DOI: https://doi.org/10.21203/rs.3.rs-992863/v1
Background The plants in the Bignoniaceae have a wide distribution in the tropics and large populations around the world. However, the research information of Bignoniaceae is still scarce or even blank. To excavating the research information of Bignoniaceae plants and provide data support for the study of plant plastid genomes.
Methods and results In this study, We have done a particular exploration of the chloroplast genome bioinformation of Campsis grandiflora. The chloroplast DNA of C. grandiflora was extracted, sequenced with HTS platform, assembled, and annotated with corresponding software. Results show that the complete chloroplast genome of C. grandiflora is 154,303 bp long, having a quadripartite structure with large single copy (LSC) of 85,064 bp and a small single copy (SSC) of 18,009 bp separated by inverted repeats (IRs) of 25,615 bp. A total of 110 genes in C. grandiflora is comprised of 79 protein-coding genes, 27 transfer RNA (tRNA) coding genes and 4 ribosomal RNA (rRNA) genes. The location and distribution of simple sequence repeats (SSRs) and long repeat sequences were determined. We finished the phylogenetic analysis based on homologous amino acid sequence among 45 species which derived from Bignoniaceae.
Conclusions The chloroplast genomes have been used for molecular markers, species identification and phylogenetic studies. The outcome strongly supported that C. grandiflora and genus Incarvillea formed a cluster within Bignoniaceae. This study identified the unique characteristics of the C. grandiflora cp genome, which will provide a theoretical basis for species identification and biological research.
The chloroplast genome is an important role of plant plastid genetic system, and its highly conserved circular quadripartite double-stranded structure which consisted of a large single-copy region (LSC; 80−90 kb) and a small single-copy region (SSC; 16−27 kb), separated by two inverted repeat regions (IRs) of 20 to 28 kb. Leading its mutation rate at a low level in the process of plant evolution. Therefore, the character that stable gene content, simple structure, nonrecombinant, and mostly maternally inherited meaning that the chloroplast genomes contain a great deal of valuable biological information as an ideal material to support phylogeny and evolution studies[1]. With the rapid development of high-throughput sequencing technology in recent years, researchers have been able to efficiently extract and sequence chloroplast genomes from plants, thus greatly advancing the process of chloroplast genome sequencing. Chloroplast genome sequencing information has been widely used to build the basis of phylogenetic analysis, and the evolutionary history of many plant groups has been deeply explored and supported[2].
The abundance of species in Bignoniaceae includes a total of 650 species in 120 genera, including Catalpa, Campsis, Adenomocalymma, Amphilophium, and Anemopaegma, etc[3]. Bignoniaceae plants, which mainly for trees, shrubs, or woody vines, are widely distributed in the tropics and subtropics and constitute an important part of tropical plants. The vast majority of species of Bignoniaceae have dazzling large and beautiful flowers, as well as a variety of exotic fruit shapes, and are cultivated in botanical gardens around the world, as ornamental, scenic, and street trees, and as an ideal shade pergola plant for the tropics[4]. Campsis grandiflora is a climbing vine affiliated with the genus Campsis, family Bignoniaceae. Distinguished from Campsis radicans, other plants of the same genus that derived from North America, C. grandiflora is mainly distributed in China and Japan, cultivated in Vietnam, India, and Pakistan[5]. Campsis grandiflora can be used for ornamental and medicinal purposes. Pharmacological studies have shown that It has antibacterial, antithrombotic, and antitumor effects[6]. According to the Chinese Pharmacopoeia (2020 Edition)[7], C. grandiflora has the functions of promoting blood circulation, and its flower is a diuretic for meridional treatment and can also cure the disease of falling and injury [8].
Although there are numerous species in the family Bignoniaceae, only more than 40 chloroplast data have been recorded[9]. In particular, the chloroplast genome study of the entire genus Campsis, an important branch of Bignoniaceae, is still blank. In this study, we gained the chloroplast genomes of the C. grandiflora by using high-throughput sequencing technology and utilized more than 40 species uploaded chloroplast genomes of the Bignoniaceae, with the aim of 1. To explore the biodiversity and evolution process of the genus Campsis. 2. To characterize the gene contents and gene loss within the family Bignoniaceae by chloroplast genome assembly and annotation. 3. To get the phylogenetic information of C. grandiflora and making valid hypotheses about homology between different lineages of Bignoniaceae. 4.To explore the gene rearrangement structure that occurred in the family Bignoniaceae.
The Campsis grandiflora sample was collected in Huazhong Medicinal Botanical Garden, China. located in 109.76 E,30.18 N, voucher sample IDs is implad201808016, IMPLAD, China. The whole-genome DNA of Campsis grandiflora was extracted using the plant genomic DNA kit (Tiangen Biotech, Beijing, China). The process of library construction and Genome sequence was completed by the Hiseq 2500 platform (Illumina, San Diego, CA, USA)[10].
The raw data of the sequence was assembled into a complete chloroplast genome with NOVOplasty(ver. 4.0.1) [11].
