海甘蓝（Crambe abyssinica）叶绿体基因组特征及其系统发育研究

doi:10.13560/j.cnki.biotech.bull.1985.2021-1078

摘要/Abstract

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。

关键词: 海甘蓝, 叶绿体基因组, 比较分析, 系统发育

Abstract:

Crambe abyssinica,belonging to Crambe genus in Brassicaceae,has been used as a potentially renewable industrial oil resource because of its high natural erucic acid content in seed. Here,the chloroplast（cp）genome of C. abyssinica was de novo assembled by Illumina Platform,and its phylogenetic relationship was detected based on the cp genome in Brassicaceae. The cp genome of C. abyssinica had a quadripartite structure of 153 754 bp in length,which were annotated a total of 111 unigenes,including 78 protein-coding genes,29 tRNA genes and 4 rRNA genes. Codon usage showed a bias of A/U-ending codons in the cp genome of C. abyssinica. A total of 41 repeat structures and 59 SSRs（simple sequence repeats）were detected in this cp genome. Comparative analysis showed that the genome sequence was conserved and the protein-coding sequence had high similarity. Synonymous and non-synonymous analysis detected strong positive selection exerted on the ndhF and ycf2 gene in the cp genome of C. abyssinica. Moreover,phylogenetic analysis showed that C. abyssinica was closely related to Brassica and formed a sister group with Sinapis species. This suggests that it is possible to transfer favorable genes from C. abyssinica to other Brassicaceae plants by distant hybridization,and also provide important molecular information for elucidating the evolutionary history of C. abyssinica.

Key words: Crambe abyssinica, chloroplast genome, comparative analysis, phylogenetic relationship

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/表 9

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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

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,petB^b,petD^b,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,atpF^b,atpH,atpI
	NADH脱氢酶亚基	ndhA^b,ndhB^a,b,ndhC,ndhD,ndhE,ndhF,ndhG,ndhH
自身复制相关基因 Genes related to self-replication	rRNA基因	rrn16^a,rrn23^a,rrn4.5^a,rrn5^a
	tRNA基因	trnA-UGC^a,b,trnC-GCA,trnD-GUC,trnE-UUC,trnF-GAA,trnfM-CAU,trnG-GCC^b,trnG-UCC,trnH-GUG,trnI-CAU^a,trnI-GAU^a,b,trnK-UUU^b,trnL-CAA^a,trnL-UAA^b,trnL-UAG,trnM-CAU,trnN-GUU^a,trnP-UGG,trnQ-UUG,trnR-ACG^a,trnR-UCU,trnS-GCU,trnS-GGA,trnS-UGA,trnT-GGU,trnT-UGU,trnV-GAC,trnV-UAC^a,b,trnW-CCA,trnY-GUA
	核糖体小亚基	rps11,rps12^a,c,rps14,rps15,rps16^b,rps18,rps19,rps2
	核糖体大亚基	rps3,rps4,rps7^a,rps8,rpl14,rpl16^b,rpl2^a,b,rpl20,rpl22,rpl23^a,rpl32,rpl33
	DNA依赖的RNA聚合酶	rpl36,rpoA,rpoB,rpoC1^b,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	clpP^c
未知功能基因 Functionally unknown genes	保守开放阅读框架	ycf1^a,ycf2^a,ycf3^c,ycf4

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,petB^b,petD^b,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,atpF^b,atpH,atpI
	NADH脱氢酶亚基	ndhA^b,ndhB^a,b,ndhC,ndhD,ndhE,ndhF,ndhG,ndhH
自身复制相关基因 Genes related to self-replication	rRNA基因	rrn16^a,rrn23^a,rrn4.5^a,rrn5^a
	tRNA基因	trnA-UGC^a,b,trnC-GCA,trnD-GUC,trnE-UUC,trnF-GAA,trnfM-CAU,trnG-GCC^b,trnG-UCC,trnH-GUG,trnI-CAU^a,trnI-GAU^a,b,trnK-UUU^b,trnL-CAA^a,trnL-UAA^b,trnL-UAG,trnM-CAU,trnN-GUU^a,trnP-UGG,trnQ-UUG,trnR-ACG^a,trnR-UCU,trnS-GCU,trnS-GGA,trnS-UGA,trnT-GGU,trnT-UGU,trnV-GAC,trnV-UAC^a,b,trnW-CCA,trnY-GUA
	核糖体小亚基	rps11,rps12^a,c,rps14,rps15,rps16^b,rps18,rps19,rps2
	核糖体大亚基	rps3,rps4,rps7^a,rps8,rpl14,rpl16^b,rpl2^a,b,rpl20,rpl22,rpl23^a,rpl32,rpl33
	DNA依赖的RNA聚合酶	rpl36,rpoA,rpoB,rpoC1^b,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	clpP^c
未知功能基因 Functionally unknown genes	保守开放阅读框架	ycf1^a,ycf2^a,ycf3^c,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