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Korean J. Pl. Taxon > Volume 52(3); 2022 > Article
PARK and XI: The complete chloroplast genome of Campsis grandiflora (Bignoniaceae)

Abstract

Campsis grandiflora (Thunb.) K. Schum is an ornamental species with various useful biological effects. The chloroplast genome of C. grandiflora isolated in Korea is 154,293 bp long (GC ratio: 38.1%) and has four subregions: 84,121 bp of large single-copy (36.2%) and 18,521 bp of small single-copy (30.0%) regions are separated by 24,332 bp of inverted repeat (42.9%) regions including 132 genes (87 protein-coding genes, eight rRNAs, and 37 tRNAs). One single-nucleotide polymorphism and five insertion and deletion (INDEL) regions (40-bp in total) were identified, indicating a low level of intraspecific variation in the chloroplast genome. All five INDEL regions were linked to the repetitive sequences. Seventy-two normal simple sequence repeats (SSRs) and 47 extended SSRs were identified to develop molecular markers. The phylogenetic trees of 29 representative Bignoniaceae chloroplast genomes indicate that the tribe-level phylogenic relationship is congruent with the findings of previous studies.

INTRODUCTION

Genus Campsis Lour. consists of only two species, Campsis grandiflora (Thunb.) distributed in East Asia and Campsis radicans (L.) Bureau found in North America (Wen and Jansen, 1995). Because of its disjunct distribution, this genus was considered as a material to understand their evolutionary history, resulting that both species was estimated to be diversified at 24.4 million years ago (Wen and Jansen, 1995). Campsis grandiflora has been utilized as an ornamental species because of their trumpet shape flowers (Jia et al., 2012). Moreover, C. grandiflora was known to have various biological effects (Yu et al., 2015; Oku et al., 2019), such as anti-oxidative and anti-inflammatory (Cui et al., 2006), and useful phytocompounds (Jin et al., 2005; Kim et al., 2007; Han et al., 2012) including triterpenoids (Kim et al., 2005). To understand intraspecific variations of C. grandiflora chloroplast genome together with the previously published chloroplast genome isolated in China (Chen et al., 2022), we completed the chloroplast genome of C. grandiflora isolated in Korea.

MATERIALS AND METHODS

Plant material

The sample was collected on Gangseo postal office, Seoul, Korea (37.565175N, 126.840624E). A specimen was deposited at the InfoBoss Cyber Herbarium (IN) under the voucher number, IB-01065. No permission is required for the collection.

DNA extraction and chloroplast genome determination

Total DNA was extracted from the fresh leaves using a DNeasy Plant Mini Kit (Qiagen, Hilden, Germany). The sequencing library was constructed using an Illumina TruSeq Nano DNA Library Preparation Kit (Illumina, San Diego, CA, USA) following the manufacturer’s recommendations with approximately 350-bp DNA fragments. 4.15-Gbp raw sequences were obtained using NovaSeq6000 at Macrogen Inc., Korea, and were filtered by Trimmomatic v0.33 (Bolger et al., 2014). The chloroplast genome was de novo assembled with Velvet v1.2.10 (Zerbino and Birney, 2008), and gaps were closed using GapCloser v1.12 (Zhao et al., 2011). The genome sequence was confirmed by aligning all raw reads against the assembled genome using BWA v0.7.17 and SAMtools v1.9 (Li et al., 2009; Li, 2013). All processes were conducted in the Genome Information System (http://geis.infoboss.co.kr) utilized in previous studies (Kim et al., 2019e, 2020; Park et al., 2019c; Park and Xi, 2021). Geneious Prime v2020.2.4 (Biomatters Ltd., Auckland, New Zealand) was used for annotation based on the Tecomaria capensis chloroplast genome (GenBank accession number: NC_037462) (Fonseca and Lohmann, 2018). A circular map of C. grandiflora chloroplast genome was drawn using OGDRAW v1.31 (Greiner et al., 2019). Large single-copy (LSC), small single-copy (SSC), and inverted repeat (IR) regions were determined by bl2seq (Tatusova and Madden, 1999).

Identification of intraspecific variations

Single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs) were identified from the pair-wise sequence alignment of the two C. grandiflora chloroplast genomes conducted by MAFFT 7.450 (Katoh and Standley, 2013) with ‘Find variations/SNPs’ implemented in Geneious Prime 2020.2.4 (Biomatters Ltd.), which has been used in the previous studies investigating intraspecific variations on organelle genomes (Kim et al., 2021a; Oh et al., 2021; Suh et al., 2021). INDEL region was defined as the continuous INDELs.

