植物学报 ›› 2018, Vol. 53 ›› Issue (1): 94-103.DOI: 10.11983/CBB16247
收稿日期:
2016-12-13
接受日期:
2017-03-29
出版日期:
2018-01-01
发布日期:
2018-08-10
通讯作者:
郭军战
基金资助:
Qiaoli Li, Na Yan, Qiong Song, Junzhan Guo*()
Received:
2016-12-13
Accepted:
2017-03-29
Online:
2018-01-01
Published:
2018-08-10
Contact:
Junzhan Guo
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。
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.
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 |
表1 4种桑属植物叶绿体基因组基本特征比较
Table 1 Comparison of chloroplast genomes among four species of Morus
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* |
表2 鲁桑叶绿体基因组注释基因信息
Table 2 Genes present in the chloroplast genome of Morus multicaulis
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 |
表3 鲁桑密码子信息
Table 3 Codon usage in Morus multicaulis
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 |
Length (bp) | Number | Morus multicaulis | M. mongolica |
---|---|---|---|
A10 | 10 | 2142, 3980, 5079, 5977, 29067, 49740, 68616, 68631, 114154 (ndhF), 116262 | 3760, 4859, 28847, 38118, 113758 (ndhF), 115866 |
A11 | 3 | 9589, 62837, 87467 | 1921, 5757, 9371, 62504, 81011 |
A12 | 3 | 4830, 53982, 85376 | 13368, 38142, 53676, 84178, 87070 |
A13 | 1 | 13596 | 4609, 73766 |
A14 | 1 | 128163 | 127468 |
A15 | 1 | 74160 | |
A16 | 1 | 8990 | |
A17 | 8772 | ||
T10 | 20 | 66, 5258, 8582, 9802, 14098, 14919, 24357, 30672, 30938, 54024, 57098 (atpB), 62610, 66927, 68743, 70892, 73958, 83130, 116784, 130487 (ycf1), 132244 (ycf1) | 5038, 7036, 9584, 24137, 30452, 30718, 53718, 56773 (atpB), 62277, 70506, 73564, 82753, 116369, 121665, 129792 (ycf1), 131549 (ycf1) |
T11 | 6 | 513, 34264, 69552, 78684, 122351, 131346 (ycf1) | 293, 8363, 57218, 59233, 66594, 68126, 69166, 74280, 78285, 130651 (ycf1) |
T12 | 5 | 27617 (rpoB), 57549, 59565, 72471, 85809 | 12476, 13966, 27397 (rpoB), 34035, 85411 |
T13 | 5 | 12703, 13286, 68491, 81352, 128585 | 8996, 13058, 51524, 72085, 127890 |
T14 | 5 | 9213, 51829, 63865, 74676, 86927 | 63532, 80953 |
T16 | 49162, 86528 | ||
T17 | 1 | 49475 | |
T19 | 1 | 116631 | 116235 |
AT5 | 1 | 11566 (ndhF) | 115270 (ndhF) |
AT6 | 2 | 118643, 118871 | 10589, 49643 |
TA6 | 2 | 5522, 21234 (rpoC2) | 5302, 21009 (rpoC2), 118243 |
TC5 | 1 | 645927 (cemA) | 64259 (cemA) |
TTC4 | 1 | 70909 | 70523 |
AAT4 | 1 | 128565 | 127870 |
ATTT3 | 1 | 62140 | |
ATTT4 | 1 | 14187 | 13957, 61807 |
AAAT3 | 2 | 24056 (rpoC1), 46731 (ycf3) | 23831(rpoC1), 46414 (ycf3) |
TATT3 | 1 | 24388 (rpoC1) | 24168 (rpoC1) |
ATTA3 | 2 | 33980, 116443 | 33751, 116047 |
TCTT3 | 1 | 111575 | 111179 |
AAAG3 | 1 | 135331 | 134636 |
