Chinese Bulletin of Botany ›› 2023, Vol. 58 ›› Issue (2): 248-260.DOI: 10.11983/CBB22026
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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: 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[J]. Chinese Bulletin of Botany, 2023, 58(2): 248-260.
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 |
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 |
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 |
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 |
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 |
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
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.
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.
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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