Identification and comparative analysis of simple sequence repeats

Simple sequence repeats (SSRs) were identified on the chloroplast genome sequence using the pipeline of the SSR database (SSRDB; http://ssrdb.infoboss.co.kr/) which has been utilized in several organelle genomic studies (Lee et al., 2020; Choi et al., 2021; Park et al., 2021d, 2022). The SSR is conventionally recognized as the nucleotide array composed of repeats with one or up to six base pair units. For example, monoSSR refers an array of nucleotide repeats containing a particular base and hexaSSR an array of nucleotide repeats containing six base pair unit. The overall length of SSR is mostly over 10 base pairs. In this study, we tried to classify SSR with more criteria which has been applied in previous analyses (Gandhi et al., 2010; Chen et al., 2015; Cheng et al., 2016; Shukla et al., 2018; Jeon and Kim, 2019; Li et al., 2019). The criteria applied are (1) ‘normal SSR’ as a conventional definition from monoSSR to hexaSSR, (2) ‘extented SSR’ referring from heptaSSR (repeats of 7 bp unit) to decaSSR (repeats of 10 bp unit), and (3) ‘potential SSR’ referring specific cases with only 2 units in pentaSSR and hexaSSR. These criteria have been applied and provided better understanding of SSR patterns in previous analyses in chloroplast genomes of Dysphania species (Kim et al., 2019f), Arabidopsis thaliana (Park et al., 2020c), Chenopodium album (Park et al., 2021b), Diarthron linifolium (Kim et al., 2021b), and mitochondrial genome of Rosa rugosa (Park et al., 2020d).

Phylogenetic analysis

Twenty-nine representative Bignoniaceae chloroplast genomes including two C. grandiflora chloroplast genomes and one outgroup species, Paulownia tomentosa (Yi and Kim, 2016), were used for calculating multiple sequence alignments of 60 conserved genes by MAFFT v7.450 (Katoh and Standley, 2013) for constructing phylogenetic trees. We used MEGA X (Kumar et al., 2018) to construct maximum likelihood (ML) and neighbor-joining (NJ) and MrBayes v3.2.6 (Ronquist et al., 2012) to carry out Bayesian inference (BI). A heuristic search was used with nearest-neighbor interchange branch swapping, the Tamura-Nei model, and uniform rates among sites to construct ML and NJ phylogenetic trees with default values for other options. To estimate the node confidences bootstrap analyses with 1,000 and 10,000 bootstrap pseudoreplicates were conducted for ML and NJ trees, respectively. For the BI analysis, the GTR (general time reversible) model with gamma rates was used as a molecular model and Markov-Chain Monte Carlo algorithm was employed for 1,000,000 generations with four chains running simultaneously. To build the consensus tree of BI, we sampled trees every 200 generations after removing 100,000 generations as a ‘burn-in’.

