Biotechnology Bulletin ›› 2021, Vol. 37 ›› Issue (5): 38-47.doi: 10.13560/j.cnki.biotech.bull.1985.2020-1380
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ZHU Bin(), GAN Chen-chen, WANG Hong-cheng()
Received:
2020-11-13
Online:
2021-05-26
Published:
2021-06-11
Contact:
WANG Hong-cheng
E-mail:zhugg130@126.com;besthongcheng@163.com
ZHU Bin, GAN Chen-chen, WANG Hong-cheng. Characteristics of the Complete Chloroplast Genome of Dendrobium thyrsiflorum and Its Phylogenetic Relationship Analysis[J]. Biotechnology Bulletin, 2021, 37(5): 38-47.
范畴 Category | 条目 Item | 描述 Description |
---|---|---|
叶绿体基因组结构 Structure of cp genome | 长编码区/bp | 84 749 |
反向重复区/bp | 26 293 | |
短编码区/bp | 14 351 | |
基因组大小/bp | 151 686 | |
基因组成 Gene content | 基因总数 | 106 |
编码基因 | 71 | |
tRNAs | 31 | |
rRNAs | 4 | |
两拷贝基因 | 19 | |
长编码区基因数 | 78 | |
反向重复区基因数 | 18 | |
短编码区基因数 | 8 | |
基因总长度/bp | 71 241 | |
基因平均长度/bp | 913 | |
基因/基因组/% | 46.97 | |
GC含量 GC content | 长编码区GC含量/% | 35.1 |
反向重复区GC含量/% | 43.43 | |
短编码区GC含量/% | 30.44 | |
平均GC含量/% | 37.55 |
Table 1 Detail chracteristics of the complete cp genome of D. thyrsiflorum
范畴 Category | 条目 Item | 描述 Description |
---|---|---|
叶绿体基因组结构 Structure of cp genome | 长编码区/bp | 84 749 |
反向重复区/bp | 26 293 | |
短编码区/bp | 14 351 | |
基因组大小/bp | 151 686 | |
基因组成 Gene content | 基因总数 | 106 |
编码基因 | 71 | |
tRNAs | 31 | |
rRNAs | 4 | |
两拷贝基因 | 19 | |
长编码区基因数 | 78 | |
反向重复区基因数 | 18 | |
短编码区基因数 | 8 | |
基因总长度/bp | 71 241 | |
基因平均长度/bp | 913 | |
基因/基因组/% | 46.97 | |
GC含量 GC content | 长编码区GC含量/% | 35.1 |
反向重复区GC含量/% | 43.43 | |
短编码区GC含量/% | 30.44 | |
平均GC含量/% | 37.55 |
基因范畴 Gene categories | 基因功能 Gene group | 基因名 Gene names |
---|---|---|
参与光合作用的基因 Genes involving in photosynthesis | 光合系统亚基 | ndhJ,pbf1,psaA,psaB,psaC,psaI,psaJ,psbA,psbB,psbC,psbD,psbE,psbF,psbH,psbI,psbJ,psbK,psbL,psbM,psbT,psbZ |
细胞色素复合体亚基 | petA,petBb,petDb,petG,petL,petN | |
二磷酸核酮糖羧化酶大亚基 | rbcL | |
ATP合成酶亚基 | atpA,atpB,atpE,atpFb,atpH,atpI | |
NADH脱氢酶亚基 | ndhA,ndhBa,b | |
自体复制相关基因 Self-replication | rRNA基因 | rrn16a,rrn23a,rrn4.5a,rrn5a |
tRNA基因 | trnA-UGCa,b,trnC-GCA,trnD-GUC,trnE-UUC,trnF-GAA,trnfM-CAU,trnG-GCCb,trnG-UCC,trnH-GUGa,trnI-CAUa,trnI-GAUa,b,trnK-UUUb,trnL-CAAa,trnL-UAAb,trnL-UAG,trnM-CAU,trnN-GUUa,trnP-UGG,trnQ-UUG,trnR-ACGa,trnR-UCU,trnS-GCU,trnS-GGA,trnS-UGA,trnT-CGU,trnT-GGU,trnT-UGU,trnV-GACa,trnV-UACa,b,trnW-CCA,trnY-GUA | |
