鲁桑叶绿体基因组序列及特征分析

doi:10.11983/CBB16247

摘要/Abstract

摘要：

鲁桑(Morus multicaulis)是亚洲地区栽培的重要经济作物。以鲁桑品种日本胡橙为实验材料, 利用高通量测序技术对鲁桑叶绿体基因组进行测序, 获得NCBI登录号(KU355297), 并研究鲁桑的叶绿体基因组结构。结合前人对蒙桑(M. mongolica)、印度桑(M. indica)和川桑(M. notabilis)的研究结果, 对鲁桑的系统进化关系进行了探讨。研究结果表明: 鲁桑叶绿体基因组是一个典型的四部分结构, 全长159 154 bp, 共注释130个基因, 包含85个蛋白质编码基因(18个基因在反向重复区重复)、37个转运RNA (tRNA)基因和8个核糖体RNA (rRNA)基因。生物信息学分析表明, 在鲁桑中共搜索到82个SSR位点, 单核苷酸、二核苷酸、三核苷酸、四核苷酸和五核苷酸重复基序个数分别为63、7、2、9和1个, 并没有发现六核苷酸; 其中单核苷酸重复在鲁桑的叶绿体基因组SSR中占76.8%。采用MEGA 6.0软件, 通过最大似然法和近邻结合法对包括4个桑属物种在内的15个物种的叶绿体基因组序列进行聚类分析, 2种方法得到的聚类结果均为鲁桑和蒙桑聚在一起。研究结果对叶绿体基因组工程研究及桑属种间的分子标记开发和优良品种培育具有一定的参考价值。

关键词: 鲁桑, 叶绿体基因组, 高通量测序, 聚类分析

Abstract:

Mulberry is an economically important crop in Asia. We determined the complete chloroplast sequence of cultivated species of Morus multicaulis. Ribenhuchen was used as experimental material. High-throughput sequencing was used to sequence the chloroplast genome and the genome structure (NCBI No.: KU355297), and we compared the chloroplast genome with those of reported sibling species (Morus mongolica, M. indica, M. notabilis). The chloroplast genome (cpDNA) of M. multicaulis with a typical quadripartite structure is 159 154 bp long. The cpDNA of M. multicaulis contains 130 genes, including 85 protein coding genes (18 genes duplicated in the inverted repeat regions), 37 transfer RNA genes and 8 ribosomal RNA genes. There are 82 simple sequence repeats, and the number of mono-, di-, tri-, tetra-, pentanucleotide repeat motifs is 63, 7, 2, 9, and 1, with no hexanucleotide repeat sequences. Mono-nucleotide repeat sequences accounted for 76.8% of the cpDNA of simple sequence repeats. MEGA 6.0 was used to construct the phylogenetic tree of 15 species and for cluster analysis of Morus plants. M. multicaulis and M. mongolica were clustered into one group. The research results have reference value for chloroplast genome research, molecular marker development and breeding of mulberry.

Key words: Morus multicaulis, chloroplast genome, high-throughput sequencing, cluster analysis

李巧丽, 延娜, 宋琼, 郭军战. 鲁桑叶绿体基因组序列及特征分析. 植物学报, 2018, 53(1): 94-103.

Qiaoli Li, Na Yan, Qiong Song, Junzhan Guo. Complete Chloroplast Genome Sequence and Characteristics Analysis of Morus multicaulis. Chinese Bulletin of Botany, 2018, 53(1): 94-103.

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链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB16247

https://www.chinbullbotany.com/CN/Y2018/V53/I1/94

图/表 7

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Genome feature	Morus indica	M. mongolica	M. notabilis	M. multicaulis
Genome size (bp)	158484	158459	158680	159154
LSC length (bp)/percent (%)/GC content (%)	87386/55.14/34.1	87367/55.14/34.0	87470/55.12/34.1	87763/55.15/33.9
SSC length (bp)/percent (%)/GC content (%)	19742/12.46/29.4	19736/12.45/29.3	19776/12.46/29.3	20035/12.59/29.3
IR length (bp)/percent (%)/GC content (%)	25678/16.20/42.9	25678/16.20/42.9	25717/16.21/42.9	25678/16.13/42.9
GC content (%)	36.4	36.3	36.4	36.2
Number of genes	133	133	129	130
Number of protein-coding genes	88	88	84	85

Genome feature	Morus indica	M. mongolica	M. notabilis	M. multicaulis
Genome size (bp)	158484	158459	158680	159154
LSC length (bp)/percent (%)/GC content (%)	87386/55.14/34.1	87367/55.14/34.0	87470/55.12/34.1	87763/55.15/33.9
SSC length (bp)/percent (%)/GC content (%)	19742/12.46/29.4	19736/12.45/29.3	19776/12.46/29.3	20035/12.59/29.3
IR length (bp)/percent (%)/GC content (%)	25678/16.20/42.9	25678/16.20/42.9	25717/16.21/42.9	25678/16.13/42.9
GC content (%)	36.4	36.3	36.4	36.2
Number of genes	133	133	129	130
Number of protein-coding genes	88	88	84	85