RESULTS AND DISCUSSION

The chloroplast genome of C. grandiflora (GenBank accession number: OM279807) is 154,293 bp (GC ratio: 38.1%) and has four subregions: 85,078 bp of LSC region (36.2%) and 18,577 bp of SSC region (33.0%) regions are separated by 25,319 bp of IR region (43.2%) (Fig. 1). Its length is shorter than that of the previous chloroplast genome by 10 bp (154,303 bp; GenBank accession number: MW430049). It contains 132 genes (87 protein-coding genes [PCGs], eight ribosomal RNAs [rRNAs], and 37 transfer RNAs [tRNA]); 19 genes (eight PCGs, four rRNAs, and seven tRNAs) are duplicated in IR regions (Fig. 1). Structural variation between C. grandiflora and T. capensis was identified using Mauve v1.1.3 (Darling et al., 2004) in LSC region: the region between 48,536 bp and 73,124 bp in C. grandiflora chloroplast genome was inverted against that of T. capensis. This phenomenon also occurred between two Incarvillea chloroplast genomes in the same family (Ma et al., 2019; Wu et al., 2021), congruent to the previous study (Chen et al., 2022). It suggests that inversion events in LSC occurred in Bignoniaceae in comparison to the other families, such as Amaranthaceae (Park et al., 2021b) and Oleaceae (Park et al., 2019f).
Interspecific variations between the two C. grandiflora chloroplast genomes were investigated. In total, one SNP and five INDEL regions (40 bp in total). One SNP was located between trnC and petN. The 20-bp deletion, which is the longest INDEL, was found in 3' end of ycf1, which expanded two more amino acids (Fig. 2A). Another 15-bp INDEL region was located in the first intron of accD, presenting the three-time repeat in the chloroplast genome assembled in this study while two-time repeat in the previous chloroplast genome (Fig. 2B). One-bp deletion was found in the intergenic region between trnK and rps16, exhibiting difference of monoSSR (Fig. 2C). The two INDEL regions were found in 16S rRNA in the IR region (Fig. 2D), showing that two-time repeat of CAT was destroyed in the chloroplast genome assembled in this study by this 2-bp deletion (Fig. 2D). Interestingly, all INDEL regions were linked to the repetitive sequences and proportion of INDEL regions related to SSRs (20%) was low. Numbers of intraspecific variations of C. grandiflora are relatively lower than those identified between the samples between Korea and China (Fig. 2E, Table 1). This result seems to be incongruent to the previous studies that estimated their genetic diversities using the classical methods (He and Gu, 1990; Wu et al., 1990; Wen and Jansen, 1995). Therefore, additional C. grandiflora chloroplast genomes will be required to evaluate its genetic diversity.
SSR has been utilized as useful molecular markers (Huang et al., 2015; Li et al., 2020a, 2020b). Seventy-two normal SSRs, 418 potential SSRs, and 47 extended SSRs were identified in both C. grandiflora chloroplast genomes (Table 2). Most of normal SSRs are monoSSRs (Fig. 3), which is similar to those of the other plant species (Kim et al., 2019f, 2021b; Park et al., 2020c, 2021b). Nine normal SSRs and 18 extended SSRs (22.68%) were identified in the genic regions of matK, atpA, rpoC2, psbC, psaI, psbB, rpoA, rpl22, ycf2, ycf1, ndhI, ndhG, and ndhD (Table 2) and 12 normal SSRs and three extended SSRs (12.61%) were found in the intronic regions of rps16, trnS-CGA, atpF, ycf3, trnL-UAA, petD, rps16, and ndhA (Table 2). Due to low number of intraspecific variations, only one monoSSR (cM0000002) displayed the differences of the number of repeats between the two chloroplast genomes. These SSRs will be useful to develop molecular makers because high genetic diversity of C. grandiflora was estimated in previous studies (He and Gu, 1990; Wu et al., 1990; Wen and Jansen, 1995).
Three phylogenetic trees showed that C. grandiflora was clustered with T. capensis/ Incarvillea with high supportive values (Fig. 4). In addition, trees presented that tribes covering more than one chloroplast genome, including Tecomeae, Catalpeae, Crescentiina, and Bignonieae, were well clustered with high supportive values (Fig. 4). It is congruent to previous phylogenetic studies, except for the Catalpeae and Oroxylae clustered in one clade with week bootstrap values (Olmstead et al., 2009). It may be caused by different coverage of samples between the two studies. Together with additional chloroplast genomes of Bignoniaceae, C. grandiflora chloroplast genome will help to understand evolutionary history of Bignoniacea.

Acknowledgments

This study was supported by the InfoBoss Research Grant (IBG-0038).

NOTES

CONFLICTS OF INTEREST
The authors declare that there are no conflicts of interest.

