全 文 ：欧亚大陆分布的大花菟丝子叶绿体基因组插入缺失分析*
王朝波1,2, 龚摇 洵1**
(1 中国科学院昆明植物研究所资源植物与生物技术重点实验室, 云南 昆明摇 650201;
2 中国科学院大学, 北京摇 100049)
摘要: 运用鸟枪法在 Illumina测序仪上对亚洲分布的大花菟丝子 (Cuscuta reflexa) 叶绿体基因组核苷酸全
序列进行测定, 并与已经发表的分布于欧洲的大花菟丝子进行了比较分析。 研究结果表明亚洲分布的大花
菟丝子叶绿体基因组总长度为 120 972 bp, 由 79 499 bp的长单拷贝区, 8 369 bp的短单拷贝区, 以及两个
16 552 bp的反向重复区组成, 其长度比欧洲分布的大花菟丝子小了 549 bp; 基因组总 GC 含量为 38. 3% ,
稍高于欧洲分布的大花菟丝子。 两地区的大花菟丝子叶绿体全基因组编码的功能基因完全相同, 且基因排列
顺序也完全一致。 另外, 经过进一步序列比对后发现亚洲分布的大花菟丝子与欧洲分布的存在 251 个插入和
210个缺失现象, 总插入缺失及碱基替换长度分别为 7 649 bp 和 3 720 bp, 最大的插入和缺失长度分别为
426 bp和 435 bp。 很多插入缺失都是单碱基, 但仍然存在四个长度超过 200 bp的大突变, 两个大的缺失发
生在 ycf2 基因中, 两个大的插入分别发生在 trnF鄄psbE和 matK鄄trnQ间隔区, 详细的对比后发现大量的插入
缺失都发生在大单拷贝区的基因间隔区, 且插入缺失在反向重复区的发生频率较低。 本研究首次报道不同
大洲分布的同种异养植物的叶绿体全基因组比较分析, 为研究这两个区域的居群多样性提供了基础资料。
关键词: 大花菟丝子; 叶绿体基因组; 插入缺失; 对比分析
中图分类号: Q 75摇 摇 摇 摇 摇 摇 文献标识码: A摇 摇 摇 摇 摇 摇 摇 摇 文章编号: 2095-0845(2013)02-158-07
Comparative Analyses of Indels Based on the Whole
Chloroplast Genome of Cuscuta reflexa between
European and Asian Populations
WANG Chao鄄Bo1,2, GONG Xun1**
(1 Key Laboratory of Economic Plant and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences,
Kunming 650201, China; 2 University of Chinese Academy of Sciences, Beijing 100049, China)
Abstract: We determined the complete nucleotide sequence of the chloroplast genome of Asian Cuscuta reflexa
which is a world distributed dodder using shotgun method at Illumina爷s Genome Analyzer, and then compared it with
the corresponding published sequence of the same species that distributed in Europe. The chloroplast genome length
was 120 972 bp, which was 549 bp shorter than the European one, with a large single copy (LSC) region of 79 499
bp, a small single copy (SSC) region of 8 369 bp and two inverted repeats (IR) of 16 552 bp each. The overall GC
content was 38. 3% , which is slightly higher than European C. reflexa. The chloroplast genome of C. reflexa from
both area encoded identical functional genes in the same order. On the other hand, detailed analyses revealed 251
insertions and 210 deletions. The length of indels substitution sum to 7 649 bp and the largest insertion and deletion
reached 426 bp and 435 bp respectively. Meanwhile, 3 720 bp base substitution events were found in the entire chlo鄄
roplast genome of Asian C. reflaxa. Majority of the indels observed were single鄄base but four large length mutations
植 物 分 类 与 资 源 学 报摇 2013, 35 (2): 158 ~ 164
Plant Diversity and Resources摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 DOI: 10. 7677 / ynzwyj201312070
*
**
Foundation item: The Joint Funds of the National Natural Science Foundation of China and Yunnan Provincial Government (U1136602)
Author for correspondence; E鄄mail: gongxun@ mail. kib. ac. cn
Received date: 2012-05-07, Accepted date: 2012-06-15
作者简介: 王朝波 (1984-) 男, 硕士, 主要从事异养植物叶绿体基因组研究。
longer than 200 bp were also detected, including two deletions in ycf2 region, one insertion in trnF鄄psbE and another
insertion in matK鄄trnQ. Most indels located in the intergenic regions of the LSC region while rare in the IR region.
