植物学报 ›› 2025, Vol. 60 ›› Issue (4): 573-585.DOI: 10.11983/CBB24146 cstr: 32102.14.CBB24146
王传永1, 庄典2, 宋正达1, 翟恒华1, 李乃伟1,*(), 张凡1,*(
)
收稿日期:
2024-09-24
接受日期:
2025-02-09
出版日期:
2025-07-10
发布日期:
2025-02-08
通讯作者:
*E-mail: linaiwei@jib.ac.cn;mumizhongfeng@126.com
基金资助:
Chuanyong Wang1, Dian Zhuang2, Zhengda Song1, Henghua Zhai1, Naiwei Li1,*(), Fan Zhang1,*(
)
Received:
2024-09-24
Accepted:
2025-02-09
Online:
2025-07-10
Published:
2025-02-08
Contact:
*E-mail: linaiwei@jib.ac.cn;mumizhongfeng@126.com
摘要: 黑涩楠(Aronia melanocarpa)因其观赏价值和经济价值而闻名, 但其与其它蔷薇科植物的系统进化关系仍不明确。该研究对黑涩楠叶绿体(cp)基因组进行测序, 并与13个蔷薇科物种的叶绿体基因组进行比较分析。结果表明, 黑涩楠的cp基因组大小为159 772 bp, 呈典型的四分结构; 其中大单拷贝区(LSC)长度为87 810 bp, 小单拷贝区(SSC)长度为19 200 bp, 中间含有2个26 381 bp的反向重复区(IRa和IRb)。共注释到132个基因, 包括87个蛋白质编码基因、37个tRNA和8个rRNA。还检测到76个简单重复序列(SSR)和50个长重复序列。系统进化分析表明, 黑涩楠与红涩楠(A. arbutifolia)的亲缘关系最近, 与榅桲(Cydonia oblonga)是姊妹支系。该研究提供的基因组信息将为后续的系统进化和种群遗传分析以及分子育种提供理论支持。
王传永, 庄典, 宋正达, 翟恒华, 李乃伟, 张凡. 黑涩楠叶绿体全基因组的结构和比较分析及系统进化推断. 植物学报, 2025, 60(4): 573-585.
Chuanyong Wang, Dian Zhuang, Zhengda Song, Henghua Zhai, Naiwei Li, Fan Zhang. Structural and Comparative Analysis of the Complete Chloroplast Genome of the Aronia melanocarpa and Its Phylogenetic Inference. Chinese Bulletin of Botany, 2025, 60(4): 573-585.
图1 黑涩楠叶绿体基因组图谱 圆圈内、外的基因分别按顺时针和逆时针方向转录。不同功能基因组用不同的颜色标记。内圈的GC和AT含量分别用深灰和浅灰色表示。
Figure 1 Map of the chloroplast genome of Aronia melanocarpa Genes inside and outside of the circle are transcribed in the clockwise and counterclockwise directions respectively. Different functional gene groups are color-coded accordingly. GC and AT content are represented on the inner circle by darker and lighter gray, respectively.
Genome features | A. melanocarpa | Genome features | A. melanocarpa |
---|---|---|---|
Genome size (bp)/GC content (%) | 159772/36.6 | Number of unique genes | 110 |
LSC size (bp)/GC content (%) | 87810/34.3 | Protein-coding genes | 87 |
SSC size (bp)/GC content (%) | 19200/30.4 | tRNAs | 37 |
IR size (bp)/GC content (%) | 52762/42.7 | rRNAs | 8 |
Total gene number | 132 | Genes duplicated in the IRs | 22 |
表1 黑涩楠叶绿体基因组特征
Table 1 The Aronia melanocarpa chloroplast genome features
Genome features | A. melanocarpa | Genome features | A. melanocarpa |
---|---|---|---|
Genome size (bp)/GC content (%) | 159772/36.6 | Number of unique genes | 110 |
LSC size (bp)/GC content (%) | 87810/34.3 | Protein-coding genes | 87 |
SSC size (bp)/GC content (%) | 19200/30.4 | tRNAs | 37 |
IR size (bp)/GC content (%) | 52762/42.7 | rRNAs | 8 |
Total gene number | 132 | Genes duplicated in the IRs | 22 |
Category | Gene group | Name of gene | Number |
---|---|---|---|
Self-replication | Proteins of the large ribosomal subunit | rpl2ab, rpl14, rpl16b, rpl20, rpl22, rpl23a, rpl32, rpl33, rpl36 | 11 |
Proteins of the small ribosomal subunit | rps2, rps3, rps4, rps7a, rps8, rps11, rps12ac, rps14, rps15, rps16b, rps18, rps19ab | 15 | |
