植物学报 ›› 2023, Vol. 58 ›› Issue (2): 248-260.DOI: 10.11983/CBB22026
包金波, 丁志杰, 苗浩宇, 李雪丽, 任书贤, 焦若岩, 李浩, 邓茜茜, 李英姿, 田新民()
收稿日期:
2022-02-10
接受日期:
2022-05-10
出版日期:
2023-03-01
发布日期:
2023-03-15
通讯作者:
*E-mail: 基金资助:
Jinbo Bao, Zhijie Ding, Haoyu Miao, Xueli Li, Shuxian Ren, Ruoyan Jiao, Hao Li;Qianqian Deng, Yingzi Li, Xinmin Tian
Received:
2022-02-10
Accepted:
2022-05-10
Online:
2023-03-01
Published:
2023-03-15
Contact:
*E-mail: 摘要:
石栗(Aleurites moluccana)是大戟科石栗属的常绿阔叶乔木, 具有能源、药用和观赏价值。为填补石栗叶绿体基因组研究的空白, 通过二代高通量全基因组测序, 组装和注释了石栗叶绿体基因组, 并进行基因组特征和系统发育分析。结果显示, 石栗叶绿体基因组为典型的四段式结构, 总长度为163 298 bp, LSC、SSC及IR的长度分别为91 301、18 501和26 748 bp。石栗叶绿体基因组共有131个基因, 包括8个rRNA基因, 37个tRNA基因, 86个蛋白质编码基因。研究发现145个SSR位点, 检测到重复单元有单核苷酸、二核苷酸、三核苷酸和四核苷酸, 数目分别为80、53、10和2个。共线性分析结果表明, 石栗叶绿体基因组存在基因倒位和重排现象。利用最大似然法和贝叶斯法构建了系统发育树, 显示石栗与油桐(Vernicia fordii)和东京桐(Deutzianthus tonkinensis)亲缘关系较近, 并形成姐妹群。利用化石时间进行定年分析, 表明石栗属、油桐属和东京桐属的分化时间为25.94 Ma (95% HPD: 24.71-63.32 Ma)。该研究丰富了石栗基因组信息, 可为石栗种质资源的开发利用提供基础遗传数据, 同时为石栗属物种鉴定及系统发育研究提供参考。
包金波, 丁志杰, 苗浩宇, 李雪丽, 任书贤, 焦若岩, 李浩, 邓茜茜, 李英姿, 田新民. 石栗叶绿体基因组研究. 植物学报, 2023, 58(2): 248-260.
Jinbo Bao, Zhijie Ding, Haoyu Miao, Xueli Li, Shuxian Ren, Ruoyan Jiao, Hao Li, Qianqian Deng, Yingzi Li, Xinmin Tian. Analysis of Chloroplast Genomes of Aleurites moluccana. Chinese Bulletin of Botany, 2023, 58(2): 248-260.
图1 石栗自然种群 (A) 花序; (B) 枝条; (C) 幼枝和幼叶; (D) 果实
Figure 1 Natural population of Aleurites moluccana (A) Inflorescence; (B) Branches; (C) Young branches and leaves; (D) Fruit
图2 石栗叶绿体基因组图谱 标注在大环外部的基因按照顺时针方向转录, 标注在大环内部的基因按照逆时针方向转录。不同颜色代表基因功能不同。内环阴影部分代表石栗叶绿体基因组的GC组成。LSC: 大单拷贝区; SSC: 小单拷贝区; IRA: 反向重复区A; IRB: 反向重复区B。* 含有内含子的基因。
Figure 2 The chloroplast genome map of Aleurites moluccana Genes on the outside of the large circle are transcribed clockwise and those on the inside are transcribed counterclockwise. The genes are color-coded based on their function. The dashed area on the inside represents the GC composition of the A. moluccana chloroplast genome. LSC: Large single-copy region; SSC: Small single-copy region; IRA: Inverted repeat region A; IRB: Inverted repeat region B. * for genes containing introns.