This research initially compared the whole chloroplast genome of same heterotrophic plants distributed in different
continents.
Key words: Cuscuta reflexa; Chloroplast genome; Indels; Comparative analysis
摇 The chloroplast genome of photosynthetic plants
consists of multiple copies of homogeneous circular
double鄄stranded DNA molecules ranging in size from
120 to 217 kb (Kumar et al., 2009; Wicke et al.,
2011), while the non鄄photosynthetic ( heterotroph鄄
ic) plants consists of a genome size less than 120 kb
in general, such as holoparasitic plant Epifagus vir鄄
giniana (Wolfe et al., 1992), Cuscuta gronovii,
C. obtusiflora, hemiparasitic plant C. reflexa, C. ex鄄
altata (Funk et al., 2007; McNeal et al., 2007),
and myco鄄heterotrophic plant Neottia nidus鄄avis
( Logacheva et al., 2011 ), Rhizanthella gardneri
(Delannoy et al., 2011). Whole chloroplast genome
of heterotrophic plant has lost all or part of their pho鄄
tosynthetic genes. Besides, the overall structure of
chloroplast genome is generally conserved despite
some mutations observed (Krause, 2011) including
small structural changes such as inversions (Saski et
al., 2005), translocations (Lee et al., 2007; Hirao
et al., 2008), indels (Asano et al., 2004; Shahid
Masood et al., 2004; Chung et al., 2006; Jo et
al., 2011), base substitutions (Morton and Clegg,
1995), and extant rearrangement (Haberle et al.,
2008; Guisinger et al., 2011) etc. Three inversions
( rpoB鄄psbD, trnT鄄petL, ccsA鄄trnL) has been found
in C. reflexa compared to the classic structure of
chloroplast genome (Funk et al., 2007).
It is reported that indels do not occur at random
locations within organelle genomes, but they are of鄄
ten associated with specific DNA sequence features.
Regions containing repeats that lead to slipped
strand mispairing and intramolecular recombination
are thought to cause the majority of indel mutations
(reviewed by ( Kelchner, 2000 )). Length muta鄄
tions have been reported in genus Saccharum (Asano
et al., 2004) and Solanum (Chung et al., 2006) and
so on. In the intergenic region of this tRNA gene
cluster, a large number of indels ranging from 1 to
811 bp in length are commonly presented. The hots鄄
pot of divergence is also recognized in the region as鄄
sociated with tRNAs and the largest deletions over
500 bp in size are found at upstream of trnC (GCA)
and trnT (GGU), and at downstream of trnD (GUC)
(Maier et al., 1995; Ogihara et al., 2002; Calsa
J俨nior et al., 2004). Another hotspot of divergence
is in the ycf1 and ycf2 gene which is conserved and
located along with ycf15 (Plader et al., 2007; Haber鄄
le et al., 2008).
Here, the entire chloroplast genome nucleotide
sequence of the C. reflexa distributed in Asia was re鄄
ported, which may interpret the worldwide spreading
of this parasitic plant. We especially focus on the
length mutations and indels located in coding region.
Our study will provide a rich source of the nucleotide
and amino acid sequence data, which can be utilized
to address phylogenetic and molecular evolutionary
question as well as to heterotrophic biology.
Materials and methods
The material of C. reflexa was collected from
Dong爷e Town (23. 6137879毅N, 102. 015824毅E),
Yuanjiang County, Yunnan Province, China. The
chloroplast DNA was isolated from 100 g fresh leaves
using an improved extraction method that includes
high ionic strength buffer at low pH (3. 6) buffer
(Triboush et al., 1998). Chloroplast DNA was se鄄
quenced with Illumina爷s Genome Analyzer at Beijing
Genomics Institute (BGI) in Shenzhen, China. Sub鄄
sequently, SOAPdenovo were used to assemble the
sequence reads of chloroplast genomes ( Li et al.,
2009). Eight small gaps were closed by PCR method
using Qiagen Taq Polymerase. Primers used for PCR
9512 期摇 摇 摇 摇 WANG and GONG: Comparative Analyses of Indels Based on the Whole Chloroplast Genome of …摇 摇 摇 摇
were designed using available information from both
ends of the gap. All primers were ordered from
Sangon Biotech (Shanghai, China) as shown in Ta鄄
ble 1. PCR products were analyzed by electrophore鄄
sis on 1% agarose gel and then sequenced using
standard Sanger protocols on ABI 3730 instruments,
and the thermal cycling program was as follows: 80
益 for 5 min; then 33 cycles of [95 益 for 45 s; 42-
52 益 (depending upon the annealing temperature)
for 45 s; 65 益, 1 min], and 65 益 for 5 min.