The genome annotation and repeat analysis works were finished by CPGAVAS2, DB 2[12].
At present, the commonly accepted phylogenetic classification of C. grandiflora is that the C. grandiflora of genus Campsis of family Bignoniaceae. We used The maximum likelihood method[13] to construct an evolutionary tree with the cpREV model of IQ-Tree[14] for 56 common protein sequences of 45 species which included genus Adenocalymma[15], Neojobertia[16], Pleonotoma[17], Amphilophium[18], Anemopaegma, Tanaecium[19], Dolichandra[20], Oroxylum[21], Catalpa[22, 23], Incarvillea[24-26], Spathodea[27] and 2 outer groups (Paulownia tomentosa[28] and Arabidopsis thaliana[29]) of species from the family Bignoniaceae. For phylogenic tree building, we used Phylosuite (version 1.2.2)[30] to extract the GenBank files of 47 species to get the common protein-coding genes information. Then we did the multiple sequence alignment by using MAFFT(v7.313) without the duplicated FASTA files. The protein-coding gene MAFFT outcome was concatenated by Gblocks(v0.91b), to select conserved blocks from multiple alignments for use in phylogenetic analysis.
After we got the contree file, the visual work of the evolutionary tree was performed by iTOL (Interactive Tree of Life) [31].
The SSR locus and distribution was identified with MISA (MIcroSAtellite identification tool)[32]. The long tandem repeats (matching parameter = 2, mismatching and indel parameter = 7, minimun identity score = 50, maximun repeat period = 500, minimum repeat size = 30bp, repeat unit similarity >= 90%) identified with TRF (Tandem Repeats Finder)[33]. The long interspersed repeats (repetition length >= 30bp, Hamming distance = 3) identified with VMATCH (The Vmatch large scale sequence analysis software)[34].
In this study, we compared each single 45 Bignoniaceae species in the phylogenic tree with A. thaliana to perform gene scale dot-plot analysis with Gepard (ver. 1.40 final.)[35].
The detailed synteny analyses of 12 species [These species are A. oligoneuron (NC_037232.1)[36], A. gnaphalanthum (NC_042903.1), T. tetragonolobum (NC_027955.1), A. paniculatum (NC_042918.1), I. compacta (NC_050666.1), I. sinensis (NC_051523.1), N. candolleana (NC_036503.1), A. allamandiflorum (NC_036494.1), A. biternatum (NC_036496.1), A. divaricatum (NC_037456.1), A. marginatum (NC_037457.1), C. grandiflora (MW430049).] with genomic structure rearrangement was revealed by Easyfig (ver. win2.1) [37]. We first got the B.O format files with blastn of particular 12 species, the contrasting species is A. thaliana. Then import the B.O files and GB or GBK files of related species into the Easyfig software. The synteny visualizes outcome will be generated.
We used the GenBank files of 12 representative species with genomic structural variations from 45 species of Bignoniaceae that were used for phylogenetic analysis to get the gene distribution on LSC, SSC, IRa, IRb border. The location of genes on the boundaries was visualized by IRSCOPE[38]
We used the aBSREL model of Hyphy Vision software to contribute the selective pressure analysis[39] among 45 species in Bignoniaceae. We first acquired the corresponding chloroplast genome GB files and FASTA files according to the accession number in NCBI. Then got 63 clusters of orthologous genes among these species to used to calculate the Ka/Ks. The outcome was listed in aBSREL.json format. In this study, we selected genes with the p-value < 0.05. The detailed information was shown in the web version of aBSREL.
The chloroplast genome sequence (GenBank accession no.: MW430049) of Campsis grandiflora was a typical circular DNA molecule with a total length of 154,303 bp. It has a conservative tetrad structure consisting of an LSC region, an SSC region, and a pair of IR regions, with lengths of 85,064 bp, 18,009 bp, and 25,615 bp, respectively (Figure 1). The G/C content of the chloroplast genome of Campsis grandiflora was 38.09 %. The G/C content in the IR region (43.17%) was higher than that in the SSC region (32.74%) and LSC region (36.16%).
The chloroplast genome of Campsis grandiflora encodes a total of 110 unique genes, including 79 protein-coding genes, 27 transfer RNA (tRNA) coding genes, and 4 ribosome RNA (rRNA) coding genes (Table 1). Among them, eight protein coding genes (rps12, ndhB, rpl2, rpl23, rps7, ycf1, ycf2, ycf15), 7 tRNA coding genes (trnA-UGC, trnE-UUC, trnL-CAA, trnM-CAU, trnN-GUU, trnR-ACG, trnV-GAC) and 4 rRNA coding genes (rrn16S, rrn23S, rrn5S, rrn4.5S) were located in IR region. 12 protein-coding genes (rps16, atpF, rpoC1, petB, petD, rpl16, rpl2 (+), rpl2(-), ndhB(+), ndhB(-), ndhA) contain one intron, and two protein-coding genes (ycf3, accD) contain two introns. 8 tRNA coding genes (trnK-UUU, trnS-CGA, trnL-UAA, trnV-UAC, trnE-UUC(-), trnE-UUC(+), trnA-UGC(-), trnA-UGC(+)) contain one intron (Table S1). In the process of counting intron and exon of gene, we found the clpP gene has lost all of its introns and exons.