Categories of genes | Group of genes | Name of genes |
---|---|---|
Genes for photosynthesis | 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, psbZ | |
Subunits of ATP synthase | atpA, atpB, atpE, atpF, atpH, atpI | |
Subunits of cytochrome | petA, petB, petD, petG, petL, petN | |
ATP-dependent protease subunits P gene | clpP | |
Large subunits of Rubisco | rbcL | |
Subunits of NADH dehydrogenase | ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK | |
Self replication | Small subunit of ribosome | rps2, rps3, rps4, rps7, rps8, rps11, rps12, rps14, rps15, rps16, rps18, rps19 |
Large subunit of ribosome | rpl2, rpl14, rpl16, rpl20, rpl2, rpl23, rpl32, rpl33, rpl36, rpl22 | |
DNA dependent RNA polymerase | rpoA, rpoB, rpoC1, rpoC2 | |
Ribosomal RNA genes | rrn5, rrn4.5, rrn16, rrn23 | |
Transfer RNA genes | trnN-GUU, trnR-ACG, trnH-GUG, trnL-CAU, trnA-UGC, trnL-GAU, trnV-GAC, trnL- CAA, trnL-CAU, trnP-UGG, trnW-CCA, trnM-CAU, trnV-UAC, trnF-GAA, trnL-UAA, trnT-UGU, trnS-GGA, trnfM-CAU, trnG-GCC, trnS-UGA, trnT-GGU, trnE-UUC, trnY-GUA, trnD-GUC, trnC-GCA, trnR-UCU, trnS-GCU, trnQ-UUG, trnK-UUU, trnL-CAA, trnV-GAC, trnL-GAU, trnR-UGC, trnL-UAG, trnR-ACG, trnN-GUU | |
Other genes | Maturase | matK |
Envelop membrane protein | cemA | |
Translation initiation factor IF-1 | infA | |
C-type cytochrome synthesis gene | ccsA | |
Unknown function | Conserved open reading frames | ycf1, ycf2, ycf3, ycf4, ycf15 |
表1 石栗叶绿体基因组功能基因注释
Table 1 Annotation of functional genes in the chloroplast genome of Aleurites moluccana
Categories of genes | Group of genes | Name of genes |
---|---|---|
Genes for photosynthesis | 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, psbZ | |
Subunits of ATP synthase | atpA, atpB, atpE, atpF, atpH, atpI | |
Subunits of cytochrome | petA, petB, petD, petG, petL, petN | |
ATP-dependent protease subunits P gene | clpP | |
Large subunits of Rubisco | rbcL | |
Subunits of NADH dehydrogenase | ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK | |
Self replication | Small subunit of ribosome | rps2, rps3, rps4, rps7, rps8, rps11, rps12, rps14, rps15, rps16, rps18, rps19 |
Large subunit of ribosome | rpl2, rpl14, rpl16, rpl20, rpl2, rpl23, rpl32, rpl33, rpl36, rpl22 | |
DNA dependent RNA polymerase | rpoA, rpoB, rpoC1, rpoC2 | |
Ribosomal RNA genes | rrn5, rrn4.5, rrn16, rrn23 | |
Transfer RNA genes | trnN-GUU, trnR-ACG, trnH-GUG, trnL-CAU, trnA-UGC, trnL-GAU, trnV-GAC, trnL- CAA, trnL-CAU, trnP-UGG, trnW-CCA, trnM-CAU, trnV-UAC, trnF-GAA, trnL-UAA, trnT-UGU, trnS-GGA, trnfM-CAU, trnG-GCC, trnS-UGA, trnT-GGU, trnE-UUC, trnY-GUA, trnD-GUC, trnC-GCA, trnR-UCU, trnS-GCU, trnQ-UUG, trnK-UUU, trnL-CAA, trnV-GAC, trnL-GAU, trnR-UGC, trnL-UAG, trnR-ACG, trnN-GUU | |
Other genes | Maturase | matK |
Envelop membrane protein | cemA | |
Translation initiation factor IF-1 | infA | |
C-type cytochrome synthesis gene | ccsA | |