Annotation of the sequenced genome was per鄄
formed using DOGMA (Wyman et al., 2004), com鄄
plement with adjustment for start and stop codons
and for intron / exon boundaries manually. Gene map
was drawn using OGDRAW 1. 2 (Lohse et al., 2007),
and each indels was mapped onto the exact position
of the map. Alignments of two C. reflexa chloroplast
genomes were performed using MAFFT version 6
(Katoh and Toh, 2008). Indels were calculated u鄄
sing DnaSP v5 (Librado and Rozas, 2009).
Result and discussion
The entire chloroplast genome is a circular doub鄄
le鄄stranded DNA molecule of 120 972 bp, which is
shorter than the European one by 549 bp (Funk et al.
, 2007). It exhibited a quadripartite structure, simi鄄
lar to typical angiosperm chloroplast genomes, with a
large single copy region of 79 499 bp, a small single
copy region of 8 369 bp and two inverted repeats of
each 16 552 bp containing four rRNA operons. The o鄄
verall GC content was 38. 3%, which is slightly high鄄
er than European C. reflexa (38. 2%) (Funk et al.,
2007). C. reflexa chloroplast genome in both area en鄄
coded identical functional genes with same gene or鄄
der. A total of 116 genes were identified, 15 (inclu鄄
ding six tRNAs and four rRNAs) of which were du鄄
plicated in IR. Ten genes contained one intron and
three of them contained two introns ( rps12, ycf3,
clpP), and four of the 13 genes with introns were tR鄄
NAs. All the ndh genes (except ndhB), infA, trnK鄄
UUU was completely loss from the chloroplast ge鄄
nome. Two ribosomal protein genes ( rpl23, rps16),
two tRNA genes ( trnV鄄UAC, trnG鄄UCC), redundant
partial of ycf2 which repeated in the IR, together with
ycf15 and ndhB remained as pseudo genes.
摇 摇 The main purpose of this study was to evaluate
the genetic diversity between two C. reflexa using en鄄
tire chloroplast DNA sequence. Comparative sequence
analysis revealed a large number of mutations
throughout the genome that includes indels and base
substitutions. In total, there were 7 649 bp Indels
(consisting of 251 insertions, 210 deletions), and
Table 1摇 Primers designed for closing gaps
No. Name Position Length Primers (5忆—3忆) Region
1 ca1fca1r
4963
5552 589
TGTTGCGCTCTTCATCTTT
TACTCGCTGCTACAATCCA
psbI
trnS鄄GCU
2 ca2fca2r
18230
18681 451
AAATCGGACGTGAATGTTT
ATTATGTTCCCGTAAGCAA
rpoC1 intron
rpoC1 intron
3 ca3fca3r
29256
30272 1016
TATCTAATGCGTTCTCCCA
TGTTACTTGACCAGCCCTC
psbC
trnS鄄UGA
4 ca4fca4r
36531
37706 1175
GAGGCATTCCCGTATCTAA
AACGAAATCCATTCTTACCA
psaA
ycf3
5 ca5fca5r
38616
39796 1180
ACTTGGCGTGTCTGTCTTT
AAATGGGTCGGTTTGAAGA
ycf3
trnS鄄GGA
6 ca6fca6r
40752
41721 969
ACCCATAGAGTTGGAAGTG
ACAGGATTTGGCTCAGGAT
trnT鄄UGU
trnL鄄UAA
7 ca7fca7r
43358
44507 1149
CGATGGTTGGCTGTTCACG
GCGGATTTGGTCAGGGAGA
psbF
petA
8 ca8fca8r
74330
75310 980
CTCTATGCCTTGCGGTAAT
TTTGGTCCACGAATCTAAT
rpl2
ycf2
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3 720 bp base substitution events in the entire chlo鄄
roplast genome of Asian C. reflaxa. Overall genome
wide indel events in Asian population relative to Eu鄄
ropean population are shown in Fig. 1. The Largest
insertion and deletion reached 426 bp and 435 bp re鄄
spectively (Fig. 2).