Function	Gene group	Gene name
Self-replication	Ribosomal RNA genes	rrn4	rrn5	rrn16	rrn23
	Transfer RNA genes	trnA-UGC trnF-GAA trnH-GUG trnL-CAA trnN-GUU trnR-UCU trnT-GGU trnW-CCA	trnC-GCA trnfM-CAU trnI-CAU trnL-UAA trnP-UGG trnS-GCU trnT-UGU trnY-GUA	trnD-GUC trnG-GCC trnI-GAU trnL-UAG trnQ-UUG trnS-GGA trnV-GAC	trnE-UUC trnG-UCC trnK-UUU trnM-CAU trnR-ACG trnS-UGA trnV-UAC
	Small subunit of ribosome	rps2 rps8 rps15	rps3 rps11 rps16*	rps4 rps12 rps18	rps7 rps14 rps19
	Lange subunit of ribosome	rpl2* rpl22 rpl36	rpl14 rpl23	rpl16* rpl32	rpl20 rpl33
	RNA polymerase subunits	rpoA	rpoB	rpoC1*	rpoC2
	NADH dehydrogenase	ndhA* ndhE ndhI	ndhB* ndhF ndhJ	ndhC ndhG ndhK	ndhD ndhH
Photosynthesis	Photosystem I	psaA psaJ	psaB	psaC	psaI
	Photosystem II	psbA psbE psbJ psbN	psbB psbF psbK psbT	psbC psbH psbL psbZ	psbD psbI psbM
	Cytochrome b/f complex	petA petL	petB* petN	petD*	petG
	ATP synthase	atpA atpH	atpB atpI	atpE	atpF*
	ATP Protease	rbcl
	Large subunit of rubisco	matK
	Maturase	clpP*
	Envelope membrane protein	cemA
Other genes	Subunit of acetyl-CoA-carboxylase	accD
	C-type cytochrome synthesis	ccsA
Unknown function	Hypothetical chloroplast reading frames	yf1	ycf3*	ycf4	ycf15
	ORFs	ycf2 ycf68*

Function	Gene group	Gene name
Self-replication	Ribosomal RNA genes	rrn4	rrn5	rrn16	rrn23
	Transfer RNA genes	trnA-UGC trnF-GAA trnH-GUG trnL-CAA trnN-GUU trnR-UCU trnT-GGU trnW-CCA	trnC-GCA trnfM-CAU trnI-CAU trnL-UAA trnP-UGG trnS-GCU trnT-UGU trnY-GUA	trnD-GUC trnG-GCC trnI-GAU trnL-UAG trnQ-UUG trnS-GGA trnV-GAC	trnE-UUC trnG-UCC trnK-UUU trnM-CAU trnR-ACG trnS-UGA trnV-UAC
	Small subunit of ribosome	rps2 rps8 rps15	rps3 rps11 rps16*	rps4 rps12 rps18	rps7 rps14 rps19
	Lange subunit of ribosome	rpl2* rpl22 rpl36	rpl14 rpl23	rpl16* rpl32	rpl20 rpl33
	RNA polymerase subunits	rpoA	rpoB	rpoC1*	rpoC2
	NADH dehydrogenase	ndhA* ndhE ndhI	ndhB* ndhF ndhJ	ndhC ndhG ndhK	ndhD ndhH
Photosynthesis	Photosystem I	psaA psaJ	psaB	psaC	psaI
	Photosystem II	psbA psbE psbJ psbN	psbB psbF psbK psbT	psbC psbH psbL psbZ	psbD psbI psbM
	Cytochrome b/f complex	petA petL	petB* petN	petD*	petG
	ATP synthase	atpA atpH	atpB atpI	atpE	atpF*
	ATP Protease	rbcl
	Large subunit of rubisco	matK
	Maturase	clpP*
	Envelope membrane protein	cemA
Other genes	Subunit of acetyl-CoA-carboxylase	accD
	C-type cytochrome synthesis	ccsA
Unknown function	Hypothetical chloroplast reading frames	yf1	ycf3*	ycf4	ycf15
	ORFs	ycf2 ycf68*

Codon	Amino acid	Number	Codon	Amino acid	Number
GGG	Gly(G)	494	TGG	Trp(W)	684
GGA	Gly(G)	759	TGA	Stop	1032
GGT	Gly(G)	599	TGT	Cys(C)	725
GGC	Gly(G)	350	TGC	Cys(C)	435
GAG	Glu(E)	550	TAG	Stop	786
GAA	Glu(E)	1368	TAA	Stop	1306
GAT	Asp(D)	1064	TAT	Try(Y)	1624
GAC	Asp(D)	425	TAC	Try(Y)	690
GTG	Val(V)	418	TTG	Leu(L)	1073
GTA	Val(V)	728	TTA	Leu(L)	1250
GTT	Val(V)	792	TTT	Phe(F)	2343
GTC	Val(V)	430	TTC	Phe(F)	1471
GCG	Ala(A)	249	TCG	Ser(S)	578
GCA	Ala(A)	430	TCA	Ser(S)	979
GCT	Ala(A)	511	TCT	Ser(S)	1273
GCC	Ala(A)	321	TCC	Ser(S)	864
AGG	Arg(R)	596	CGG	Arg(R)	350
AGA	Arg(R)	1044	CGA	Arg(R)	596
AGT	Ser(S)	718	CGT	Arg(R)	363
AGC	Ser(S)	478	CGC	Arg(R)	236
AAG	Lys(K)	1039	CAG	Gln(Q)	440
AAA	Lys(K)	2280	CAA	Gln(Q)	1013
AAT	Asn(N)	1883	CAT	His(H)	945
AAC	Asn(N)	728	CAC	His(H)	362
ATG	Met(M)	855	CTG	Leu(L)	489
ATA	Ile(I)	1729	CTA	Leu(L)	799
ATT	Ile(I)	1965	CTT	Leu(L)	1065
ATC	Ile(I)	1083	CTC	Leu(L)	581
ACG	Thr(T)	399	CCG	Pro(P)	400
ACA	Thr(T)	689	CCA	Pro(P)	738
ACT	Thr(T)	690	CCT	Pro(P)	730
ACC	Thr(T)	587	CCC	Pro(P)	580