Fig. 1.
Circular map of Campsis grandiflora complete chloroplast genome. The genes located outside of the circle are transcribed clockwise, while those located inside are transcribed counterclockwise. The dark gray plot in the inner circle corresponds to GC content. Large singlecopy (LSC), small single-copy (SSC), and inverted repeat (IR) are indicated with LSC, SSC, and IR (IRA and IRB), respectively.
kjpt-52-3-156f1.jpg
Fig. 2.
Intraspecific variations identified from the two Campsis grandiflora chloroplast genomes. AD. Consensus sequences were displayed with different background colors of each base. Insertions and deletions were presented as orange-colored boxes. Yellow and red arrows indicate protein-coding genes (PCGs) and rRNAs, respectively. Amino acid sequences in PCG were displayed below the nucleotide sequences. Blue arrows and lines indicate repetitive sequences found in insertions and deletions. E. X-axis means the number of single nucleotide polymorphism (SNPs) and Y-axis indicates insertion and deletion (INDEL) coverage (bp). Blue-colored circle indicates the number of intraspecific variations identified in C. grandiflora chloroplast genomes. Orange, gray, and yellow-colored circles presented those identified between Chinese and Korean isolates, Chinese and Chinese isolates, and Korean and Korean isolates, respectively.
kjpt-52-3-156f2.jpg
Fig. 3.
Distribution of simple sequence repeats (SSRs) along with types identified from Campsis grandiflora chloroplast genome. X-axis presented SSR types of normal SSRs, potential SSRs, and extended SSRs. Y-axis indicates the number of SSRs.
kjpt-52-3-156f3.jpg
Fig. 4.
Phylogenetic trees of the 29 representative Bignoniaceae chloroplast genomes including two Campsis grandiflora chloroplast genomes. Phylogenetic tree was drawn based on the maximum likelihood phylogenetic tree. The numbers above the branches correspond to the bootstrap support values from the maximum likelihood and neighbor-joining methods, as well as posterior probability from the Bayesian inference.
kjpt-52-3-156f4.jpg
Table 1.
List of numbers of intraspecific variations in the chloroplast genomes identified from the samples isolated from Korea and China.
Family Species name Source Target No. of SNPs INDEL length (bp) Reference
Selaginellaceae Selaginella tamariscina Korean isolate (MN894555) Chinese isolate (NC_041646) 1,223 1,635 Park et al. (2020a), Xu et al. (2018)
Rosaceae Hagenia abyssinica Chinese isolate (KX008604) Chinese isolate (KY420026) 82 262 Gichira et al. (2017), Zhang et al. (2017)
Sanguisorba officinalis Chinese isolate (NC_044694) Korean isolate (MZ145058) 85 301
Chinese isolate (NC_044694) Korean isolate (MK696193) 75 290 Meng et al. (2018)
Korean isolate (MZ145058) Korean isolate (MK696193) 10 105
Sanguisorba tenuifolia Chinese isolate (NC_044692) Chinese isolate (NC_042223) 27 138
Chinese isolate (NC_044692) Korean isolate (MK696194) 91 338 Meng et al. (2018), Park et al. (2018)
Chinese isolate (NC_042223) Korean isolate (MK696194) 89 344
Sanguisorba stipulata Korean isolate (MZ145059) Korean isolate (MK696195) 78 367
Sanguisorba filiformis Chinese isolate (NC_044693) Chinese isolate (KY419920) 45 478 Meng et al. (2018), Zhang et al. (2017)
Amaranthaceae Chenopodium album Korean isolate (MW446246) Korean isolate (MW446245) 28 19 Hong et al. (2017), Park et al. (2021b)
Korean isolate (MW446246) Korean isolate (MW446243) 2 2
Korean isolate (MW446246) Korean isolate (MW446241) 27 315
