 bp, 具有典型被子植物叶绿体基因组环状四分体结构; 共注释得到129个基因, 包括8个核糖体RNA (rRNA)基因、37个转运RNA (tRNA)基因和84个蛋白质编码基因。直刺变豆菜在叶绿体基因组结构、基因种类、排列顺序上与其他伞形科植物基本一致。直刺变豆菜叶绿体全基因组测序的成功为变豆菜属植物完整叶绿体基因组组装及其特征分析提供了新的方法。
陈志祥,姚雪莹,Stephen R.Downie,王奇志 (2019) 直刺变豆菜叶绿体全基因组及其特征. 生物多样性, 27, 366-372. DOI: 10.17520/biods.2018332.
Chen Zhixiang,Yao Xueying,Stephen R. Downie,Wang Qizhi (2019) Assembling and analysis of Sanicula orthacantha chloroplast genome. Biodiversity Science, 27, 366-372. DOI: 10.17520/biods.2018332.
图1 直刺变豆菜叶绿体全基因组。外圈基因逆时针方向转录, 内圈基因顺时针方向转录, 不同的颜色表明基因不同的功能, 小圈中深灰色表示GC含量, 浅灰色表示AT含量。
Fig. 1 Sequence map of the Sanicula orthacantha chloroplast genome. Genes drawn outside of the circle are transcribed counter-clockwise, while genes shown on the inside of the circle are transcribed clockwise. Genes belonging to different functional groups are color-coded. The dark gray in the inner circle indicates GC content, while the light gray corresponds to AT content.
基因分类 Category for genes | 基因分组 Group of genes | 基因名称 Name of genes |
---|---|---|
表达相关基因 Self replication | 核糖体RNA基因 Ribosomal RNAs | rrn4.5(×2), rrn5(×2), rrn16(×2), rrn 23(×2) |
转运RNA基因 Transfer RNAs | trnA-UGC(×2), trnC-GCA, trnD-GUG, trnE-UCC, trnF-GAA, trnfM-CAU, trnG-GCC, trnG-UCC, trnH-GUG, trnI-CAU(×2), trnI-GAU(×2), trnK- UUU, trnL-CAA(×2), trnL-UAA, trnL-UAG, trnM-CAU, trnN-GUU (×2) trnP-UGG, trnQ-UUC, trnR-ACG(×2) trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC(×2), trnV-UAC, trnW-CCA, trnY-GUA | |
核糖体小亚基基因 Ribosomal small subunit (SSU) | rps16, rps2, rps14, rps4, rps18, rps11, rps8, rps3, rps19, rps7(×2), rps12, rps15 | |
核糖体大亚基基因 Ribosomal large subuni (LSU) | rpl33, rpl20, rpl36, rpl14, rpl16, rpl22, rpl2(×2), rpl23(×2), rpl32 | |
RNA聚合酶亚基基因 RNA polymerase | rpoA, rpoB, rpoC1, rpoC2 | |
光合作用相关基因 Genes for photosynthesis | 光合系统I基因 Photosystem I | psaA, psaB, psaC, psaI, psaJ |
光合系统II基因 Photosystem II | psbA, psbB, psbK, psbI, psbM, psbD, psbC, psbE, psbJ, psbL, psbT, psbH, psbN, psbF, psbZ, psbJ | |
细胞色素复合物基因 Cytochrome b/f complex | petA, petD, petG, petL, petN | |
ATP合酶基因 ATP synthase | atpA, atpF, atpH, atpI, atpE, atpB | |
依赖ATP的蛋白酶单元p基因 ATP-dependent protease subunit p gene | clpP | |
二磷酸核酮糖羧化酶大亚基基因 RubiscoCO large subunit | rbcL | |
NADH脱氢酶基因 NADH dehydrogenase | ndhJ, ndhK, ndhC, ndhB(×2), ndhF, ndhD, ndhE, ndhG, ndhI, ndhA, ndhH | |
其他基因 Other genes | 成熟酶基因 Maturase | matK |
包裹膜蛋白基因 Envelop membrane protein | cemA | |
乙酰辅酶A羧化酶亚基基因 Subunit of acetyl-CoA-carboxylase | accD | |
c型细胞色素合成基因 c-type cytochrome synthesis ccsA gene | ccsA | |
转录起始因子基因 Transcription initiation factor IF-1 | InfA | |
未知功能基因 Genes of unknown function | 保守开放阅读框 Conserved open reading frames | ycf1, ycf2(×2), ycf3, ycf4 |
表1 直刺变豆菜叶绿体基因组所编码的基因
Table 1 List of genes found in Sanicula orthacantha chloroplast genome
基因分类 Category for genes | 基因分组 Group of genes | 基因名称 Name of genes |
---|---|---|
表达相关基因 Self replication | 核糖体RNA基因 Ribosomal RNAs | rrn4.5(×2), rrn5(×2), rrn16(×2), rrn 23(×2) |
转运RNA基因 Transfer RNAs | trnA-UGC(×2), trnC-GCA, trnD-GUG, trnE-UCC, trnF-GAA, trnfM-CAU, trnG-GCC, trnG-UCC, trnH-GUG, trnI-CAU(×2), trnI-GAU(×2), trnK- UUU, trnL-CAA(×2), trnL-UAA, trnL-UAG, trnM-CAU, trnN-GUU (×2) trnP-UGG, trnQ-UUC, trnR-ACG(×2) trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC(×2), trnV-UAC, trnW-CCA, trnY-GUA | |
核糖体小亚基基因 Ribosomal small subunit (SSU) | rps16, rps2, rps14, rps4, rps18, rps11, rps8, rps3, rps19, rps7(×2), rps12, rps15 | |
核糖体大亚基基因 Ribosomal large subuni (LSU) | rpl33, rpl20, rpl36, rpl14, rpl16, rpl22, rpl2(×2), rpl23(×2), rpl32 | |
RNA聚合酶亚基基因 RNA polymerase | rpoA, rpoB, rpoC1, rpoC2 | |
光合作用相关基因 Genes for photosynthesis | 光合系统I基因 Photosystem I | psaA, psaB, psaC, psaI, psaJ |
光合系统II基因 Photosystem II | psbA, psbB, psbK, psbI, psbM, psbD, psbC, psbE, psbJ, psbL, psbT, psbH, psbN, psbF, psbZ, psbJ | |
细胞色素复合物基因 Cytochrome b/f complex | petA, petD, petG, petL, petN | |
ATP合酶基因 ATP synthase | atpA, atpF, atpH, atpI, atpE, atpB | |
依赖ATP的蛋白酶单元p基因 ATP-dependent protease subunit p gene | clpP | |
二磷酸核酮糖羧化酶大亚基基因 RubiscoCO large subunit | rbcL | |
NADH脱氢酶基因 NADH dehydrogenase | ndhJ, ndhK, ndhC, ndhB(×2), ndhF, ndhD, ndhE, ndhG, ndhI, ndhA, ndhH | |
其他基因 Other genes | 成熟酶基因 Maturase | matK |
包裹膜蛋白基因 Envelop membrane protein | cemA | |
乙酰辅酶A羧化酶亚基基因 Subunit of acetyl-CoA-carboxylase | accD | |
c型细胞色素合成基因 c-type cytochrome synthesis ccsA gene | ccsA | |
转录起始因子基因 Transcription initiation factor IF-1 | InfA | |
未知功能基因 Genes of unknown function | 保守开放阅读框 Conserved open reading frames | ycf1, ycf2(×2), ycf3, ycf4 |
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