核糖体小亚基 | rps11,rps12a,c,rps14,rps15,rps16b,rps18,rps19a,rps2 | |
核糖体大亚基 | rps3,rps4,rps7a,rps8,rpl14,rpl16b,rpl2a,b,rpl20,rpl22,rpl23a,rpl32,rpl33 | |
DNA依赖的RNA聚合酶 | rpl36,rpoA,rpoB,rpoC1b,rpoC2 | |
其它功能基因 Other genes | 成熟酶 | matK |
翻译起始因子 | infA | |
蛋白质膜基因 | cemA | |
乙酰辅酶A亚基 | accD | |
C类型细胞色素合成基因 | ccsA | |
蛋白酶 | clpPc | |
未知功能基因 Nonfunctional genes | 保守的开放阅读框 | ycf1,ycf2a,ycf3c,ycf4 |
Table 2 Summary of assembled gene functions of D. thyrsiflorum cp genome
基因范畴 Gene categories | 基因功能 Gene group | 基因名 Gene names |
---|---|---|
参与光合作用的基因 Genes involving in photosynthesis | 光合系统亚基 | ndhJ,pbf1,psaA,psaB,psaC,psaI,psaJ,psbA,psbB,psbC,psbD,psbE,psbF,psbH,psbI,psbJ,psbK,psbL,psbM,psbT,psbZ |
细胞色素复合体亚基 | petA,petBb,petDb,petG,petL,petN | |
二磷酸核酮糖羧化酶大亚基 | rbcL | |
ATP合成酶亚基 | atpA,atpB,atpE,atpFb,atpH,atpI | |
NADH脱氢酶亚基 | ndhA,ndhBa,b | |
自体复制相关基因 Self-replication | rRNA基因 | rrn16a,rrn23a,rrn4.5a,rrn5a |
tRNA基因 | trnA-UGCa,b,trnC-GCA,trnD-GUC,trnE-UUC,trnF-GAA,trnfM-CAU,trnG-GCCb,trnG-UCC,trnH-GUGa,trnI-CAUa,trnI-GAUa,b,trnK-UUUb,trnL-CAAa,trnL-UAAb,trnL-UAG,trnM-CAU,trnN-GUUa,trnP-UGG,trnQ-UUG,trnR-ACGa,trnR-UCU,trnS-GCU,trnS-GGA,trnS-UGA,trnT-CGU,trnT-GGU,trnT-UGU,trnV-GACa,trnV-UACa,b,trnW-CCA,trnY-GUA | |
核糖体小亚基 | rps11,rps12a,c,rps14,rps15,rps16b,rps18,rps19a,rps2 | |
核糖体大亚基 | rps3,rps4,rps7a,rps8,rpl14,rpl16b,rpl2a,b,rpl20,rpl22,rpl23a,rpl32,rpl33 | |
DNA依赖的RNA聚合酶 | rpl36,rpoA,rpoB,rpoC1b,rpoC2 | |
其它功能基因 Other genes | 成熟酶 | matK |
翻译起始因子 | infA | |
蛋白质膜基因 | cemA | |
乙酰辅酶A亚基 | accD | |
C类型细胞色素合成基因 | ccsA | |
蛋白酶 | clpPc | |
未知功能基因 Nonfunctional genes | 保守的开放阅读框 | ycf1,ycf2a,ycf3c,ycf4 |
重复单元 Repeats units | 类型 Types | 数量 Number | 最长重复序列 The largest repeats |
---|---|---|---|
1 | T | 16 | 14 |
A | 17 | 12 | |
G | 1 | 10 | |
C | 1 | 10 | |
2 | AT | 5 | 16 |
TA | 6 | 12 | |
GA | 1 | 10 | |
3 | TAT | 1 | 15 |
ATA | 1 | 15 | |
4 | AGAA | 2 | 12 |
AGAT | 1 | 12 | |
ATTA | 1 | 12 | |
TTCT | 1 | 12 | |
GTCT | 1 | 12 | |
5 | ATATG | 1 | 15 |
6 | CCATCT | 1 | 18 |
Total | 17 | 58 | — |
Table 3 Summary of simple sequence repeats inD. thyrsiflorum cp genome
重复单元 Repeats units | 类型 Types | 数量 Number | 最长重复序列 The largest repeats |
---|---|---|---|
1 | T | 16 | 14 |
A | 17 | 12 | |
G | 1 | 10 | |
C | 1 | 10 | |
2 | AT | 5 | 16 |
