生物技术通报 ›› 2022, Vol. 38 ›› Issue (6): 174-186.doi: 10.13560/j.cnki.biotech.bull.1985.2021-1078
收稿日期:
2021-08-21
出版日期:
2022-06-26
发布日期:
2022-07-11
作者简介:
钱方,男,硕士研究生,研究方向:油菜远缘杂交及种质资源创新;E-mail: 基金资助:
QIAN Fang(), GAO Zuo-min, HU Li-juan, WANG Hong-cheng()
Received:
2021-08-21
Published:
2022-06-26
Online:
2022-07-11
摘要:
海甘蓝(Crambe abyssinica)为十字花科(Brassicaceae)海甘蓝属(Crambe)植物,其种子富含芥酸,被视为一种重要的可再生工业油用资源。本研究基于Illumina HiSeq 测序数据从头组装了(de novo)海甘蓝的叶绿体(chloroplast,cp)基因组,并分析其在十字花科植物中的系统发育位置。结果表明,海甘蓝叶绿体基因组大小为153 754 bp,呈典型的四分体结构;其包含111个基因,包括78个编码基因、29个tRNA基因以及4个rRNA基因。通过密码子偏好性分析,海甘蓝叶绿体基因组中末端为A/U的密码子使用存在偏倚。SSR及长重复片段分析检测到41个重复序列和59个SSR位点。与近缘种比较,发现其叶绿体基因组序列高度保守,尤其蛋白质编码序列相似度极高。同义与非同义核苷酸替代率分析表明,除ndhB和ycf2基因外,其余编码基因普遍存在纯化选择压力。此外,系统发育分析发现海甘蓝与芸薹属重要的经济作物亲缘关系密切,与白芥属植物形成姊妹类群。这为海甘蓝与芸薹属植物的种间杂交提供了遗传支撑,同时也为阐明海甘蓝的进化史提供了重要的分子信息。
钱方, 高作敏, 胡利娟, 王洪程. 海甘蓝(Crambe abyssinica)叶绿体基因组特征及其系统发育研究[J]. 生物技术通报, 2022, 38(6): 174-186.
QIAN Fang, GAO Zuo-min, HU Li-juan, WANG Hong-cheng. Characteristics of Crambe abyssinica Chloroplast Genome and Its Phylogenetic Relationship in Brassicaceae[J]. Biotechnology Bulletin, 2022, 38(6): 174-186.
图1 海甘蓝叶绿体全基因组图谱 圆圈外面的基因是顺时针转录,而圆圈里面的基因是逆时针转录。不同功能组的基因以不同的颜色显示。内圈深灰色对应GC含量,浅灰色对应AT含量
Fig.1 Circle gene map of the C. abyssinica cp genome Genes drawn outside and inside of the circle are transcribed clockwise and counterclockwise,respectively. Genes belonging to different functional groups are color coded. The dark gray in the inner circle corresponds to GC content,and light grey to AT content
类别 Category | 条目 Item | 说明 Description |
---|---|---|
叶绿体基因组结构 | 大单拷贝区/bp | 83 622 |
Structure of cp genome | 反向重复区/bp | 26 176 |
小单拷贝区/bp | 17 780 | |
基因组大小/bp | 153 754 | |
基因组成 | 基因总数 | 111 |
Gene composition | 编码基因 | 78 |
tRNAs | 29 | |
rRNAs | 4 | |
双拷贝基因 | 19 | |
大单拷贝区基因数 | 81 | |
反向重复区基因数 | 18 | |
小单拷贝区基因数 | 13 | |
GC含量 | 大单拷贝区GC含量/% | 34.14 |
GC content | 反向重复区GC含量/% | 42.36 |
小单拷贝区GC含量/% | 29.29 | |
平均GC含量/% | 36.37 | |
单碱基含量 | A/% | 31.35 |
Single nucleotide content | T/% | 32.28 |
C/% | 18.51 | |
G/% | 17.86 |
表1 海甘蓝叶绿体基因组的详细特征
Table 1 Detailed characteristics of the chloroplast genome of C. abyssinica
类别 Category | 条目 Item | 说明 Description |
---|---|---|
叶绿体基因组结构 | 大单拷贝区/bp | 83 622 |
Structure of cp genome | 反向重复区/bp | 26 176 |
小单拷贝区/bp | 17 780 | |
基因组大小/bp | 153 754 | |
基因组成 | 基因总数 | 111 |
Gene composition | 编码基因 | 78 |
tRNAs | 29 | |
rRNAs | 4 | |
双拷贝基因 | 19 | |
大单拷贝区基因数 | 81 | |
反向重复区基因数 | 18 | |
小单拷贝区基因数 | 13 | |
GC含量 | 大单拷贝区GC含量/% | 34.14 |
GC content | 反向重复区GC含量/% | 42.36 |
小单拷贝区GC含量/% | 29.29 | |
平均GC含量/% | 36.37 | |
单碱基含量 | A/% | 31.35 |
Single nucleotide content | T/% | 32.28 |
C/% | 18.51 | |
G/% | 17.86 |
基因功能分类 Category for genes | 基因功能 Groups of genes | 基因名 Names of genes |
---|---|---|
参与光合作用的基因 Genes involving in photosynthesis | 光合系统亚基 | ndhI,ndhJ,ndhK,psaA,psaB,psaC,psaI,psaJ,psbA,psbB,psbC,psbD,psbE,psbF,psbH,psbI,psbJ,psbK,psbL,psbM,psbN,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 | ndhAb,ndhBa,b,ndhC,ndhD,ndhE,ndhF,ndhG,ndhH | |
自身复制相关基因 Genes related to 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-GUG,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-GGU,trnT-UGU,trnV-GAC,trnV-UACa,b,trnW-CCA,trnY-GUA | |
核糖体小亚基 | rps11,rps12a,c,rps14,rps15,rps16b,rps18,rps19,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 | |
