Chin Bull Bot ›› 2018, Vol. 53 ›› Issue (1): 94-103.doi: 10.11983/CBB16247

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Complete Chloroplast Genome Sequence and Characteristics Analysis of Morus multicaulis

Qiaoli Li, Na Yan, Qiong Song, Junzhan Guo*()   

  1. College of Forestry, Northwest A & F University, Yangling 712100, China
  • Received:2016-12-13 Accepted:2017-03-29 Online:2018-08-10 Published:2018-01-01
  • Contact: Junzhan Guo E-mail:guojunzhan@163.com

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

Figure 1

Gene map of the chloroplast genome of Morus multicaulis"

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

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*

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

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

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"

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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