Korean isolate (MW446246) Korean isolate (MW446242) 21 18
Korean isolate (MW446246) Korean isolate (MW446244) 14 33
Korean isolate (MW446246) Korean isolate (NC_034950) 17 36
Korean isolate (MW446245) Korean isolate (MW446243) 30 35
Korean isolate (MW446245) Korean isolate (MW446241) 0 298
Korean isolate (MW446245) Korean isolate (MW446242) 21 15
Korean isolate (MW446245) Korean isolate (MW446244) 30 40
Korean isolate (MW446245) Korean isolate (NC_034950) 33 37
Korean isolate (MW446243) Korean isolate (MW446241) 29 331
Korean isolate (MW446243) Korean isolate (MW446242) 23 34
Korean isolate (MW446243) Korean isolate (MW446244) 16 49
Korean isolate (MW446243) Korean isolate (NC_034950) 19 52
Korean isolate (MW446241) Korean isolate (MW446242) 21 309
Korean isolate (MW446241) Korean isolate (MW446244) 30 336
Korean isolate (MW446241) Korean isolate (NC_034950) 33 333
Korean isolate (MW446242) Korean isolate (MW446244) 23 39
Korean isolate (MW446242) Korean isolate (NC_034950) 26 36
Korean isolate (MW446244) Korean isolate (NC_034950) 18 57
Dysphania pumilio Korean isolate (MH936550) Korean isolate (MK541016) 25 2 Kim et al. (2019b), Park and Kim (2019)
Suaeda japonica Korean isolate (MK764271) Korean isolate (MK558824) 3 3 Kim et al. (2019g), Kang et al. (2020)
Magnoliaceae Magnolia kobus Korean isolate (NC_023237) Korean isolate (MN894553) 50 63
Liriodendron tulipifera Korean isolate (MK477550) Chinese isolate (NC_008326) 12 0 Cai et al. (2006), Kwon et al. (2019b)
Theaceae Camellia japonica Korean isolate (MK353210) Korean isolate (MK353211) 25 2 Kim et al. (2017), Kwon et al. (2019a), Li et al. (2019), Min et al. (2019b)
Korean isolate (MK353210) Korean isolate (KU951523) 25 2
Korean isolate (MK353211) Korean isolate (KU951523) 25 0
Chinese isolate (MW602996) Korean isolate (MK353210) 8 36
Chinese isolate (MW602996) Korean isolate (MK353211) 8 38
Chinese isolate (MW602996) Korean isolate (KU951523) 33 38
Chinese isolate (NC_036830) Korean isolate (MK353210) 78 644
Chinese isolate (NC_036830) Korean isolate (MK353211) 78 645
Chinese isolate (NC_036830) Korean isolate (KU951523) 103 645
Chinese isolate (NC_036830) Chinese isolate (MW602996) 80 671
Fagaceae Fagus multinervis Korean isolate (OM373199) Korean isolate (MZ962344) 4 1 Park and Oh (2020), Park et al. (2019a), Yang et al. (2020), Park et al. (unpubl. data)
Korean isolate (OM373199) Korean isolate (MK518070) 1 2
Korean isolate (OM373199) Korean isolate (MN894556) 1 0
Korean isolate (OM373199) Korean isolate (MT762296) 1 2
Korean isolate (MZ962344) Korean isolate (MK518070) 3 3
Korean isolate (MZ962344) Korean isolate (MN894556) 5 1
Korean isolate (MZ962344) Korean isolate (MT762296) 3 3
Korean isolate (MK518070) Korean isolate (MT762296) 0 0
Korean isolate (MK518070) Korean isolate (MN894556) 2 2
Korean isolate (MN894556) Korean isolate (MT762296) 2 2
Fagus japonica Korean isolate (NC_053352) Korean isolate (MT762295) 1 32 Yang et al. (2020), Park et al. (unpubl. data)
Caryophyllaceae Pseudostellaria palibiniana Korean isolate (MK120981) Korean isolate (MK309611) 84 175 Kim et al. (2019c, 2019d)
Salicaceae Salix koriyanagi Korean isolate (MK541017) Korean isolate (MK120982) 0 0 Kim et al. (2019a), Park et al. (2019d)
Rosaceae Pyrus ussuriensis Korean isolate (MK507863) Korean isolate (MK172841) 121 781 Cho et al. (2019), Gil et al. (2019)
Asteraceae Artemisia fukudo Korean isolate (NC_044156) Korean isolate (MG951488) 7 12 Lee et al. (2016), Min et al. (2019c),