Fig. 1摇 Comparative sequence analysis of the two C. reflexa chloroplast genomes. Gene order and content of Asian C. reflexa are the same with
the European C. reflexa chloroplast genomes. Genes shown inside the circle are transcribed clockwise and those outside are transcribed
counterclockwise. Dashed area of the inner circle drew the GC content of the chloroplast genome. Red arrows indicate deletion event
in Asian C. reflexa, and black arrows indicate insertion event in Asian C. reflexa. Length of arrow indicates the size of indel event
Fig. 2摇 The length of each indel scored as a character for two C. reflexa. Frequency is the observed number of indel events with certain length
1612 期摇 摇 摇 摇 WANG and GONG: Comparative Analyses of Indels Based on the Whole Chloroplast Genome of …摇 摇 摇 摇
摇 Of the 251 insertion events, only 28 (11. 2% )
were identified in the coding region, 47 (18. 7% )
in intron and 176 (70. 1% ) in the intergenic region
(Table 2). Most of the insertions (49) were single鄄
base, however multi鄄nucleotide insertions were also
identified. As shown in Table 3, most of the inser鄄
tions that located in the coding region had a triplex
type, which wouldn爷t disrupt the coding sequence.
However, two small insertions of 7鄄bp and 1鄄bp were
found before the stop codon of rpl20, leading to a
42鄄bp delayed of stop codon. Most insertions in the
intron and intergenic region were short, 11 bases or
less, and located in the LSC region. The two largest
insertions located within the single copy part of ycf2,
with no influence on the gene function.
The deletion events in three regions ( coding,
intergenic and intron) were also given in Table 2.
Among 210 deletion events, 30 (14. 3% ) were lo鄄
cated in the coding region, 37 in the intron (17. 6%)
and 143 (68. 1%) in the intergenic region. Similar to
insertions, numerous single base pair deletions (26)
existed in the chloroplast genome of C. reflaxa. A
single large deletion of 157鄄bp was located in the
coding region of pseudo gene ycf15. Since ycf15 in
both area had no function, this deletion was assumed
to cause parasitic lifestyle of C. reflaxa. Single鄄base
Table 2摇 Indel events in the IR, LSC, and SSC region of C. reflexa chloroplast genome
Region Type IR (Ins / Del) LSC (Ins / Del) SSC (Ins / Del) Total (Percentage) (Ins / Del)
Coding region 2 / 6 18 / 12 8 / 12 28(11. 2) / 30(14. 3)
Intron 2 / 0 45 / 37 0 / 0 47(18. 7) / 37(17. 6)
Intergenic region 19 / 10 168 / 143 13 / 17 176(70. 1) / 143(68. 1)
The values in parentheses represent proportion (% ). IR= inverted repeat, LSC= large single copy, SSC=small single copy. Ins=Number of inser鄄
tion, Del =Number of deletion
Table 3摇 Counted number and length of indels
located in coding region
Gene Ins Lenth / bp Dels Lenth / bp
matK 1 3 2 24, 36
rpoC2 3 9, 6, 21 1 8
trnS鄄GGA 0 1 3
trnG鄄UCC 1 16 0
petA 0 1 1
accD 0 2 9, 54
atpE 1 6 0
trnV鄄UAC 0 1 37
rps18 1 12 0
rpl20 2 1, 7 0
rpoA 0 1 9
rps8 0 1 21
rpl2 1 6 0
rpl23 2 6, 15 1 8
ycf2 6 3 (2) 9, 24, 9 (24, 9)
ycf15 0 1 (1) 157 (157)
ycf1 8 9, 9, 6, 12,6, 3, 21, 3摇 12
36, 12, 12, 24, 9, 9,
6, 6, 9, 42, 6, 9
ndhB 1 (1) 2 (2) 0
The values in parentheses represent indels repeated in the IR region.