The coding sequence (CDS) in the Chloroplast genome of C. grandiflora was 79,170 bp, accounting for 51.31% of the total genome length. The length of the rRNA gene was 9,388 bp, accounting for 6.08% of the whole genome length. The length of the tRNA gene was 2,811 bp, accounting for 1.82% of the whole genome length. The non-coding region of the Campsis grandiflora chloroplast genome mainly includes introns and gene spacers, whose length accounts for 40.79% of the whole genome length.
The repeat sequences are particular nucleic characteristic sequences repeat units that have multiple copies in the genome. On the one hand, these repeats might play a significant role in the evolution of the chloroplast genome. On the other hand, they can also be used for species identification and molecular breeding as molecular markers. The repeat sequences are respectively classified into simple sequence repeat (SSR), long tandem repeats, and long interspersed repeated sequence 3 forms according to their length and correlation[1].
The SSR is also named microsatellite sequence. It is a piece of DNA that consists of multiple duplicate basic repeat units made of 1-6 nucleotides. The SSR is widespread all around the different places of the gene. Their length usually below 200bp. In the chloroplast genome of C. grandiflora, the SSR is mainly A/T type, with 54. The second and third types are C/G and AT/AT, with 3 and 2 respectively (Table S2). Besides, we analyzed and listed the quantity, type, size, and locus of SSRs in the chloroplast genome of C. grandiflora. In total, there were 51 SSRs identified in the C. grandiflora chloroplast genome. These SSRs are mainly composed of mononucleotide repeat units and dinucleotide repeat units (Table S3). Beyond that, we found no other forms like tri-, tetra-, penta-, hexa-nucleotide repeat units. Among 51 SSRs we found, most of them appear in intergenic spacers (35 SSRs), 9 SSRs located in the coding sequence, and 7 SSRs situated in the non-coding region of particular genes.
The long tandem repeats refer to the repeated repetition of a sequence on a chromosome. A total of 40 tandem repeats have been found, satisfying the two conditions that the total length is over 20bp and the similarity between repeating units is greater than or equal to 90% (Table S4). We also listed the related property in the table. Among the long tandem repeats, more than half (22) repeats were located in IGS, and 13 repeats were shown in the CDS, the remainder 5 repeats were located in the non-coding region.
Interspersed repeats are another kind of repeated sequence which are different from tandem repeats. It include palindromic repeats and direct repeats. With the e-value less than 1E-4 as the threshold, the scattered repeats of plumbic chloroplast genomes included 49 direct repeats. It's worth mentioning that all of the interspersed repeats of C. grandiflora chloroplast genome are D type (direct repeat sequence), and these interspersed repeats are all in the range of 62,500-63,700 of accD gene and almost all of them are located in the non-coding region except one sequence that its repeat unit I in the CDS of accD (Table 2).
To get the phylogenetic information of C. grandiflora and making valid hypotheses about homology between different lineages of Bignoniaceae. We used 45 Bignoniaceae species and 2 outgroup species chloroplast genomes to build the phylogenetic tree of Bignoniaceae. (Figure 2)
The tree shows that that two primary branches initially diverged from the tree root There are 15 species from the genus Adenocalymma, Neojobertia and Pleonotoma gathered into a branch on top of the tree. 11 species of the genus Amphilophium converged into a branch. 8 species of the genus Anemopaegma got into a branch. Then the genus Amphilophium, Anemopaegma, Tanaecium, and Dolichandra gathered into a big branch with Adenocalymma, Neojobertia, and Pleonotoma. Furthermore, the grand branch congregated a branch with genus Oroxylum, and then the genus Spathodea. At the bottom of the tree, 2 species of genus Catalpa gathered to a branch. From this view, the eight genera mentioned above have contributed to the upper grand branch of the evolutionary tree of the family Bignoniaceae. In the remaining part of the tree, 3 species of the genus Incarvillea gathered into a branch, then the sole branch Tecomaria have aggregated a branch with the genus Incarvillea. At last, the genus Campsis, Incarvillea, Tecomaria have converged into another grand branch of the tree.
In the phylogenetic tree of the family Bignoniaceae, the bootstrap scores of all branches of the evolutionary tree were high (> 47%), indicating that the evolutionary tree has high reliability. The results of the phylogenetic analysis are consistent.
The initial study of C. grandiflora chloroplast genome rearrangement structure started from synteny analysis[40]. We first performed a genome comparing dot plot by using Gepard (ver. 1.40 final). The visualization result shows that the rearrangement was occurred at about 48 772-73 286bp in the C. grandiflora chloroplast genome (Figure S1).