AAGGA3 | 1 | 14021 (atpF) | 13792 (atpF) |
ATTTC3 | 24071 |
表4 鲁桑和蒙桑中简单重复序列(SSR)位点对比
Table 4 Comparison of simple sequence repeats (SSR) loci in Morus multicaulis and M. mongolica
Length (bp) | Number | Morus multicaulis | M. mongolica |
---|---|---|---|
A10 | 10 | 2142, 3980, 5079, 5977, 29067, 49740, 68616, 68631, 114154 (ndhF), 116262 | 3760, 4859, 28847, 38118, 113758 (ndhF), 115866 |
A11 | 3 | 9589, 62837, 87467 | 1921, 5757, 9371, 62504, 81011 |
A12 | 3 | 4830, 53982, 85376 | 13368, 38142, 53676, 84178, 87070 |
A13 | 1 | 13596 | 4609, 73766 |
A14 | 1 | 128163 | 127468 |
A15 | 1 | 74160 | |
A16 | 1 | 8990 | |
A17 | 8772 | ||
T10 | 20 | 66, 5258, 8582, 9802, 14098, 14919, 24357, 30672, 30938, 54024, 57098 (atpB), 62610, 66927, 68743, 70892, 73958, 83130, 116784, 130487 (ycf1), 132244 (ycf1) | 5038, 7036, 9584, 24137, 30452, 30718, 53718, 56773 (atpB), 62277, 70506, 73564, 82753, 116369, 121665, 129792 (ycf1), 131549 (ycf1) |
T11 | 6 | 513, 34264, 69552, 78684, 122351, 131346 (ycf1) | 293, 8363, 57218, 59233, 66594, 68126, 69166, 74280, 78285, 130651 (ycf1) |
T12 | 5 | 27617 (rpoB), 57549, 59565, 72471, 85809 | 12476, 13966, 27397 (rpoB), 34035, 85411 |
T13 | 5 | 12703, 13286, 68491, 81352, 128585 | 8996, 13058, 51524, 72085, 127890 |
T14 | 5 | 9213, 51829, 63865, 74676, 86927 | 63532, 80953 |
T16 | 49162, 86528 | ||
T17 | 1 | 49475 | |
T19 | 1 | 116631 | 116235 |
AT5 | 1 | 11566 (ndhF) | 115270 (ndhF) |
AT6 | 2 | 118643, 118871 | 10589, 49643 |
TA6 | 2 | 5522, 21234 (rpoC2) | 5302, 21009 (rpoC2), 118243 |
TC5 | 1 | 645927 (cemA) | 64259 (cemA) |
TTC4 | 1 | 70909 | 70523 |
AAT4 | 1 | 128565 | 127870 |
ATTT3 | 1 | 62140 | |
ATTT4 | 1 | 14187 | 13957, 61807 |
AAAT3 | 2 | 24056 (rpoC1), 46731 (ycf3) | 23831(rpoC1), 46414 (ycf3) |
TATT3 | 1 | 24388 (rpoC1) | 24168 (rpoC1) |
ATTA3 | 2 | 33980, 116443 | 33751, 116047 |
TCTT3 | 1 | 111575 | 111179 |
AAAG3 | 1 | 135331 | 134636 |
AAGGA3 | 1 | 14021 (atpF) | 13792 (atpF) |
ATTTC3 | 24071 |
图2 4个桑属物种叶绿体基因组反向重复区(IR)、大单拷贝区(LSC)和小单拷贝区(SSC)边界比对MT: 鲁桑, MI: 印度桑; MM: 蒙桑; MN: 川桑
Figure 2 Comparison of the junction between inverted repeat region (IR), large single copy-region (LSC) and small single copy- region (SSC) of chloroplast genome among four Morus species MT: Morus multicaulis; MI: M. indica; MM: M. mongolica; MN: M. notabilis
图3 基于叶绿体全基因组的桑属4个物种及其近缘种的最大似然法(ML) (A)和近邻结合法(NJ) (B)聚类结果
Figure 3 Cluster analysis of four species of Morus using complete chloroplast genome sequence by the maximum likelihood (ML) method (A) and neighbor-joining (NL) method (B)
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