Erigeron canadensis Korean isolate (MT806101) Chinese isolate (NC_046789) 103 208 Park et al. (unpubl. data), Zhang et al. (2019)
Chrysanthemum zawadskii Korean isolate (MW539687) Chinese isolate (MG799556) 110 251 Baek et al. (2021), Hongmei et al. (2021)
Orchidaceae Goodyera schlechtendaliana Korean isolate (MK144665) Korean isolate (MK134679) 200 511 Niu et al. (2017), Oh et al. (2019a, 2019b)
Chinese isolate (NC_029364) Korean isolate (MK144665) 842 1,779
Chinese isolate (NC_029364) Korean isolate (MK134679) 740 1,470
Chinese isolate (LC085346) Chinese isolate (NC_029364) 514 2,133
Chinese isolate (LC085346) Korean isolate (MK144665) 700 1,366
Chinese isolate (LC085346) Korean isolate (MK134679) 597 1,065
Chinese isolate Chinese isolate 445 415
(AB893949) (LC085346)
Chinese isolate (AB893949) Chinese isolate (NC_029364) 864 2,045
Chinese isolate (AB893949) Korean isolate (MK144665) 282 1,060
Chinese isolate Korean isolate 163 652
(AB893949) (MK134679)
Gastrodia elata Korean isolate (MN026874) Korean isolate (MN296709) 324 630 Kang et al. (2020), Park et al. (2020b), Yuan et al. (2018)
Chinese isolate (NC_037409) Korean isolate (MN026874) 493 651
Chinese isolate (NC_037409) Korean isolate (MN296709) 457 671
Oleaceae Abeliophyllum distichum Korean isolate (NC_031445) Korean isolate (MN127986) 93 57 Min et al. (2019a), Park et al. (2019e, 2019f, 2021c)
Korean isolate (NC_031445) Korean isolate (MK616470) 93 64
Korean isolate (NC_031445) Korean isolate (MF407183) 93 57
Korean isolate (NC_031445) Korean isolate (MN116559) 102 64
Korean isolate (NC_031445) Korean isolate (MW426545) 99 72
Korean isolate (MN127986) Korean isolate (MK616470) 0 0
Korean isolate (MN127986) Korean isolate (MF407183) 0 1
Korean isolate (MN127986) Korean isolate (MN116559) 9 12
Oleaceae Abeliophyllum distichum Korean isolate (MN127986) Korean isolate (MW426545) 6 20 Min et al. (2019a), Park et al. (2019e, 2019f, 2021c)
Korean isolate (MK616470) Korean isolate (MF407183) 0 1
Korean isolate (MK616470) Korean isolate (MN116559) 9 11
Korean isolate (MK616470) Korean isolate (MW426545) 6 19
Korean isolate (MF407183) Korean isolate (MN116559) 9 11
Korean isolate (MF407183) Korean isolate (MW426545) 6 21
Korean isolate (MN116559) Korean isolate (MW426545) 7 23
Adoxaceae Viburnum erosum Korean isolate (MN641480) Korean isolate (MN218778) 16 50 Choi et al. (2020), Park et al. (2019b)
Brasicaceae Arabidopsis thaliana Korean isolate (MK353213) Chinese isolate (MK380719) 10 33 Park et al. (2020c)
Ranunculaceae Aconitum coreanum Korean isolate (NC_031421) Korean isolate (KU318669) 29 61 Kim et al. (2019h), Park et al. (2017)
Korean isolate (NC_031421) Korean isolate (MN400660) 5 52
Korean isolate (MN400660) Korean isolate (KU318669) 19 92
Thymelaeaceae Daphne genkwa Korean isolate (MT754180) Korean isolate (Unpub) 59 404 Yoo et al. (2021)
Korean isolate (MT754180) Chinese isolate (NC_045891) 69 772
Korean isolate (Unpub) Chinese isolate (NC_045891) 85 543
Campanulaceae Campanula takesimana Korean isolate (MW013763) Korean isolate (NC_026203) 33 662 Cheon et al. (2016), Park et al. (2021a)
Poaceae Zoysia japonica Korean isolate (MW690657) Korean isolate (NC_036827) 68 50 Lee and Park (2021)
Zoysia macrostachya Korean isolate (MZ233426) Korean isolate (NC_042189) 29 18 Cheon et al. (2021), Oh et al. (2021)
Staphyleaceae Euscaphis japonica Chinese isolate (MN159078) Korean isolate (NC_052922) 424 809 Oh and Park (2020), Xiang et al. (2019)