This study explores whether there is a correlation between gene loss and the rearrangement of genome structure. We made detailed statistics of the protein-coding gene loss in the particular plants of Bignoniaceae (Table 3). All the plants involved in the statistics are derived from phylogenetic trees (Figure 2 with supplement Figure 4). The genes listed in the table are all existed quantity varies. Oppositely, genes that did not differ in number were not listed. The result of the statistic shows: The number of genes in 8 species from the genus Anemopaegma was highly conserved and consistent. In terms of gene loss, the accD gene has been lost in the genus Incarvillea. The clpP gene was found lost in I. arguta , T. tetragonolobum but also found incomplete structure in C. grandiflora. The ndhD gene was found lost in T. tetragonolobum and I. arguta. The petB, rpl16, rpoA gene has lost in T. tetragonolobum, I. arguta. The I. sinensis was also found to have lost the petB and rpl16 gene. The rpl32 gene was found only missing in C. grandiflora. The rps16 was found lost in T. tetragonolobum, I. compacta, I. arguta. The rps19 gene was found only lost in I. sinensis. The rps4 gene has lost in T. tetragonolobum. The ycf4 gene has been lost in A. peregrinum and A. biternatum. And the ycf15 gene was only found in T. tetragonolobum, I. arguta, and C. grandiflora. The ycf1 gene was found only lost in A. gnaphalanthum. In general, the majority of gene loss occurs in the genus Incarvillea and Tanaecium.
In genetics, Ka/Ks or dN/dS represents the ratio between non-synonymous replacement (Ka) and synonymous replacement (Ks). This ratio can be used to determine whether there is selective pressure acting on the protein-coding gene[41].
Nucleotide variations that do not lead to amino acid changes are called synonymous mutations, whereas non-synonymous mutations occur. It is generally believed that synonymous mutations are not subject to natural selection, while non-synonymous mutations are. In evolutionary analysis, it makes sense to understand the rate at which synonymous and non-synonymous mutations occur[41].
In this study, we used the phylogenetic tree (Figure 2) as species reference, and we utilized the aBSREL (adaptive branch-site random effects likelihood) model of software Hyphy to carry the selection pressure analysis of protein-coding genes (Table S5). A total of 6 Bignoniaceae genes were positively selected: ndhG, rbcL, rpl22, rpl23, rps12, rps15. In species A. bracteatum, the ndhG gene is positively selected. In species A. glaucum, A. divaricatum, the rbcL gene was positively selected. The rpl22 gene was positively selected in species A. steyermarkii, D. cynanchoides. In species A. allamandiflorum, A. chamberlaynii, rpl23 gene was positively selected. In C. ovata, rps12 and rps15 are positively selected. In species C. grandiflora, rps15 is positively selected.
To unravel the gene distribution of junction sites border, and compare the distinction between C. grandiflora and other species which have genome rearrangement structure in the family Bignoniaceae. We have visualized the gene distribution with IRSCOPE (Figure S5).
In the result of the visualizing analysis, we can see the complete genome was divide into 5 parts with 4 vertical bars. The 5 parts are respective LSC, IRb, SSC, IRa, LSC. In the 4 species from the genus Adenocalymma, the rps15 gene has crossed the JSA between SSC and IRa, and the gene distribution in genome boundary is highly conservative. The bp number of each gene from the boundary or across the boundary is highly consistent or similar. In the I. sinensis, the ndhF was found to cross the JSB between IRb and SSC region. In the I. compacta, the gene located in the boundary between IRb/IRa and SSC is trnN. It’s worth mentioning that, there are significant differences in the length of SSC and IR regions between these two species from the genus Incarvillea. The SSC region in the I. sinensis was only 8,666 bp, and the IR regions were 35,394 bp respectively. But in the I. compacta, the SSC region has reached 21,925 bp. This difference in the length of genomic regions has also occurred in A. paniculatum and A. oligoneuron. Their IR regions have reached 37,372 bp and 39,614 bp respectively, much longer than the normal length of the IR region. Accordingly, in the A. paniculatum, the gene that crossed the IRb and LSC are petD, and in the A. oligoneuron, the counterpart gene is petB.
In this study, we extracted, assembled, sequenced, and annotated the complete chloroplast genome of C. grandiflora, filling in the gaps in chloroplast genome information of genus Campsis. The phylogenetic analysis not only reveals the phylogenetic information of Bignoniaceae but also shows the overall evolutionary history of 45 species of the family. And the repeat sequence analysis provided us the genetic characteristic information. The Ka/Ks analysis indicated the direction of evolution of Bignoniaceae. We conducted a detailed and in-depth analysis of the chloroplast genome of C. grandiflora, and found that the chloroplast genome has an inverted rearrangement structure through synteny analysis, We also found and sorted out the rearrangement structures of 12 chloroplast genomes of Bignoniaceae from the available data by synteny analysis. which was of great significance to the phylogenetic information of C. grandiflora. Then the gene loss analysis inspired us to the relationship between rearrangement structure and the gene quantity variation.