TA | 6 | 12 | |
GA | 1 | 10 | |
3 | TAT | 1 | 15 |
ATA | 1 | 15 | |
4 | AGAA | 2 | 12 |
AGAT | 1 | 12 | |
ATTA | 1 | 12 | |
TTCT | 1 | 12 | |
GTCT | 1 | 12 | |
5 | ATATG | 1 | 15 |
6 | CCATCT | 1 | 18 |
Total | 17 | 58 | — |
密码子 Codon | 数目 Number | 氨基酸 Amino acids | 密码子比例 Ratio/% | 氨基酸数目 Number of amino acids | 氨基酸比例 Ratio/% | 相对密码子使用度 RSCU |
---|---|---|---|---|---|---|
GCA | 369 | 丙氨酸 Ala | 1.55 | 1 235 | 5.2 | 1.2 |
GCC | 176 | 0.74 | 0.57 | |||
GCG | 122 | 0.51 | 0.4 | |||
GCU | 568 | 2.39 | 1.84 | |||
AGA | 489 | 精氨酸 Arg | 2.06 | 1 509 | 6.35 | 1.94 |
AGG | 160 | 0.67 | 0.64 | |||
CGA | 333 | 1.4 | 1.32 | |||
CGC | 84 | 0.35 | 0.33 | |||
CGG | 102 | 0.43 | 0.41 | |||
CGU | 341 | 1.44 | 1.36 | |||
AAC | 257 | 天冬酰胺Asn | 1.08 | 1 114 | 4.69 | 0.46 |
AAU | 857 | 3.61 | 1.54 | |||
GAC | 181 | 天冬氨酸Asp | 0.76 | 998 | 4.2 | 0.36 |
GAU | 817 | 3.44 | 1.64 | |||
UGC | 72 | 半胱氨酸Cys | 0.3 | 279 | 1.17 | 0.52 |
UGU | 207 | 0.87 | 1.48 | |||
CAA | 655 | 谷氨酰胺Gln | 2.76 | 872 | 3.67 | 1.5 |
CAG | 217 | 0.91 | 0.5 | |||
GAA | 964 | 谷氨酸 Glu | 4.06 | 1 317 | 5.55 | 1.46 |
GAG | 353 | 1.49 | 0.54 | |||
GGA | 636 | 甘氨酸 Gly | 2.68 | 1 585 | 6.67 | 1.61 |
GGC | 152 | 0.64 | 0.38 | |||
GGG | 286 | 1.2 | 0.72 | |||
GGU | 511 | 2.15 | 1.29 | |||
CAC | 130 | 组氨酸 His | 0.55 | 599 | 2.52 | 0.43 |
CAU | 469 | 1.97 | 1.57 | |||
AUA | 581 | 异亮氨酸 Ile | 2.44 | 1 959 | 8.25 | 0.89 |
AUC | 434 | 1.83 | 0.66 | |||
AUU | 944 | 3.98 | 1.45 | |||
CUA | 352 | 亮氨酸 Leu | 1.48 | 2 410 | 10.15 | 0.88 |
CUC | 169 | 0.71 | 0.42 | |||
CUG | 172 | 0.72 | 0.43 | |||
CUU | 509 | 2.14 | 1.27 | |||
UUA | 716 | 3.02 | 1.78 | |||
UUG | 492 | 2.07 | 1.22 | |||
AAA | 972 | 赖氨酸 Lys | 4.09 | 1 353 | 5.7 | 1.44 |
AAG | 381 | 1.6 | 0.56 | |||
AUG | 549 | 甲硫氨酸Met | 2.31 | 549 | 2.31 | 1 |
UUC | 509 | 苯丙氨酸Phe | 2.14 | 1 328 | 5.59 | 0.77 |
UUU | 819 | 3.45 | 1.23 | |||
CCA | 268 | 脯氨酸 Pro | 1.13 | 970 | 4.08 | 1.11 |
CCC | 217 | 0.91 | 0.89 | |||
CCG | 112 | 0.47 | 0.46 | |||
CCU | 373 | 1.57 | 1.54 | |||
AGC | 99 | 丝氨酸 Ser | 0.42 | 1 891 | 7.96 | 0.31 |
AGU | 377 | 1.59 | 1.2 | |||
UCA | 366 | 1.54 | 1.16 | |||
UCC | 322 | 1.36 | 1.02 | |||
UCG | 161 | 0.68 | 0.51 | |||
UCU | 566 | 2.38 | 1.8 | |||
UAA | 35 | 终止密码子TER | 0.15 | 78 | 0.33 | 1.35 |
UAG | 26 | 0.11 | 1 | |||
UGA | 17 | 0.07 | 0.65 | |||