Table 2.
List of normal SSRs and extended SSRs identified in the C. grandiflora chloroplast genomes isolated in Korea.
No. Name SSRType Type Start End Unit sequence Repeat No. Gene Position
1 cO0000001 ExtendedSSR OctaSSR 2551 2566 ATAATTGG 2 matK Genic
2 cM0000001 SSR MonoSSR 4417 4427 A 11 - -
3 cM0000002 SSR MonoSSR 4729 4739 G 11 - -
4 cM0000003 SSR MonoSSR 4807 4817 T 11 - -
5 cM0000004 SSR MonoSSR 5226 5235 T 10 rps16 Intronic
6 cM0000005 SSR MonoSSR 5249 5258 A 10 rps16 Intronic
7 cO0000002 ExtendedSSR OctaSSR 6472 6487 AAATAGAT 2 - -
8 cM0000006 SSR MonoSSR 6513 6522 T 10 - -
9 cD0000001 SSR DiSSR 7299 7310 AT 6 - -
10 cM0000007 SSR MonoSSR 8095 8105 T 11 - -
11 cHe0000001 ExtendedSSR HeptaSSR 8479 8492 AATGTAA 2 - -
12 cD0000002 SSR DiSSR 8530 8539 TA 5 - -
13 cM0000008 SSR MonoSSR 8698 8709 T 12 - -
14 cM0000009 SSR MonoSSR 9087 9096 A 10 trnS-CGA Intronic
15 cM0000010 SSR MonoSSR 9287 9298 A 12 trnS-CGA Intronic
16 cO0000003 ExtendedSSR OctaSSR 10230 10245 TACGTAAG 2 atpA Genic
17 cTe0000001 SSR TetraSSR 11104 11115 GTCT 3 atpA Genic
18 cM0000011 SSR MonoSSR 12359 12371 T 13 atpF Intronic
19 cN0000001 ExtendedSSR NonaSSR 13024 13041 TCTTTTTTA 2 - -
20 cM0000012 SSR MonoSSR 13054 13063 T 10 - -
21 cHe0000003 ExtendedSSR HeptaSSR 14205 14218 ATTTATT 2 - -
22 cHe0000004 ExtendedSSR HeptaSSR 14480 14493 ATTTTTT 2 - -
23 cM0000013 SSR MonoSSR 16315 16327 T 13 - -
24 cP0000031 SSR PentaSSR 16455 16469 CAAAT 3 - -
25 cHe0000005 ExtendedSSR HeptaSSR 17159 17172 CAACCCT 2 rpoC2 Genic
26 cM0000014 SSR MonoSSR 18522 18532 T 11 rpoC2 Genic
27 cD0000003 SSR DiSSR 19907 19916 AT 5 rpoC2 Genic
28 cHe0000006 ExtendedSSR HeptaSSR 27420 27433 TGTATAA 2 - -
29 cHe0000007 ExtendedSSR HeptaSSR 27459 27472 TGTATAA 2 - -
30 cM0000015 SSR MonoSSR 30555 30567 A 13 - -
31 cHe0000008 ExtendedSSR HeptaSSR 30733 30746 AAAGAAA 2 - -
32 cHe0000009 ExtendedSSR HeptaSSR 30834 30847 TATTGGA 2 - -
33 cT0000001 SSR TriSSR 35063 35074 TTC 4 psbC Genic
34 cM0000016 SSR MonoSSR 35277 35291 T 15 - -
35 cO0000004 ExtendedSSR OctaSSR 35310 35325 TCGATTTT 2 - -
36 cM0000017 SSR MonoSSR 35664 35673 A 10 - -
37 cM0000018 SSR MonoSSR 36062 36072 C 11 - -
38 cM0000019 SSR MonoSSR 36073 36084 A 12 - -
39 cM0000020 SSR MonoSSR 36178 36187 A 10 - -
40 cHe0000011 ExtendedSSR HeptaSSR 42112 42125 TTAATAT 2 - -
41 cM0000021 SSR MonoSSR 42252 42261 A 10 - -
42 cTe0000002 SSR TetraSSR 42470 42481 TAAA 3 - -
43 cM0000022 SSR MonoSSR 43350 43361 T 12 ycf3 Intronic
44 cO0000005 ExtendedSSR OctaSSR 44658 44673 ATCCTAAT 2 - -
45 cM0000023 SSR MonoSSR 45132 45146 A 15 - -
46 cM0000024 SSR MonoSSR 46347 46359 T 13 - -
47 cD0000004 SSR DiSSR 46520 46533 TA 7 - -
48 cHe0000012 ExtendedSSR HeptaSSR 46676 46689 AAAAAAT 2 - -
49 cM0000025 SSR MonoSSR 46996 47007 T 12 - -
50 cHe0000013 ExtendedSSR HeptaSSR 47052 47065 TATATTT 2 - -
51 cM0000026 SSR MonoSSR 47199 47212 A 14 - -
52 cHe0000014 ExtendedSSR HeptaSSR 47362 47375 TCCTATA 2 - -
53 cM0000027 SSR MonoSSR 47393 47402 T 10 - -
54 cM0000028 SSR MonoSSR 47671 47681 A 11 trnL-UAA Intronic
55 cHe0000015 ExtendedSSR HeptaSSR 47801 47814 ATATCAA 2 trnL-UAA Intronic
56 cHe0000016 ExtendedSSR HeptaSSR 48224 48237 AATTAAG 2 - -
57 cN0000006 ExtendedSSR NonaSSR 48587 48604 ATGATAAAG 2 - -
58 cN0000007 ExtendedSSR NonaSSR 48643 48660 AAAGTGAAT 2 - -
59 cM0000029 SSR MonoSSR 50718 50730 A 13 - -
60 cHe0000017 ExtendedSSR HeptaSSR 51214 51227 ATTAGTT 2 - -