There are a lot of species in the Bignoniaceae, but only a drop in the bucket of information that is currently available. The results of this study are based on all the released chloroplast genome sequences available so far. Please correct any irregularities or gaps. With the acceleration of sequencing progress, the database of Bignoniaceae will be enriched day by day in the future, and there will be more discoveries, new features, and breakthroughs.
CL conceived the study; MJ collected samples of C. grandiflora, extracted DNA for next-generation sequencing, assembled and validated the genome; ZEC performed data analysis and drafted the manuscript; HMC and QD reviewed the manuscript critically. All authors have read and agreed the contents of the manuscript.
Funding
This work was supported by the National Science &Technology Fundamental Resources Investigation Program of China [2018FY100705], National Science Foundation Funds [81872966],Chinese Academy of Medical Sciences, Innovation Funds for Medical Sciences (CIFMS) [2017-I2M-1-013], Qinghai Provincial Key Laboratory of Phytochemistry of Qinghai Tibet Plateau [2020-ZJ-Y20]. The funders were not involved in the study design, data collection, analysis, decision to publish, or manuscript preparation.
Compliance with ethical standards
Conflict of interest All the authors declare no conflicts of interest.
Ethical approval This article does not contain any studies with human participants performed by any of the authors.
Data availability statement
The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at (https://www.ncbi.nlm.nih.gov/) under the accession no.MW430049. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA704532, and SAMN18043523 respectively.
ORCID
Chang Liu: 0000-0003-3879-7302
Qing Du: 0000-0002-0732-3377
Mei Jiang: 0000-0002-8266-7233
Zhuoer Chen: 0000-0001-7782-6992
1. Liu C, Huang L-F (2020) Chloroplast genomic mapping of Chinese medicinal plants [M]. Science Press: Beijing, China. Vol.1, pp 3-4.
2. Liu L, Li Y, Li S, Hu N, He Y, Pong R, Lin D, Lu L, Law M (2012) Comparison of next-generation sequencing systems. J Biomed Biotechnol, 2012:251364. https://doi.org/10.1155/2012/251364
3. Lohmann, Lúcia G (2006) Untangling the phylogeny of neotropical lianas (Bignonieae, Bignoniaceae). Am J Bot, 93(2):304-318. https://doi.org/10.3732/ajb.93.2.304
4. Flora of China (2021) Bignoniaceae. IBCAS Publishing iPlant.http://www.iplant.cn/info/Bignoniaceae?t=z.Accessed 07 Jan 2021
5. Flora of China (2021) Campsis grandiflora. IBCAS Publishing iPlant.http://www.iplant.cn/info/Campsis%20grandiflora?t=foc. Accessed 07 Jan 2021
6. Cui XY, Kim JH, Zhao X, Chen BQ, Lee BC, Pyo HB, Yun YP, Zhang YH (2006) Antioxidative and acute anti-inflammatory effects of Campsis grandiflora flower. J Ethnopharmacol, 103(2):223-228. 10. https://doi.org/1016/j.jep.2005.08.007
7. National Pharmacopoeia Commission (2015) The Pharmacopoeia of the People's Republic of China (2015 edition) [S]. Medical Technology Publishing House: Beijing, China, vol.1, pp 299
8. Xiao P-g, Zhao Z-z (2018) Encyclopedia of Medicinal Plants[M]. World Book Inc: Beijing, China, pp 11-14.
9. Schoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S, Khovanskaya R, Leipe D, McVeigh R, O'Neill K, Robbertse Bet al (2020) NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database : the journal of biological databases and curation. 2020. https://doi.org/10.1093/database/baaa062
10. Steemers FJ, Gunderson KL (2005) Illumina, Inc. Pharmacogenomics, 6(7):777-782. https://doi.org/10.2217/14622416.6.7.777
11. Dierckxsens N, Mardulyn P, Smits G (2017) NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res, 45(4):e18. https://doi.org/10.1093/nar/gkw955
12. Shi L, Chen H, Jiang M, Wang L, Wu X, Huang L, Liu C (2019) CPGAVAS2, an integrated plastome sequence annotator and analyzer. Nucleic Acids Res, 47(W1):W65-W73. https://doi.org/10.1093/nar/gkz345