Subunits of RNA polymerase | rpoA, rpoB, rpoC1b, rpoC2 | 4 | |
rRNAs | rrn23Sa, rrn16Sa, rrn5Sa, rrn4.5Sa | 8 | |
tRNAs | trnH-GUG, trnK-UUUb, trnQ-UUG, trnS-GCU, trnG- GCCab, trnR-UCU, trnC-GCA, trnD-GUC, trnY-GUA, trnE- UUC, trnT-GGU, trnS-UGA, trnfM, trnS-GGA, trnS-GGA, trnT-UGU, trnL-UAAb, trnF-GAA, trnV-UACb, trnM-CAU, trnW-CCA, trnP-UGG, trnI-CAUa, trnL-CAAa, trnV-GACa, trnI-GAUab, trnA-UGCab, trnR-ACGa, trnN-GUUa, trnL-UAG | 37 | |
Photosynthesis | Subunits of photosystem I | psaA, psaB, psaIa, psaJ | 5 |
Subunits of photosystem II | psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbIa, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ | 15 | |
Subunits of NADH dehydrogenase | ndhAb, ndhBab, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK | 12 | |
Subunits of cytochrome b/f complex | petA, petBb, petDb, petG, petL, petN | 6 | |
Subunits of ATP synthase | atpA, atpB, atpE, atpFb, atpH, atpI | 6 | |
Large subunit of Rubisco | rbcL | 1 | |
Biosynthesis | Maturase | matK | 1 |
Protease | clpPc | 1 | |
Envelope membrane protein | cemA | 1 | |
Acetyl-CoA carboxylase | accD | 1 | |
C-type cytochrome synthesis gene | ccsA | 1 | |
Translation initiation factor | infA | 1 | |
Unknown function | Conserved hypothetical chloroplast reading frames | ycf1a, ycf2a, ycf3c, ycf4 | 6 |
表2 本研究测序的黑涩楠叶绿体基因组中的基因
Table 2 Genes in the chloroplast genome of Aronia melanocarpa sequenced in this study
Category | Gene group | Name of gene | Number |
---|---|---|---|
Self-replication | Proteins of the large ribosomal subunit | rpl2ab, rpl14, rpl16b, rpl20, rpl22, rpl23a, rpl32, rpl33, rpl36 | 11 |
Proteins of the small ribosomal subunit | rps2, rps3, rps4, rps7a, rps8, rps11, rps12ac, rps14, rps15, rps16b, rps18, rps19ab | 15 | |
Subunits of RNA polymerase | rpoA, rpoB, rpoC1b, rpoC2 | 4 | |
rRNAs | rrn23Sa, rrn16Sa, rrn5Sa, rrn4.5Sa | 8 | |
tRNAs | trnH-GUG, trnK-UUUb, trnQ-UUG, trnS-GCU, trnG- GCCab, trnR-UCU, trnC-GCA, trnD-GUC, trnY-GUA, trnE- UUC, trnT-GGU, trnS-UGA, trnfM, trnS-GGA, trnS-GGA, trnT-UGU, trnL-UAAb, trnF-GAA, trnV-UACb, trnM-CAU, trnW-CCA, trnP-UGG, trnI-CAUa, trnL-CAAa, trnV-GACa, trnI-GAUab, trnA-UGCab, trnR-ACGa, trnN-GUUa, trnL-UAG | 37 | |
Photosynthesis | Subunits of photosystem I | psaA, psaB, psaIa, psaJ | 5 |
Subunits of photosystem II | psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbIa, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ | 15 | |
Subunits of NADH dehydrogenase | ndhAb, ndhBab, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK | 12 | |
Subunits of cytochrome b/f complex | petA, petBb, petDb, petG, petL, petN | 6 | |
Subunits of ATP synthase | atpA, atpB, atpE, atpFb, atpH, atpI | 6 | |
Large subunit of Rubisco | rbcL | 1 | |
Biosynthesis | Maturase | matK | 1 |
Protease | clpPc | 1 | |
Envelope membrane protein | cemA | 1 | |
Acetyl-CoA carboxylase | accD | 1 | |
C-type cytochrome synthesis gene | ccsA | 1 | |