ACA | 352 | 苏氨酸 Thr | 1.48 | 1197 | 5.04 | 1.18 |
ACC | 219 | 0.92 | 0.73 | |||
ACG | 148 | 0.62 | 0.49 | |||
ACU | 478 | 2.01 | 1.6 | |||
UGG | 415 | 色氨酸 Trp | 1.75 | 415 | 1.75 | 1 |
UAC | 166 | 络氨酸 Tyr | 0.7 | 822 | 3.46 | 0.4 |
UAU | 656 | 2.76 | 1.6 | |||
GUA | 454 | 缬氨酸 Val | 1.91 | 1267 | 5.34 | 1.43 |
GUC | 164 | 0.69 | 0.52 | |||
GUG | 215 | 0.91 | 0.68 | |||
GUU | 434 | 1.83 | 1.37 |
Table. 4 Summary of codon usage and amino acids patterns of D. thyrsiflorum cp genome
密码子 Codon | 数目 Number | 氨基酸 Amino acids | 密码子比例 Ratio/% | 氨基酸数目 Number of amino acids | 氨基酸比例 Ratio/% | 相对密码子使用度 RSCU |
---|---|---|---|---|---|---|
GCA | 369 | 丙氨酸 Ala | 1.55 | 1 235 | 5.2 | 1.2 |
GCC | 176 | 0.74 | 0.57 | |||
GCG | 122 | 0.51 | 0.4 | |||
GCU | 568 | 2.39 | 1.84 | |||
AGA | 489 | 精氨酸 Arg | 2.06 | 1 509 | 6.35 | 1.94 |
AGG | 160 | 0.67 | 0.64 | |||
CGA | 333 | 1.4 | 1.32 | |||
CGC | 84 | 0.35 | 0.33 | |||
CGG | 102 | 0.43 | 0.41 | |||
CGU | 341 | 1.44 | 1.36 | |||
AAC | 257 | 天冬酰胺Asn | 1.08 | 1 114 | 4.69 | 0.46 |
AAU | 857 | 3.61 | 1.54 | |||
GAC | 181 | 天冬氨酸Asp | 0.76 | 998 | 4.2 | 0.36 |
GAU | 817 | 3.44 | 1.64 | |||
UGC | 72 | 半胱氨酸Cys | 0.3 | 279 | 1.17 | 0.52 |
UGU | 207 | 0.87 | 1.48 | |||
CAA | 655 | 谷氨酰胺Gln | 2.76 | 872 | 3.67 | 1.5 |
CAG | 217 | 0.91 | 0.5 | |||
GAA | 964 | 谷氨酸 Glu | 4.06 | 1 317 | 5.55 | 1.46 |
GAG | 353 | 1.49 | 0.54 | |||
GGA | 636 | 甘氨酸 Gly | 2.68 | 1 585 | 6.67 | 1.61 |
GGC | 152 | 0.64 | 0.38 | |||
GGG | 286 | 1.2 | 0.72 | |||
GGU | 511 | 2.15 | 1.29 | |||
CAC | 130 | 组氨酸 His | 0.55 | 599 | 2.52 | 0.43 |
CAU | 469 | 1.97 | 1.57 | |||
AUA | 581 | 异亮氨酸 Ile | 2.44 | 1 959 | 8.25 | 0.89 |
AUC | 434 | 1.83 | 0.66 | |||
AUU | 944 | 3.98 | 1.45 | |||
CUA | 352 | 亮氨酸 Leu | 1.48 | 2 410 | 10.15 | 0.88 |
CUC | 169 | 0.71 | 0.42 | |||
CUG | 172 | 0.72 | 0.43 | |||
CUU | 509 | 2.14 | 1.27 | |||
UUA | 716 | 3.02 | 1.78 | |||
UUG | 492 | 2.07 | 1.22 | |||
AAA | 972 | 赖氨酸 Lys | 4.09 | 1 353 | 5.7 | 1.44 |
AAG | 381 | 1.6 | 0.56 | |||
AUG | 549 | 甲硫氨酸Met | 2.31 | 549 | 2.31 | 1 |
UUC | 509 | 苯丙氨酸Phe | 2.14 | 1 328 | 5.59 | 0.77 |
UUU | 819 | 3.45 | 1.23 | |||
CCA | 268 | 脯氨酸 Pro | 1.13 | 970 | 4.08 | 1.11 |
CCC | 217 | 0.91 | 0.89 | |||
CCG | 112 | 0.47 | 0.46 | |||
CCU | 373 | 1.57 | 1.54 | |||
AGC | 99 | 丝氨酸 Ser | 0.42 | 1 891 | 7.96 | 0.31 |