Unknown function | Conserved open reading frames | ycf1, ycf2, ycf3, ycf4, ycf15 |
SSR repeat type (number of copies) | SSR repeat sequence | Number of copies | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16-30 | Total | ||
Mononucleotide (80) | A/T | 24 | 17 | 7 | 14 | 3 | 3 | 68 | ||||||
C/G | 7 | 3 | 2 | 12 | ||||||||||
Dinucleotide (53) | AT/TA/AC/CA/AG/GA | 18 | 7 | 6 | 4 | 6 | 2 | 2 | 45 | |||||
CG/GC | 4 | 2 | 1 | 1 | 8 | |||||||||
Trinucleotide (10) | CGG/AAG | 2 | 2 | 1 | 5 | |||||||||
TGT/TTA | 1 | 2 | 3 | |||||||||||
ATT/AAT | 1 | 1 | 2 | |||||||||||
Tetranucleotide (2) | TACA/TGGT | 1 | 1 | 2 |
表2 石栗叶绿体基因组简单重复序列(SSR)信息
Table 2 Information of simple sequence repeat (SSR) identified in the chloroplast genome of Aleurites moluccana
SSR repeat type (number of copies) | SSR repeat sequence | Number of copies | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16-30 | Total | ||
Mononucleotide (80) | A/T | 24 | 17 | 7 | 14 | 3 | 3 | 68 | ||||||
C/G | 7 | 3 | 2 | 12 | ||||||||||
Dinucleotide (53) | AT/TA/AC/CA/AG/GA | 18 | 7 | 6 | 4 | 6 | 2 | 2 | 45 | |||||
CG/GC | 4 | 2 | 1 | 1 | 8 | |||||||||
Trinucleotide (10) | CGG/AAG | 2 | 2 | 1 | 5 | |||||||||
TGT/TTA | 1 | 2 | 3 | |||||||||||
ATT/AAT | 1 | 1 | 2 | |||||||||||
Tetranucleotide (2) | TACA/TGGT | 1 | 1 | 2 |
图3 石栗叶绿体基因组重复序列长度及类型 (A) 重复序列长度; (B) 重复序列类型
Figure 3 The length and type of repeat sequences in the chloroplast genome of Aleurites moluccana (A) The length of repeat sequences; (B) The type of repeat sequences
Amino acid | Codon | No. of codon | RSCU | Amino acid | Codon | No. of codon | RSCU |
---|---|---|---|---|---|---|---|
Ala | GCU | 431 | 1.20 | Cys | UGU | 698 | 1.20 |
GCC | 306 | 0.86 | UGC | 468 | 0.80 | ||
GCA | 427 | 1.19 | Glu | GAA | 1416 | 1.40 | |
GCG | 267 | 0.75 | GAG | 611 | 0.60 | ||
Asp | GAU | 1073 | 1.41 | Gly | GGU | 534 | 0.93 |
GAC | 448 | 0.59 | GGC | 382 | 0.67 | ||
Phe | UUU | 2457 | 1.26 | GGA | 803 | 1.40 | |
UUC | 1452 | 0.74 | GGG | 572 | 1.00 | ||
His | CAU | 874 | 1.36 | Ile | AUU | 1927 | 1.19 |
CAC | 412 | 0.64 | AUC | 1184 | 0.73 | ||
Lys | AAA | 2578 | 1.38 | AUA | 1728 | 1.07 | |
AAG | 1162 | 0.62 | Leu | UUA | 1299 | 1.46 | |
Trp | UGG | 748 | 1.00 | UUG | 1125 | 1.26 | |
Asn | AAU | 2122 | 1.43 | CUU | 1021 | 1.15 | |
AAC | 843 | 0.57 | CUC | 577 | 0.65 | ||
Arg | CGU | 341 | 0.58 | CUA | 844 | 0.95 | |
CGC | 246 | 0.42 | CUG | 442 | 0.50 | ||
CGA | 590 | 1.00 | Pro | CCU | 568 | 1.02 | |
CGG | 412 | 0.70 | CCC | 556 | 1.00 | ||
AGA | 1253 | 2.12 | CCA | 699 | 1.25 | ||
AGG | 702 | 1.19 | CCG | 408 | 0.73 | ||
Thr | ACU | 683 | 1.18 | Met | AUG | 887 | 1.00 |
ACC | 550 | 0.95 | Gln | CAA | 1041 | 1.38 | |
ACA | 696 | 1.20 | CAG | 463 | 0.62 | ||
ACG | 383 | 0.66 | Ser | UCU | 1070 | 1.36 | |
Val | GUU | 737 | 1.34 | UCC | 840 | 1.07 | |
GUC | 402 | 0.73 | UCA | 1002 | 1.27 | ||
GUA | 667 | 1.21 | UCG | 565 | 0.72 | ||
GUG | 393 | 0.71 | AGU | 720 | 0.92 | ||
Tyr | UAU | 1842 | 1.43 | AGC | 521 | 0.66 | |