Translation initiation factor | infA | 1 | |
Unknown function | Conserved hypothetical chloroplast reading frames | ycf1a, ycf2a, ycf3c, ycf4 | 6 |
Nucleotide(s) | Number of repeats | |||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
6 | 7 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | Total | |
A | - | - | 5 | 5 | 4 | 2 | 2 | 4 | 2 | - | - | - | 1 | 25 |
C | - | - | 2 | 1 | - | 1 | - | - | - | - | - | - | - | 4 |
G | - | - | 1 | 1 | - | - | - | - | - | - | - | - | - | 2 |
T | - | - | 13 | 9 | 6 | 2 | 1 | 4 | 1 | 2 | 2 | 1 | - | 41 |
AT | 2 | - | - | - | - | - | - | - | - | - | - | - | 2 | |
TA | 1 | 1 | - | - | - | - | - | - | - | - | - | - | - | 2 |
表3 黑涩楠叶绿体基因组中简单重复序列(SSR)的鉴定频率
Table 3 The frequency of identified of simple sequence repeats (SSRs) in the Aronia melanocarpa chloroplast genome
Nucleotide(s) | Number of repeats | |||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
6 | 7 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | Total | |
A | - | - | 5 | 5 | 4 | 2 | 2 | 4 | 2 | - | - | - | 1 | 25 |
C | - | - | 2 | 1 | - | 1 | - | - | - | - | - | - | - | 4 |
G | - | - | 1 | 1 | - | - | - | - | - | - | - | - | - | 2 |
T | - | - | 13 | 9 | 6 | 2 | 1 | 4 | 1 | 2 | 2 | 1 | - | 41 |
AT | 2 | - | - | - | - | - | - | - | - | - | - | - | 2 | |
TA | 1 | 1 | - | - | - | - | - | - | - | - | - | - | - | 2 |
Amino acids | Codon | No. | RSCU | Amino acids | Codon | No. | RSCU |
---|---|---|---|---|---|---|---|
Phe | UUU | 975 | 1.3 | Ala | GCU | 645 | 1.84 |
Phe | UUC | 526 | 0.7 | Ala | GCC | 217 | 0.62 |
Leu | UUA | 912 | 1.95 | Ala | GCA | 390 | 1.11 |
Leu | UUG | 565 | 1.21 | Ala | GCG | 148 | 0.42 |
Leu | CUU | 593 | 1.27 | TER | UAA | 51 | 1.76 |
Leu | CUC | 186 | 0.4 | TER | UAG | 21 | 0.72 |
Leu | CUA | 363 | 0.78 | TER | UGA | 15 | 0.52 |
Leu | CUG | 181 | 0.39 | His | CAU | 493 | 1.55 |
Ile | AUU | 1123 | 1.47 | His | CAC | 145 | 0.45 |
Ile | AUC | 440 | 0.58 | Gln | CAA | 727 | 1.54 |
Ile | AUA | 730 | 0.96 | Gln | CAG | 217 | 0.46 |
Met | AUG | 627 | 1 | Asn | AAU | 987 | 1.53 |
Val | GUU | 524 | 1.44 | Asn | AAC | 305 | 0.47 |
Val | GUC | 167 | 0.46 | Lys | AAA | 1068 | 1.49 |
Val | GUA | 552 | 1.52 | Lys | AAG | 364 | 0.51 |
Val | GUG | 208 | 0.57 | Asp | GAU | 889 | 1.62 |
Ser | UCU | 573 | 1.69 | Asp | GAC | 208 | 0.38 |
Ser | UCC | 330 | 0.97 | Glu | GAA | 1035 | 1.48 |
Ser | UCA | 408 | 1.2 | Glu | GAG | 363 | 0.52 |
Ser | UCG | 190 | 0.56 | Cys | UGU | 226 | 1.49 |
Ser | AGU | 411 | 1.21 | Cys | UGC | 77 | 0.51 |
Ser | AGC | 128 | 0.38 | Trp | UGG | 458 | 1 |
Pro | CCU | 421 | 1.56 | Arg | CGU | 340 | 1.27 |
Pro | CCC | 201 | 0.74 | Arg | CGC | 112 | 0.42 |
Pro | CCA | 310 | 1.15 | Arg | CGA | 370 | 1.38 |
Pro | CCG | 149 | 0.55 | Arg | CGG | 121 | 0.45 |
Thr | ACU | 551 | 1.6 | Arg | AGA | 493 | 1.84 |
Thr | ACC | 251 | 0.73 | Arg | AGG | 173 | 0.65 |
Thr | ACA | 423 | 1.23 | Gly | GGU | 589 | 1.31 |
Thr | ACG | 153 | 0.44 | Gly | GGC | 183 | 0.41 |