The values in bold represent indels that does not happened in triplex
type. Ins= insertions, Dels=deletions
deletion located before stop codon of petA, which
made stop codon of this photosynthesis gene 489 bp
afterward. The effect of this deletion to the expres鄄
sion of protein is unknown yet. Another 8鄄bp dele鄄
tion was found within rpoC2 which was also present
in the LSC region; resulting in the ahead of stop co鄄
don by 12 bp.
Overall, the indels were observed more fre鄄
quently in the intergenic region rather than intron
and coding region. It is known that direct repeats
contribute significantly to variability of chloroplast
genomes (Wolfe et al., 1992; Ogihara et al., 2002).
Shashid et al. (2004) and Hiratsuka et al. (1989)
also identified many indels in the intergenic region
when comparing rice and tobacco. Our research
showed that heterotrophic plant undergone a much
relaxed selective constraint compared to autotrophic
plant, especially in the intergenic region.
A total of 39 ( only 8. 5% ) indel events hap鄄
pened within IR region, suggesting that IR region
contributed greatly to the conservation of nucleotide
sequence (Wicke et al., 2011). The complete a鄄
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lignment of chloroplast genome sequences revealed a
reasonable number of indels in the intron and inter鄄
genic spacer regions in C. reflexa, but there were fe鄄
wer indels occurred in 18 genes ( Table 3) when
compared with Eropean C. reflexa. Comparison of
accD genes between two C. reflexa is similar to that
of seven Solanaceae species, two deletion events of 9
and 54 bp were observed. The accD gene encodes
the beta鄄carboxyl transferase subunits of acetyl鄄CoA鄄
carboxylase (ACCase) and is present in the plastids
of most land plants. The tobacco ACCase is essen鄄
tial for leaf development, leaf longevity, and seed
yield (Madoka et al., 2002). C. reflexa lost leaves
through their entire lifecycle, we still observed the
relatively long deletion (54 bp) which kept accD as
a functional gene, showed that accD gene maybe im鄄
portant at seedling stage. Additional indels did take
place in ycf1 and ycf2. Most vascular plants contain
these two genes, which appear to be essential for
cell survival, and often seemed to be housekeeping
genes ( Krause, 2011 ). A total of 20 indels oc鄄
curred within ycf1 and 11 within ycf2; contributing
to 53. 4% of the indels within coding region. Our
observation consistent with former report that these
two genes varied greatly among land plants (Moore
et al., 2010).
As for the intergenic and intron region, most
multi鄄nucleotide deletions were 2 to 11 bp. Seven
remarkable mutation regions identified including
trnM鄄trnV, trnS鄄trnR, rpl16鄄rps3, clpP鄄psbB, trnC鄄
psbD, matK鄄trnQ, and ycf3 introns. Striking feature
of C. reflexa was two largest deletions, of which 232鄄
bp deletion was in matK鄄trnQ and a 426鄄bp deletion
in trnF鄄psbE.
A coarse comparison of our results with those of
the Poaceae plants showed that the length mutation
was bounded with the tRNA cluster. In addition, the
indel events in C. reflexa is about 3 times more than
that between wild and cultivated rice (Matsuoka et
al., 2002), suggesting that parasitic plants underg鄄
one relaxed selective constraint on chloroplast ge鄄
nome along evolutionary history.
In conclusion, the Asian C. reflexa chloroplast
genome is very similar to European one even though
a great number of insertion / deletion and base substi鄄
tution events were detected. A substantial amount of
polymorphism, mainly resulting from indels, was ob鄄
served within in C. reflexa of two areas. Further鄄
more, the indel events in the intergenic region were
quite frequent comparing with other plant. Taken to鄄
gether, our data obtained from Asian C. reflexa pro鄄
vide potential molecular markers to evaluate genetic
diversity as well as evolutionary processes in hetero鄄
trophic plants.
Acknowledgements: We are grateful to Yu Jiaojun and Guan
Mengmeng for critically reading the manuscript. The skillful
technical assistance of Dr. Ma Pengfei is gratefully acknowl鄄
edged. We are thankful to lab members for their generous help.