13. Hasegawa M, Kishino H, Saitou N (1991) On the maximum likelihood method in molecular phylogenetics. J Mol Evol, 32(5):443-445. https://doi.org/10.1007/BF02101285
14. Nguyen, L. T, Schmidt H. A, Von Haeseler A, Minh, B. Q (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol, 32(1):268-274. https://doi.org/10.1093/molbev/msu300
15. Fonseca LHM, Lohmann LG (2017) Plastome Rearrangements in the “Adenocalymma-Neojobertia” Clade (Bignonieae, Bignoniaceae) and Its Phylogenetic Implications.Front Plant Sci. 8:1875. https://doi.org/10.3389/fpls.2017.01875
16. Fonseca LHM, Lohmann LG (2018) Combining high-throughput sequencing and targeted loci data to infer the phylogeny of the "Adenocalymma-Neojobertia" clade (Bignonieae, Bignoniaceae). Molecular phylogenetics and evolution. 123:1-15. https://doi.org/10.1016/j.ympev.2018.01.023
17. Fonseca LHM, Lohmann LG (2019) An updated synopsis of Adenocalymma (Bignonieae, Bignoniaceae): new combinations, synonyms, and lectotypifications. Systematic Botany. 44(4):893-912. https://doi.org/10.1600/036364419X15710776741341
18. Thode VA, Lohmann LG (2019) Comparative Chloroplast Genomics at Low Taxonomic Levels: A Case Study Using Amphilophium (Bignonieae, Bignoniaceae). Frontiers in plant science. 10:796. https://doi.org/10.3389/fpls.2019.00796
19. Nazareno AG, Carlsen M, Lohmann LG (2015) Complete Chloroplast Genome of Tanaecium tetragonolobum: The First Bignoniaceae Plastome. PloS one. 10(6):e0129930. https://doi.org/10.1371/journal.pone.0129930
20. Fonseca LH, Cabral SM, Agra Mde F, Lohmann LG (2015) Taxonomic updates in Dolichandra Cham. (Bignonieae, Bignoniaceae). PhytoKeys.(46):35-43. https://doi.org/10.3897/phytokeys.46.8421
21. Jiang Y, Wang J, Qian J, Xu L, Duan BZ (2020) The complete chloroplast genome sequence of Oroxylum indicum (L.) Kurz (Bignoniaceae) and its phylogenetic analysis. Mitochondrial DNA Part B. 5(2):1429-1430. https://doi.org/10.1080/23802359.2020.1736961
22. Ma Q-g, Zhang J-g, Zhang J-p (2020) The complete chloroplast genome of Catalpa ovata G. Don.(Bignoniaceae). Mitochondrial DNA Part B. 5(2):1800-1801. https://doi.org/10.1080/23802359.2020.1750979
23. Yang J, Wang S, Huang Z, Guo P (2020): The complete chloroplast genome sequence of Catalpa bungei (Bignoniaceae): a high-quality timber species from China. Mitochondrial DNA Part B. 5(4):3854-3855. https://doi.org/10.1080/23802359.2020.1841581
24. Wu X, Li H, Chen St (2021) Characterization of the chloroplast genome and its inference on the phylogenetic position of Incarvillea sinensis Lam.(Bignoniaceae). Mitochondrial DNA Part B.6(1):263-264. https://doi.org/10.1080/23802359.2020.1860722
25. Ma G-T, Yang J-G, Zhang Y-F, Guan T-X (2019) Characterization of the complete chloroplast genome of Incarvillea arguta (Bignoniaceae). Mitochondrial DNA Part B.4(1):1603-1604. https://doi.org/10.1080/23802359.2019.1601529
26. Wu X, Peng C, Li Z, Chen S (2019) The complete plastome genome of Incarvillea compacta (Bignoniaceae), an alpine herb endemic to China. Mitochondrial DNA Part B.4(2):3786-3787. https://doi.org/10.1080/23802359.2019.1681916
27. Wang Y, Yuan X, Li Y, Zhang J (2019) The complete chloroplast genome sequence of Spathodea campanulata. Mitochondrial DNA Part B.4(2):3469-3470. https://doi.org/10.1080/23802359.2019.1674710
28. Yi D-K, Kim K-J (2016) Two complete chloroplast genome sequences of genus Paulownia (Paulowniaceae): Paulownia coreana and P. tomentosa. Mitochondrial DNA Part B.1(1):627-629. https://doi.org/10.1080/23802359.2016.1214546
29. Sato S, Nakamura Y, Kaneko T, Asamizu E, Tabata Satoshi (1999) Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Research 6(5):283-290. https://doi.org/10.1093/dnares/6.5.283
30. Zhang D, Gao F, Jakovlic I, Zou H, Zhang J, Li WX, Wang GT (2020) PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol Ecol Resour. 20(1):348-355. https://doi.org/10.1111/1755-0998.13096
31. Letunic I, Bork P (2021) Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Nucleic acids research. 49(W1):W293-W296. https://doi.org/10.1093/nar/gkab301