61 cDe0000004 ExtendedSSR DecaSSR 51678 51697 TATGAGAAAA 2 - -
62 cM0000030 SSR MonoSSR 51739 51748 T 10 - -
63 cTe0000003 SSR TetraSSR 52184 52195 GTTT 3 - -
64 cO0000006 ExtendedSSR OctaSSR 53336 53351 ATATATAA 2 - -
65 cM0000031 SSR MonoSSR 54063 54073 A 11 - -
66 cM0000032 SSR MonoSSR 56504 56514 A 11 - -
67 cO0000007 ExtendedSSR OctaSSR 59209 59224 TATCAAAA 2 - -
68 cM0000033 SSR MonoSSR 59479 59489 A 11 - -
69 cTe0000004 SSR TetraSSR 59496 59507 TTTC 3 - -
70 cM0000034 SSR MonoSSR 59697 59709 A 13 - -
71 cO0000008 ExtendedSSR OctaSSR 60779 60794 ATAAAGAA 2 psaI Genic
72 cTe0000005 SSR TetraSSR 63789 63800 TTTA 3
73 cM0000035 SSR MonoSSR 66657 66666 A 10 atpB Genic
74 cDe0000005 ExtendedSSR DecaSSR 68648 68667 AAAATCAATA 2 - -
75 cM0000036 SSR MonoSSR 70334 70344 A 11 - -
76 cM0000037 SSR MonoSSR 70396 70405 A 10 - -
77 cM0000038 SSR MonoSSR 72938 72949 A 12 - -
78 cHe0000021 ExtendedSSR HeptaSSR 72980 72993 ATTTAAG 2 - -
79 cTe0000006 SSR TetraSSR 73132 73143 AAAG 3 - -
80 cHe0000022 ExtendedSSR HeptaSSR 73526 73539 CTGGTTG 2 psbB Genic
81 cHe0000023 ExtendedSSR HeptaSSR 73990 74003 GGCGTGG 2 psbB Genic
82 cM0000039 SSR MonoSSR 75085 75094 C 10 - -
83 cM0000040 SSR MonoSSR 75096 75108 A 13 - -
84 cM0000041 SSR MonoSSR 76129 76140 A 12 - -
85 cO0000011 ExtendedSSR OctaSSR 77589 77604 ATACAGAA 2 petD Intronic
86 cM0000042 SSR MonoSSR 79112 79125 T 14 rpoA Genic
87 cN0000009 ExtendedSSR NonaSSR 79940 79957 TTTCTCTTG 2 - -
88 cM0000043 SSR MonoSSR 81025 81035 T 11 - -
89 cM0000044 SSR MonoSSR 81538 81550 T 13 - -
90 cM0000045 SSR MonoSSR 82710 82725 T 16 rpl16 Intronic
91 cM0000046 SSR MonoSSR 82788 82800 A 13 rpl16 Intronic
92 cO0000012 ExtendedSSR OctaSSR 83219 83234 TTTCTCTC 2 rpl16 Intronic
93 cHe0000026 ExtendedSSR HeptaSSR 84484 84497 TTACTAA 2 rpl22 Genic
94 cM0000047 SSR MonoSSR 85098 85107 T 10 - -
95 cN0000010 ExtendedSSR NonaSSR 89648 89665 GGAACATTT 2 ycf2 Genic
96 cN0000011 ExtendedSSR NonaSSR 92241 92258 GATATTGAT 2 ycf2 Genic
97 cN0000012 ExtendedSSR NonaSSR 92285 92302 TATTGATGC 2 ycf2 Genic
98 cHe0000027 ExtendedSSR HeptaSSR 92995 93008 ACTTGGA 2 ycf2 Genic
99 cM0000048 SSR MonoSSR 112535 112544 A 10 ycf1 Genic
100 cM0000049 SSR MonoSSR 113091 113102 A 12 ycf1 Genic
101 cTe0000007 SSR TetraSSR 115405 115416 GATT 3 - -
102 cM0000050 SSR MonoSSR 118228 118239 T 12 ndhA Intronic
103 cM0000051 SSR MonoSSR 118287 118296 A 10 ndhA Intronic
104 cM0000052 SSR MonoSSR 118446 118455 T 10 ndhA Intronic
105 cHe0000030 ExtendedSSR HeptaSSR 119608 119621 ATTGGAA 2 ndhI Genic
106 cTe0000008 SSR TetraSSR 120108 120119 TTCA 3 - -
107 cHe0000031 ExtendedSSR HeptaSSR 120362 120375 TATTCTA 2 ndhG Genic
108 cM0000053 SSR MonoSSR 121803 121816 T 14 - -
109 cN0000013 ExtendedSSR NonaSSR 122187 122204 CTACTTTAG 2 ndhD Genic
110 cTe0000009 SSR TetraSSR 123187 123198 TATT 3 ndhD Genic
111 cM0000054 SSR MonoSSR 125479 125488 T 10 - -
112 cM0000055 SSR MonoSSR 125903 125915 A 13 - -
113 cHe0000032 ExtendedSSR HeptaSSR 126066 126079 TTTTTTA 2 - -
114 cM0000056 SSR MonoSSR 128639 128648 A 10 - -
115 cHe0000034 ExtendedSSR HeptaSSR 146362 146375 GTTCCAA 2 ycf2 Genic
116 cN0000014 ExtendedSSR NonaSSR 147070 147087 GCATCAATA 2 ycf2 Genic
117 cN0000015 ExtendedSSR NonaSSR 147110 147127 TATCATCAA 2 ycf2 Genic
118 cN0000016 ExtendedSSR NonaSSR 149707 149724 AAATGTTCC 2 ycf2 Genic
119 cM0000057 SSR MonoSSR 154265 154274 A 10

SSR, simple sequence repeat.

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