References:
Asano T, Tsudzuki T, Takahashi S et al., 2004. Complete nucleotide
sequence of the sugarcane ( Saccharum officinarum) chloroplast
genome: a comparative analysis of four monocot chloroplast ge鄄
nomes [J] . DNA Research, 11 (2): 93—99
Calsa J俨nior T, Carraro DM, Benatti MR et al., 2004. Structural fea鄄
tures and transcript鄄editing analysis of sugarcane (Saccharum offi鄄
cinarum L. ) chloroplast genome [J] . Current Genetics, 46 (6):
366—373
Chung HJ, Jung JD, Park HW et al., 2006. The complete chloroplast
genome sequences of Solanum tuberosum and comparative analy鄄
sis with Solanaceae species identified the presence of a 241鄄bp
deletion in cultivated potato chloroplast DNA sequence [ J] .
Plant Cell Reports, 25 (12): 1369—1379
Delannoy E, Fujii S, Colas des Francs鄄Small C et al., 2011. Ram鄄
pant gene loss in the underground orchid Rhizanthella gardneri
highlights evolutionary constraints on plastid genomes [ J] . Mo鄄
lecular Biology and Evolution, 28 (7): 2077—2086
Funk HT, Berg S, Krupinska K et al., 2007. Complete DNA se鄄
quences of the plastid genomes of two parasitic flowering plant
species, Cuscuta reflexa and Cuscuta gronovii [J] . BMC Plant
Biology, 7 (45): 1—12
Guisinger MM, Kuehl JV, Boore JL et al., 2011. Extreme reconfigu鄄
ration of plastid genomes in the angiosperm family Geraniaceae:
rearrangements, repeats, and codon usage [J] . Molecular Biolo鄄
gy and Evolution, 28 (1): 583—600
Haberle RC, Fourcade HM, Boore JL et al., 2008. Extensive rear鄄
rangements in the chloroplast genome of Trachelium caeruleum
are associated with repeats and tRNA genes [J] . Journal of Mo鄄
3612 期摇 摇 摇 摇 WANG and GONG: Comparative Analyses of Indels Based on the Whole Chloroplast Genome of …摇 摇 摇 摇
lecular Evolution, 66 (4): 350—361
Hirao T, Watanabe A, Kurita M et al., 2008. Complete nucleotide
sequence of the Cryptomeria japonica D. Don. chloroplast genome
and comparative chloroplast genomics: diversified genomic struc鄄
ture of coniferous species [ J] . BMC Plant Biology, 8 (70):
1—20
Hiratsuka J, Shimada H, Whittier R et al., 1989. The complete se鄄
quence of the rice (Oryza sativa) chloroplast genome: intermo鄄
lecular recombination between distinct tRNA genes accounts for a
major plastid DNA inversion during the evolution of the cereals
[J] . Molecular and General Genetics, 217 (2-3): 185—194
Jo YD, Park J, Kim J et al., 2011. Complete sequencing and com鄄
parative analyses of the pepper (Capsicum annuum L. ) plastome
revealed high frequency of tandem repeats and large insertion / de鄄
letions on pepper plastome [ J] . Plant Cell Reports, 30 (2):
217—229
Katoh K, Toh H, 2008. Recent developments in the MAFFT multiple
sequence alignment program [J] . Briefings in Bioinformatics, 9
(4): 286—298
Kelchner SA, 2000. The evolution of non鄄coding chloroplast DNA and
its application in plant systematics [ J] . Annals of The Missouri
Botanical Garden, 87 (4): 482—498
Krause K, 2011. Piecing together the puzzle of parasitic plant plas鄄
tome evolution [J] . Planta, 234 (4): 647—656
Kumar S, Hahn FM, McMahan CM et al., 2009. Comparative analy鄄
sis of the complete sequence of the plastid genome of Parthenium
argentatum and identification of DNA barcodes to differentiate
Parthenium species and lines [ J ] . BMC Plant Biology, 9
(131): 1—12
Lee HL, Jansen RK, Chumley TW et al., 2007. Gene relocations
within chloroplast genomes of Jasminum and Menodora (Oleace鄄
ae) are due to multiple, overlapping inversions [ J] . Molecular
Biology and Evolution, 24 (5-6): 1161—1180
Li RQ, Yu C, Li YR et al., 2009. SOAP2: an improved ultrafast tool
for short read alignment [J] . Bioinformatics, 25 (15): 1966—
1967
Librado P, Rozas J, 2009. DnaSP v5: a software for comprehensive
analysis of DNA polymorphism data [ J ] . Bioinformatics, 25
(11): 1451—1452
Logacheva MD, Schelkunov MI, Penin AA, 2011. Sequencing and a鄄
nalysis of plastid genome in mycoheterotrophic orchid Neottia ni鄄
dus鄄avis [J] . Genome Biology and Evolution, 3 (1): 1296—
1303
Lohse M, Drechsel O, Bock R, 2007. OrganellarGenomeDRAW
(OGDRAW): a tool for the easy generation of high鄄quality cus鄄
tom graphical maps of plastid and mitochondrial genomes [ J] .