Tyr | UAU | 801 | 1.61 | Gly | GGA | 725 | 1.62 |
Tyr | UAC | 194 | 0.39 | Gly | GGG | 295 | 0.66 |
表4 黑涩楠叶绿体基因组中的密码子用法
Table 4 Codon usage in the Aronia melanocarpa chloroplast genome
Amino acids | Codon | No. | RSCU | Amino acids | Codon | No. | RSCU |
---|---|---|---|---|---|---|---|
Phe | UUU | 975 | 1.3 | Ala | GCU | 645 | 1.84 |
Phe | UUC | 526 | 0.7 | Ala | GCC | 217 | 0.62 |
Leu | UUA | 912 | 1.95 | Ala | GCA | 390 | 1.11 |
Leu | UUG | 565 | 1.21 | Ala | GCG | 148 | 0.42 |
Leu | CUU | 593 | 1.27 | TER | UAA | 51 | 1.76 |
Leu | CUC | 186 | 0.4 | TER | UAG | 21 | 0.72 |
Leu | CUA | 363 | 0.78 | TER | UGA | 15 | 0.52 |
Leu | CUG | 181 | 0.39 | His | CAU | 493 | 1.55 |
Ile | AUU | 1123 | 1.47 | His | CAC | 145 | 0.45 |
Ile | AUC | 440 | 0.58 | Gln | CAA | 727 | 1.54 |
Ile | AUA | 730 | 0.96 | Gln | CAG | 217 | 0.46 |
Met | AUG | 627 | 1 | Asn | AAU | 987 | 1.53 |
Val | GUU | 524 | 1.44 | Asn | AAC | 305 | 0.47 |
Val | GUC | 167 | 0.46 | Lys | AAA | 1068 | 1.49 |
Val | GUA | 552 | 1.52 | Lys | AAG | 364 | 0.51 |
Val | GUG | 208 | 0.57 | Asp | GAU | 889 | 1.62 |
Ser | UCU | 573 | 1.69 | Asp | GAC | 208 | 0.38 |
Ser | UCC | 330 | 0.97 | Glu | GAA | 1035 | 1.48 |
Ser | UCA | 408 | 1.2 | Glu | GAG | 363 | 0.52 |
Ser | UCG | 190 | 0.56 | Cys | UGU | 226 | 1.49 |
Ser | AGU | 411 | 1.21 | Cys | UGC | 77 | 0.51 |
Ser | AGC | 128 | 0.38 | Trp | UGG | 458 | 1 |
Pro | CCU | 421 | 1.56 | Arg | CGU | 340 | 1.27 |
Pro | CCC | 201 | 0.74 | Arg | CGC | 112 | 0.42 |
Pro | CCA | 310 | 1.15 | Arg | CGA | 370 | 1.38 |
Pro | CCG | 149 | 0.55 | Arg | CGG | 121 | 0.45 |
Thr | ACU | 551 | 1.6 | Arg | AGA | 493 | 1.84 |
Thr | ACC | 251 | 0.73 | Arg | AGG | 173 | 0.65 |
Thr | ACA | 423 | 1.23 | Gly | GGU | 589 | 1.31 |
Thr | ACG | 153 | 0.44 | Gly | GGC | 183 | 0.41 |
Tyr | UAU | 801 | 1.61 | Gly | GGA | 725 | 1.62 |
Tyr | UAC | 194 | 0.39 | Gly | GGG | 295 | 0.66 |
图2 14种蔷薇科植物叶绿体基因组比较 图中纵坐标和横坐标分别代表50%-100%的相同率和序列长度。注释基因显示在顶部。
Figure 2 A comparison of the chloroplast genomes among 14 Rosaceae species The vertical scale and horizontal axes in the figure represent the percentage of identity ranging from 50% to 100% and the sequence length, respectively. Annotated genes are displayed on the top.
图3 蔷薇科14个物种的LSC、SSC和IR区域的边界距离比较 LSC、SSC和IR同表1。
Figure 3 Comparisons of the boundary distances for LSC, SSC, and IR regions among 14 species from the Rosaceae LSC, SSC, and IR are the same as shown in Table 1.
图4 利用完整的叶绿体基因组对60个蔷薇科物种进行系统进化分析 左侧为利用iQTree构建的系统发育树, 节点上方的数字为自展支持率; 右侧为利用FastTree构建的系统发育树, 节点上方的数字为SH-like local支持率。
Figure 4 Phylogenetic analyses on 60 Rosaceae species using their complete chloroplast genomes On the left, phylogenetic tree was constructed by iQTree, numbers above the nodes are bootstrap values; on the right, phylogenetic tree was constructed by FastTree, numbers above the nodes are SH-like local values.
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