32. Beier S, Thiel T, Münch T, Scholz U, Mascher M (2017) MISA-web: a web server for microsatellite prediction. Bioinformatics. 33(16):2583-2585. https://doi.org/10.1093/bioinformatics/btx198
33. Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic acids research. 27(2):573-580. https://doi.org/10.1093/nar/27.2.573
34. Gojman B, DeHon A (2009) VMATCH: Using logical variation to counteract physical variation in bottom-up, nanoscale systems. In: 2009 International Conference on Field-Programmable Technology. IEEE. 2009: 78-87. https://doi.org/10.1109/FPT.2009.5377684
35. Krumsiek J, Arnold R, Rattei T (2007) Gepard: a rapid and sensitive tool for creating dotplots on genome scale. Bioinformatics. 23(8):1026-1028. https://doi.org/10.1093/bioinformatics/btm039
36. Firetti F, Zuntini AR, Gaiarsa JW, Oliveira RS, Lohmann LG, Van Sluys MA (2017) Complete chloroplast genome sequences contribute to plant species delimitation: A case study of the Anemopaegma species complex. American Journal of Botany. 104(10):1493-1509. https://doi.org/10.3732/ajb.1700302
37. Sullivan MJ, Petty NK, Beatson SA (2011) Easyfig: a genome comparison visualizer. Bioinformatics. 27(7):1009-1010. https://doi.org/10.1093/bioinformatics/btr039
38. Amiryousefi A, Hyvönen J, Poczai P (2018) IRscope: an online program to visualize the junction sites of chloroplast genomes. Bioinformatics. 34(17):3030-3031. https://doi.org/10.1093/bioinformatics/bty220
39. Smith MD, Wertheim JO, Weaver S, Murrell B, Scheffler K, Kosakovsky Pond SL (2015) Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection. Molecular biology and evolution. 32(5):1342-1353. https://doi.org/10.1093/molbev/msv022
40. Tang H, Bowers JE, Wang X, Ming R, Alam M, Paterson AH (2008) Synteny and collinearity in plant genomes. SCIENCE.320(5875):486-488. https://doi.org/10.1126/science.1153917
41. Zhang Z, Li J, Zhao X-Q, Wang J, Wong GK-S, Yu J (2006) KaKs_Calculator: calculating Ka and Ks through model selection and model averaging. Genomics, Proteomics & Bioinformatics.4(4):259-263. https://doi.org/10.1016/S1672-0229(07)60007-2
42. Firetti F, Zuntini AR, Gaiarsa JW, Oliveira RS, Lohmann LG, Van Sluys MA: Complete chloroplast genome sequences contribute to plant species delimitation: A case study of the Anemopaegma species complex. Am J Bot2017, 104(10): 1493-1509. https://doi.org/10.3732/ajb.1700302
Table 1. Gene contents in the chloroplast of Campsis grandiflora.
|
Category of genes |
Group of genes |
Name of genes |
|
rRNA |
rRNA genes |
rrn16S(×2), rrn23S(×2), rrn5S(×2), rrn4.5S(×2) |
|
tRNA |
tRNA genes |
27 trn genes |
|
Self-replication |
Small subunit of ribosome |
rps11, rps12(×2), rps14, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7(×2), rps8 |
|
Large subunit of ribosome |
rpl14, rpl16, rpl2(×2), rpl20, rpl22, rpl23(×2), rpl33, rpl36 |
|
|
DNA dependent RNA polymerase |
rpoA, rpoB, rpoC1, rpoC2 |
|
|
Genes for photo- synthesis |
Subunits of NADH-dehydrogenase
|
ndhA, ndhB(×2), ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK |
|
Subunits of photosystem Ⅰ |
psaA, psaB, psaC, psaI, psaJ |
|
|
Subunits of photosystem Ⅱ |
psbA, psbB, psbC, psbD, psbE, psbF, psbI, psbJ, psbK psbL, psbM, psbN, psbT, psbZ, ycf3 |
|
|
Subunits of cytochrome b/f complex |
petA, petB, petD, petG, petL, petN |
|
|
Subunits of ATP synthase |
atpA, atpB, atpE, atpF, atpH, atpI |
|
|
Large subunit of rubisco |
rbcL |
|
|
Other genes |
Maturase |
matK |
|
Translational initiation factor |
infA |
|
|
Envelope membrane protein |
cemA |
|
|
Protease |
ΨclpP |
|
|
Subunit of Acetyl-CoA-carboxylase |
accD |
|
|
c-type cytochrom synthesis gene |
ccsA |
|
|
Unkown Conserved open reading frames |
ycf1(×2), ycf2(×2), ycf4, ycf15(×2) |
|
Table 3. Gene loss of protein-coding genes in the chloroplast genomes of the structurally variant species in family Bignoniaceae. a genome rearrangement structure type. b normal structure without rearrangement. a: gene quantity is 1. b: gene located in IR region. c: the gene is not found in this species.