Current Genetics, 52 (5-6): 267—274
Madoka Y, Tomizawa K, Mizoi J et al., 2002. Chloroplast transfor鄄
mation with modified accD operon increases acetyl鄄CoA carboxyl鄄
ase and causes extension of leaf longevity and increase in seed
yield in tobacco [ J] . Plant and Cell Physiology, 43 (12):
1518—1525
Maier RM, Neckermann K, Igloi GL et al., 1995. Complete se鄄
quence of the maize chloroplast genome: gene content, hotspots
of divergence and fine tuning of genetic information by transcript
editing [J] . Journal of Molecular Biology, 251 (5): 614—628
Matsuoka Y, Yamazaki Y, Ogihara Y et al., 2002. Whole chloroplast
genome comparison of rice, maize, and wheat: implications for
chloroplast gene diversification and phylogeny of cereals [ J] .
Molecular Biology and Evolution, 19 (12): 2084—2091
McNeal JR, Kuehl JV, Boore JL et al., 2007. Complete plastid ge鄄
nome sequences suggest strong selection for retention of photo鄄
synthetic genes in the parasitic plant genus Cuscuta [ J] . BMC
Plant Biology, 7 (57): 1—22
Moore MJ, Soltis PS, Bell CD et al., 2010. Phylogenetic analysis of
83 plastid genes further resolves the early diversification of eud鄄
icots [J] . Proceedings of the National Academy of Sciences, 107
(10): 4623—4628
Ogihara Y, Isono K, Kojima T et al., 2002. Structural features of a
wheat plastome as revealed by complete sequencing of chloroplast
DNA [J] . Molecular Genetics and Genomics, 266 (5): 740—
746
Plader W, Yukawa Y, Sugiura M et al., 2007. The complete struc鄄
ture of the cucumber (Cucumis sativus L. ) chloroplast genome:
its composition and comparative analysis [J] . Cellular & Molec鄄
ular Biology Letters, 12 (4): 584—594
Saski C, Lee SB, Daniell H et al., 2005. Complete chloroplast ge鄄
nome sequence of Gycine max and comparative analyses with other
legume genomes [J] . Plant Molecular Biology, 59 (2): 309—
322
Shahid MM, Nishikawa T, Fukuoka S et al., 2004. The complete nu鄄
cleotide sequence of wild rice ( Oryza nivara) chloroplast ge鄄
nome: first genome wide comparative sequence analysis of wild
and cultivated rice [J] . Gene, 340 (1): 133—139
Triboush SO, Danilenko NG, Davydenko OG, 1998. A method for i鄄
solation of chloroplast DNA and mitochondrial DNA from sun鄄
flower [J] . Plant Molecular Biology, 16 (2): 183—183
Wicke S, Schneeweiss GM, dePamphilis CW et al., 2011. The evo鄄
lution of the plastid chromosome in land plants: gene content,
gene order, gene function [J] . Plant Molecular Biology, 76 (3
-5): 273—297
Wolfe KH, Morden CW, Palmer JD, 1992. Function and evolution of
a minimal plastid genome from a nonphotosynthetic parasitic plant
[ J] . Proceedings of the National Academy of Sciences, 89 (22):
10648—10652
Wyman S, Jansen R, Boore J, 2004. Automatic annotation of or鄄
ganellar genomes with DOGMA [ J] . Bioinformatics, 20 (1):
3252—3255
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