Highly variable chloroplast genome from two endangered Papaveraceae lithophytes Corydalis saxicola and C. tomentella

doi:10.21203/rs.3.rs-18411/v1

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Highly variable chloroplast genome from two endangered Papaveraceae lithophytes Corydalis saxicola and C. tomentella

https://doi.org/10.21203/rs.3.rs-18411/v1

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published 19 Mar, 2021

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Backgroud: Corydalis DC., the largest genus of Papaveraceae, is recognized as one of the most taxonomically challenging plant taxa. However, no complete chloroplast (cp) genome for this genus has been reported to date.

Results: We sequenced four complete cp genomes of two affinities Corydalis saxicola and C. tomentellav of the genus Corydalis, compared these cp genomes with each other and others from Papaveraceae, and analyzed the phylogenetic relationships based on the sequences of common CDS. The cp genomes are 189,029 to 190,247 bp in length, possessing a quadripartite structure and with two highly expanded inverted repeat (IR) regions (length: 41,955 to 42,350 bp). Comparison between the cp genomes of C. tomentella, C. saxicola and Papaveraceae species revealed high variability in genome sizes, genome structures, gene content, and gene arrangements. Five NADH dehydrogenase-like genes with psaC, rpl32, ccsA and trnL-UAG normally located in the SSC region have migrated to IRs resulting in IR expansion and gene duplication. An up to 9 kb inversion involving five genes (rpl23, ycf2, ycf15, trnI-CAU and trnL-CAA) was found within IR regions. In addition, the accD gene was found to be absent. The ycf1 gene has shifted from the IR/SSC border to the SSC region as a single copy. Phylogenetic analysis showed that genus Corydalis is quite distantly related to the other genera of Papaveraceae, supporting for recent advocacy to establish a separate Fumariaceae family.

Conclusions: Our results provide a useful resource for classification of this taxonomically complicated genus, and will be valuable for understanding Papaveraceae evolutionary relationships.

Plant Molecular Biology and Genetics

Corydalis saxicola

Corydalis tomentella

Papaveraceae

taxonomic study

cp genome

Chloroplasts (cp), generally considered to have originated from ancient cyanobacteria, are the main site of photosynthesis and energy conversion in plant cells, containing all necessary enzyme systems for photosynthesis and a complete, highly conserved genome [1–2]. With the development of high-throughput sequencing technology, cp genomics has made rapid progress [3]. The National Center for Biotechnology Information (NCBI) database included 377 complete cp genome sequences in 2010 and had more than 10,381 sequences in 2020 (https://www.ncbi. nlm.nih.gov/genome/browse/), a nearly 30-fold increase over 10 years. Currently, cp genomics research is an intense area of botanical and genomic study [4].

Correct understanding of the relationship between different biological groups is the main focus of phylogenetic biology, the basis of taxonomy and naming, and a foundation for research in other branches of biology [5]. Compared with traditional molecular markers, the cp genomes provide specific advantages for establishing plant phylogenetic relationships and taxonomic research [6]. The length of cp genomes is usually 115–165 kb, a modest size that is easily sequenced, and an appropriate nucleotide substitution frequency has produced sufficient mutagenesis for analysis. Relatively conserved gene sequences allow produce co-linearity among plant groups, and the evolution rates of coding regions and non-coding regions are significantly different to be suited for phylogenetic analysis of different ranks [7]. Taxonomists have widely used cp genomes to study plant phylogenetics and advocated for use of cp genomes as a super DNA barcode for species identification [6].

A large number of cp genome sequences have been sequenced, providing abundant data that can be used for plant phylogeny research to more accurately reveal the true evolutionary relationships between species and effectively solve difficult phylogenetic relationship problems in the study of complex taxa. Rorbert et al. clarified long-confusing phylogenetic relationships in rosids by comparing the whole cp genomes of 28 rosid species [8]. Zhang et al. analyzed plastomes from 130 species of 87 genera and offered new insights into deep phylogenetic relationships and the diversification history of Rosaceae [9]. On the basis of more abundant information sites, cp genomes have been successfully used as a "super barcode" to identify several taxonomically difficult species. Guo et al. found that the rpl32 gene in the Epimedium wushanense cp genome was deleted, and they successfully identified 11 Epimedium species by studying the evolutionary relationship of rpl32 genes [10]. Cui et al. analyzed eight cp genomes from Amomum to accurately identify Amomum villosum and related species [11]. Analysis of Lycium barbarum, L. chinense, and L. rutenicum cp genomes showed that these three plants could be successfully identified by cp genomics [12]. With the reduced cost of sequencing and the development of bioinformatics technology, cp genome analysis will be extensively used in future studies of plant systematic relationships and taxonomy.

Corydalis is the largest genus in Papaveraceae [13]. There are more than 400 Corydalis species that are widely distributed in the North Temperate Zone [14]. Corydalis has extremely complex morphological variation because of typical reticulate evolution and intense differentiation during evolution [13], including extensive interspecific hybridization and gene introgression [13–15]. Taxonomic study of the genus on the basis of morphological characteristics and DNA barcoding has been very difficult and slow, and a complete classification system has not yet been established in Corydalis [16]. Consequently, it is considered to be one of the most taxonomically complex taxa. Though cp genomes have been proven effective for phylogenetic research of many taxonomically complex taxa [2, 8–12], there currently are no published reports about cp genomes of genus Corydalis.

In this study, high-throughput sequencing and comparative genomics were used to study the cp genomes of two important medicinal plants in genus Corydalis: C. saxicola and C. tomentella. They have a very special habitat (Fig. 1), grow in dry cracks of limestone and are critically endangered. We sequenced four complete cp genome sequences from these two species, described their genomic characteristics, conducted comparisons between these genomes and other Papaveraceae cp genomes, analyzed the phylogenetic relationships on the basis of common CDS in the cp genomes.