|
typea |
Name of species |
acc D |
clp P |
inf A |
ndhD |
pet B |
pet D |
rpl 14 |
rpl 16 |
rpl 20 |
rpl 22 |
rpl 32 |
rpl 36 |
rpo A |
rps 11 |
rps 12 |
rps 15 |
rps 16 |
rps 19 |
rps 3 |
rps 4 |
rps 8 |
ycf 1 |
ycf 4 |
ycf 15 |
|
type1 |
Anemopaegma. oligoneuron |
1a |
1 |
2b |
1 |
2 |
2 |
2 |
2 |
1 |
2 |
1 |
2 |
2 |
2 |
2 |
2 |
1 |
2 |
2 |
1 |
2 |
2 |
1 |
0c |
|
Anemopaegma. acutifolium |
1 |
1 |
2 |
1 |
2 |
2 |
2 |
2 |
1 |
2 |
1 |
2 |
2 |
2 |
2 |
2 |
1 |
2 |
2 |
1 |
2 |
2 |
1 |
0 |
|
|
Anemopaegma. album |
1 |
1 |
2 |
1 |
2 |
2 |
2 |
2 |
1 |
2 |
1 |
2 |
2 |
2 |
2 |
2 |
1 |
2 |
2 |
1 |
2 |
2 |
1 |
0 |
|
|
Anemopaegma. arvense |
1 |
1 |
2 |
1 |
2 |
2 |
2 |
2 |
1 |
2 |
1 |
2 |
2 |
2 |
2 |
2 |
1 |
2 |
2 |
1 |
2 |
2 |
1 |
0 |
|
|
Anemopaegma. chamberlaynii |
1 |
1 |
2 |
1 |
2 |
2 |
2 |
2 |
1 |
2 |
1 |
2 |
2 |
2 |
2 |
2 |
1 |
2 |
2 |
1 |
2 |
2 |
1 |
0 |
|
|
Anemopaegma. foetidum |
1 |
1 |
2 |
1 |
2 |
2 |
2 |
2 |
1 |
2 |
1 |
2 |
2 |
2 |
2 |
2 |
1 |
2 |
2 |
1 |
2 |
2 |
1 |
0 |
|
|
Anemopaegma. glaucum |
1 |
1 |
2 |
1 |
2 |
2 |
2 |
2 |
1 |
2 |
1 |
2 |
2 |
2 |
2 |
2 |
1 |
2 |
2 |
1 |
2 |
2 |
1 |
0 |
|
|
Anemopaegma. prostratum |
1 |
1 |
2 |
1 |
2 |
2 |
2 |
2 |
1 |
2 |
1 |
2 |
2 |
2 |
2 |
2 |
1 |
2 |
2 |
1 |
2 |
2 |
1 |
0 |
|
|
type2 |
Amphilophium. gnaphalanthum |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
2 |
2 |
1 |
1 |
1 |
1 |
1 |
0 |
1 |
0 |
|
type3 |
Amphilophium. paniculatum |
1 |
1 |
2 |
1 |
1 |
2 |
2 |
2 |
1 |
2 |
1 |
2 |
2 |
2 |
2 |
2 |
1 |
2 |
2 |
1 |
2 |
2 |
1 |
0 |
|
Nb |
Amphilophium. dusenianum |
1 |
1 |
2 |
1 |
1 |
2 |
2 |
2 |
1 |
2 |
1 |
2 |
2 |
2 |
2 |
2 |
1 |
2 |
2 |
1 |
2 |
2 |
1 |
0 |
|
type4 |
Tanaecium. tetragonolobum |
0 |
0 |
1 |
0 |
0 |
1 |
1 |
0 |
1 |
1 |
1 |
1 |
0 |
1 |
1 |
1 |
0 |
1 |
1 |
0 |
1 |
2 |
1 |
2 |
|
type5 |
Incarvillea. compacta |
0 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
0 |
1 |
1 |
1 |
1 |
1 |
1 |
0 |
|
type6 |
Incarvillea. sinensis |
0 |
1 |
1 |
1 |
0 |
1 |
1 |
0 |
1 |
1 |
1 |
1 |
1 |
1 |
2 |
2 |
1 |
0 |
1 |
1 |
1 |
2 |
1 |
0 |
|
N |
Incarvillea. arguta |
0 |
0 |
1 |
0 |
0 |
1 |
1 |
0 |
1 |
1 |
1 |
1 |
0 |
1 |
1 |
1 |
0 |
2 |
1 |
0 |
1 |
2 |
1 |
1 |
|
type7 |
Neojobertia. candolleana |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
2 |
1 |
1 |
1 |
1 |
1 |
2 |
1 |
0 |
|
type8 |
Adenocalymma. allamandiflorum |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
2 |
1 |
1 |
1 |
1 |
1 |
2 |
1 |
0 |
|
type9 |
Adenocalymma. biternatum |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
2 |
1 |
1 |
1 |
1 |
1 |
2 |
0 |
0 |
|
type10 |
Adenocalymma. divaricatum |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
2 |
2 |
1 |
1 |
1 |
1 |
1 |
2 |
1 |
0 |
|
type11 |
Adenocalymma. marginatum |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
2 |
1 |
0 |
|
N |
Adenocalymma. peregrinum |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
2 |
1 |
1 |
1 |
1 |
1 |
2 |
0 |
0 |
|
type12 |
Campsis. grandiflora |
1 |
Ψ1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
0 |
1 |
1 |
1 |
2 |
1 |
1 |
1 |
1 |
1 |
1 |
2 |
1 |
2 |
|
N |
Arabidopsis. thaliana |
1 |
1 |
0 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
2 |
1 |
1 |
1 |
1 |
1 |
1 |
2 |
1 |
0 |
Due to technical limitations, Table 2 is only available as a download in the Supplemental Files section.
FigureS5 is not available with this version.