AGU | 377 | 1.59 | 1.2 | |||
UCA | 366 | 1.54 | 1.16 | |||
UCC | 322 | 1.36 | 1.02 | |||
UCG | 161 | 0.68 | 0.51 | |||
UCU | 566 | 2.38 | 1.8 | |||
UAA | 35 | 终止密码子TER | 0.15 | 78 | 0.33 | 1.35 |
UAG | 26 | 0.11 | 1 | |||
UGA | 17 | 0.07 | 0.65 | |||
ACA | 352 | 苏氨酸 Thr | 1.48 | 1197 | 5.04 | 1.18 |
ACC | 219 | 0.92 | 0.73 | |||
ACG | 148 | 0.62 | 0.49 | |||
ACU | 478 | 2.01 | 1.6 | |||
UGG | 415 | 色氨酸 Trp | 1.75 | 415 | 1.75 | 1 |
UAC | 166 | 络氨酸 Tyr | 0.7 | 822 | 3.46 | 0.4 |
UAU | 656 | 2.76 | 1.6 | |||
GUA | 454 | 缬氨酸 Val | 1.91 | 1267 | 5.34 | 1.43 |
GUC | 164 | 0.69 | 0.52 | |||
GUG | 215 | 0.91 | 0.68 | |||
GUU | 434 | 1.83 | 1.37 |
Fig.3 Phylogenetic analysis of 27 Dendrobium species based on the common CDs of selected cp genomes Dotted line refers to the classification of selected Dendrobium sp.
种名 Species | 登录号 Accession number | 基因组大小 Genome size/bp | 长编码区 LSC/bp | 短编码区 SSC/bp | 反向重复区 IR/bp | 基因数目 Numuber of genes | GC含量 GC content/% |
---|---|---|---|---|---|---|---|
球花石斛 D. thyrsiflorum | MN413199 | 151 686 | 84 749 | 14 351 | 26 293 | 125 | 37.55 |
矮石斛 D. bellatulum | NC037700 | 152 107 | 90 299 | 14 516 | 23 646 | 128 | 37.48 |
玫瑰石斛 D. crepidatum | NC035331 | 151 717 | 117 317 | 14 382 | 10 009 | 132 | 37.57 |
齿瓣石斛 D. devonianum | NC035325 | 151 945 | 84 966 | 14 435 | 26 272 | 132 | 37.55 |
反瓣石斛 D. ellipsophyllum | NC035340 | 152 026 | 84 930 | 14 488 | 26 306 | 132 | 37.50 |
霍山石斛 D. huoshanense | NC028430 | 153 188 | 85 614 | 14 524 | 26 525 | 129 | 37.49 |
Table 5 Comparison of six chloroplast genomes of Dendrobium species
种名 Species | 登录号 Accession number | 基因组大小 Genome size/bp | 长编码区 LSC/bp | 短编码区 SSC/bp | 反向重复区 IR/bp | 基因数目 Numuber of genes | GC含量 GC content/% |
---|---|---|---|---|---|---|---|
球花石斛 D. thyrsiflorum | MN413199 | 151 686 | 84 749 | 14 351 | 26 293 | 125 | 37.55 |
矮石斛 D. bellatulum | NC037700 | 152 107 | 90 299 | 14 516 | 23 646 | 128 | 37.48 |
玫瑰石斛 D. crepidatum | NC035331 | 151 717 | 117 317 | 14 382 | 10 009 | 132 | 37.57 |
齿瓣石斛 D. devonianum | NC035325 | 151 945 | 84 966 | 14 435 | 26 272 | 132 | 37.55 |
反瓣石斛 D. ellipsophyllum | NC035340 | 152 026 | 84 930 | 14 488 | 26 306 | 132 | 37.50 |
霍山石斛 D. huoshanense | NC028430 | 153 188 | 85 614 | 14 524 | 26 525 | 129 | 37.49 |
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