UAC | 737 | 0.57 |
表3 石栗叶绿体基因组密码子使用偏好性
Table 3 Codon usage bias in the chloroplast genome of Aleurites moluccana
Amino acid | Codon | No. of codon | RSCU | Amino acid | Codon | No. of codon | RSCU |
---|---|---|---|---|---|---|---|
Ala | GCU | 431 | 1.20 | Cys | UGU | 698 | 1.20 |
GCC | 306 | 0.86 | UGC | 468 | 0.80 | ||
GCA | 427 | 1.19 | Glu | GAA | 1416 | 1.40 | |
GCG | 267 | 0.75 | GAG | 611 | 0.60 | ||
Asp | GAU | 1073 | 1.41 | Gly | GGU | 534 | 0.93 |
GAC | 448 | 0.59 | GGC | 382 | 0.67 | ||
Phe | UUU | 2457 | 1.26 | GGA | 803 | 1.40 | |
UUC | 1452 | 0.74 | GGG | 572 | 1.00 | ||
His | CAU | 874 | 1.36 | Ile | AUU | 1927 | 1.19 |
CAC | 412 | 0.64 | AUC | 1184 | 0.73 | ||
Lys | AAA | 2578 | 1.38 | AUA | 1728 | 1.07 | |
AAG | 1162 | 0.62 | Leu | UUA | 1299 | 1.46 | |
Trp | UGG | 748 | 1.00 | UUG | 1125 | 1.26 | |
Asn | AAU | 2122 | 1.43 | CUU | 1021 | 1.15 | |
AAC | 843 | 0.57 | CUC | 577 | 0.65 | ||
Arg | CGU | 341 | 0.58 | CUA | 844 | 0.95 | |
CGC | 246 | 0.42 | CUG | 442 | 0.50 | ||
CGA | 590 | 1.00 | Pro | CCU | 568 | 1.02 | |
CGG | 412 | 0.70 | CCC | 556 | 1.00 | ||
AGA | 1253 | 2.12 | CCA | 699 | 1.25 | ||
AGG | 702 | 1.19 | CCG | 408 | 0.73 | ||
Thr | ACU | 683 | 1.18 | Met | AUG | 887 | 1.00 |
ACC | 550 | 0.95 | Gln | CAA | 1041 | 1.38 | |
ACA | 696 | 1.20 | CAG | 463 | 0.62 | ||
ACG | 383 | 0.66 | Ser | UCU | 1070 | 1.36 | |
Val | GUU | 737 | 1.34 | UCC | 840 | 1.07 | |
GUC | 402 | 0.73 | UCA | 1002 | 1.27 | ||
GUA | 667 | 1.21 | UCG | 565 | 0.72 | ||
GUG | 393 | 0.71 | AGU | 720 | 0.92 | ||
Tyr | UAU | 1842 | 1.43 | AGC | 521 | 0.66 | |
UAC | 737 | 0.57 |
图5 石栗叶绿体基因组共线性分析 LSC、SSC、IRA和IRB同图2。
Figure 5 Collinear analysis of Aleurites moluccana chloroplast genome LSC, SSC, IRA, and IRB are the same as in Figure 2.
图6 石栗叶绿体基因组反向重复区的收缩与扩张 LSC、SSC、IRA和IRB同图2。JLB: LSC与IRB的边界; JSB: SSC与IRB的边界; JSA: SSC与IRA的边界; JLA: LSC与IRA的边界
Figure 6 Contraction and expansion of inverted repeat region in the chloroplast genome of Aleurites moluccana LSC, SSC, IRA, and IRB are the same as in Figure 2. JLB: Boundary between LSC and IRB; JSB: Boundary between SSC and IRB; JSA: Boundary between SSC and IRA; JLA: Boundary between LSC and IRA
图7 基于蛋白编码序列构建的石栗与其它19个物种贝叶斯系统发育树 分支上的数值为后验概率。
Figure 7 Bayesian phylogenetic tree of Aleurites moluccana and other 19 species based on protein coding sequence The values on the branch are posteriori probability.
图8 基于蛋白编码序列构建的石栗与其它19个物种最大似然(ML)系统发育树 分支上的数值为后验概率。
Figure 8 Maximum likelihood (ML) phylogenetic tree of Aleurites moluccana and other 19 species based on protein coding sequence The values on the branch are posteriori probability.
图9 基于宽松分子钟模型构建的石栗与其它19个物种系统发育时间树 分支上的数值为分化时间(单位: 百万年前)。
Figure 9 Phylogenetic dating tree of Aleurites moluccana and other 19 species based on relax molecular clock model The values on the branch are the differentiation time (unit: million years ago).
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