其他功能基因 Other functional genes | 成熟酶 | matK |
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 Functionally unknown genes | 保守开放阅读框架 | ycf1a,ycf2a,ycf3c,ycf4 |
表2 海甘蓝叶绿体基因组基因功能总结
Table 2 Summary of assembled gene functions of C. abyssinica chloroplast genome
基因功能分类 Category for genes | 基因功能 Groups of genes | 基因名 Names of genes |
---|---|---|
参与光合作用的基因 Genes involving in photosynthesis | 光合系统亚基 | ndhI,ndhJ,ndhK,psaA,psaB,psaC,psaI,psaJ,psbA,psbB,psbC,psbD,psbE,psbF,psbH,psbI,psbJ,psbK,psbL,psbM,psbN,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 | ndhAb,ndhBa,b,ndhC,ndhD,ndhE,ndhF,ndhG,ndhH | |
自身复制相关基因 Genes related to 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-GUG,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-GGU,trnT-UGU,trnV-GAC,trnV-UACa,b,trnW-CCA,trnY-GUA | |
核糖体小亚基 | rps11,rps12a,c,rps14,rps15,rps16b,rps18,rps19,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 | |
其他功能基因 Other functional genes | 成熟酶 | matK |
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 Functionally unknown genes | 保守开放阅读框架 | ycf1a,ycf2a,ycf3c,ycf4 |
基因组结构 Genome features | 海甘蓝 C. abyssinica | 拟南芥 A. thaliana | 克拉里克海甘蓝 C. kralikii | 甘蓝型油菜 B. napus | 萝卜 R. sativus | 白菜 B. rapa |
---|---|---|---|---|---|---|
基因组大小Genome size/bp | 153 754 | 154 478 | 153 919 | 152 860 | 153 368 | 153 482 |
大单拷贝区LSC length/bp | 83 622 | 84 170 | 83 688 | 83 030 | 83 170 | 83 282 |
小单拷贝区SSC length/bp | 17 780 | 17 780 | 17 769 | 17 760 | 17 764 | 17 775 |
反向重复区IR length/bp | 26 176 | 26 264 | 26 231 | 26 035 | 26 217 | 26 213 |
GC含量GC content/% | 36.37 | 36.29 | 36.35 | 36.32 | 36.34 | 36.36 |
基因数量Number of genes | 111 | 113 | 113 | 113 | 113 | 113 |
蛋白编码基因Protein-coding gene | 78 | 79 | 79 | 79 | 79 | 79 |
rRNA | 4 | 4 | 4 | 4 | 4 | 4 |
tRNA | 29 | 30 | 30 | 30 | 30 | 30 |
表3 6种十字花科物种叶绿体基因组特征比较
Table 3 Comparison of six chloroplast genomes of Brassicaceae species
基因组结构 Genome features | 海甘蓝 C. abyssinica | 拟南芥 A. thaliana | 克拉里克海甘蓝 C. kralikii | 甘蓝型油菜 B. napus | 萝卜 R. sativus | 白菜 B. rapa |
---|---|---|---|---|---|---|
基因组大小Genome size/bp | 153 754 | 154 478 | 153 919 | 152 860 | 153 368 | 153 482 |
大单拷贝区LSC length/bp | 83 622 | 84 170 | 83 688 | 83 030 | 83 170 | 83 282 |
小单拷贝区SSC length/bp | 17 780 | 17 780 | 17 769 | 17 760 | 17 764 | 17 775 |
反向重复区IR length/bp | 26 176 | 26 264 | 26 231 | 26 035 | 26 217 | 26 213 |
GC含量GC content/% | 36.37 | 36.29 | 36.35 | 36.32 | 36.34 | 36.36 |
基因数量Number of genes | 111 | 113 | 113 | 113 | 113 | 113 |
蛋白编码基因Protein-coding gene | 78 | 79 | 79 | 79 | 79 | 79 |
rRNA | 4 | 4 | 4 | 4 | 4 | 4 |
tRNA | 29 | 30 | 30 | 30 | 30 | 30 |
图2 以海甘蓝为参考与其他5个近缘物种的序列比对结果 灰色箭头和粗黑线表明基因定位。紫色条代表外显子,蓝色条代表非翻译区(UTR),粉色条代表非编码序列(CNS),灰色条代表mRNA,白色峰代表基因组学差异。y轴表示同一性百分比(显示:50%-100%)
Fig.2 Sequence alignment of 5 chloroplast genomes of Brassicaceae,with the annotation of C. abyssinica as reference Gray arrows above the alignment indicate the position and direction of each gene. The Y-scale represents the percent of identity between 50% and 100%. Genome regions are color coded as exon,tRNA,rRNA and conserved noncoding sequences(CNS)
图5 海甘蓝与十字花科5个近缘物种叶绿体基因组中75个蛋白编码基因的Ka/Ks值
Fig.5 Ka/Ks ratios of 75 PCGs of the C. abyssinica chloroplast genome versus 5 closely related species of Brassicaceae
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