Organization and features of tomentella and saxicola genomes

The complete C. tomentella genomes were 190,198–190,247 bp long and exhibited a typical angiosperm circular cp structure, containing four regions: large single-copy region (LSC: 96,530 − 96,701 bp), small single-copy region (SSC: 9,636-9,664 bp), and a pair of inverted repeats (IR: 41,955 − 42,002 bp) (Fig. 1). The GC content of the genome and each genomic region was also typical of the angiosperm cp style. Specific lengths and contents are shown in Fig. 1 and Table 1. The lengths of the two complete C. saxicola genomes were 189,029 bp and 189,155 bp, which were slightly smaller than those of C. tomentella. The cp genome structure, size of each region, and GC content were similar between the two species (Table 1).

Table 1

Summary of chloroplast genome features of *C. tomentella* and *C. saxicola*
Species	Voucher No.	Genbank No.	Total	Length (bp)			GC content (%)
Species	Voucher No.	Genbank No.	Total	IR	LSC	SSC	Total	IR	LSC	SSC
Corydalis tomentella	MHJ1	MT093187	190247	41955	96701	9636	40.3	42.2	39.2	35.4
Corydalis tomentella	MHJ2	MT077878	190198	42002	96530	9664	40.2	42.2	39.0	35.4
Corydalis saxicola	YHL1	MT077877	189155	42350	94744	9711	40.2	42.2	39.1	35.1
Corydalis saxicola	YHL2	MT077879	189029	42164	94993	9708	40.3	42.2	39.1	35.1

CPGAVAS2 was used to annotate the cp genomes of C. tomentella and C. saxicola. Removing duplicate genes, a total of 119 annotated genes (Fig. 2, Table 2 and S1), including 78 protein-coding genes, 37 tRNA genes, and four rRNA genes, were identified from the C. tomentella. There were 28 genes in the IR region, of which 15 were involved in gene expression. Introns greatly affect regulated selective splicing in the genome. There were 19 genes that contain introns in the C. tomentella cp genome. Most intron genes contained only one intron, while the ycf3 gene contained two introns. There were 12 introns with a length of more than 700 bp, and the longest gene was trnK-UUU with a length of 2,478 bp. The gene features of C. saxicola cp genome were similar to those of C. tomentella. The C. saxicola cp genome contained 120 genes, including 78 protein-coding genes, 38 tRNA genes, and four rRNA genes. Nineteen genes contained introns. The longest intron gene in the C. saxicola cp genome was trnK-UUU, and its length was also 2,478 bp (Fig. 2, Table 2 and S1).

Table 2

List of genes in the two *Corydalis* chloroplast genomes
Group of genes	Gene names	Number of Genes
Photosystem I	psaA, psaB, psaC(× 2), psaI(× 2), psaJ	5(2)
Photosystem II	psbA, psbB, psbC, psbD, psbE, psbF, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ	14
Cytochrome b/f complex	petA, petB, petD, petG, petL, petN	6
ATP synthase	atpA, atpB, atpE, atpF, atpH, atp*I	6
NADH-dehydrogenase	ndhA, ndhB(× 2), ndhC, ndhD(× 2), ndhE(× 2), ndhF(× 2), ndhG(× 2), ndhH, ndhI(× 2), ndhJ, ndhK,	11(6)
RubisCO large subunit	rbcL	1
DNA dependent RNA polymerase	rpoA, rpoB, rpoC1, rpo*C2	4
Small subunit of ribosome	rps2, rps3, rps4, rps7(× 2), rps8, rps11, rps12(× 2), rps14, rps15, rps16, rps18, rps19	12(2)
Large subunit of ribosome	rpl2(× 2), rpl14, rpl16, rpl20, rpl22, rpl23(× 2), rpl32(× 2), rpl33, rpl36	9(3)
Proteins of unknown function	ycf1, ycf2(× 2), ycf3*, ycf4, ycf*15(× 2)	5(2)
Other genes	ccsA(× 2), cemA, infA, matK, clpP**	5(1)
Transfer RNAs	37 tRNAs(C. tomentella); 38 tRNAs(C. saxicola)	37/38
Ribosomal RNAs	rrn16S(× 2), rrn23S(× 2), rrn4.5S(× 2), rrn5S(× 2)	4(4)
*One or two asterisks followed genes indicate the number of contained introns, respectively. (× 2) indicates the number of the repeat unit is 2. The numbers in parenthesis at the line of ‘Number’ indicate the total number of repeated genes.

Codon usage bias, SSRs analysis, and repeat sequences

Coding sequence codon usage patterns for the C. tomentella and C. saxicola cp genomes were calculated on the basis of relative synonymous codon usage (RSCU) values. We defined codons with RSCU values greater than 1.00 to be used more frequently, and vice versa. All protein-coding genes in the C. tomentella and C. saxicola cp genomes were encoded by 52,244 codons and 51,125 codons, respectively (Table S2). The most prevalent amino acid was Leucine in the cp genomes of C. tomentella (5,656; 10.83%) and C. saxicola (5,528; 10.81%). Conversely, the least frequently utilized amino acid was Cysteine in the cp genomes of these two species(591–634; 1.16–1.18%). The third position nucleotides in each codon of all the coding genes had a high AT content, at 65.83% and 65.91% for C. tomentella and C. saxicola, respectively.

SSRs are short tandem repeats of 1–6 bp DNA sequences that are widely distributed throughout the cp genome [17]. In this study, CPGAVAS2 software was used to analyze the sequences and the classification statistics of SSRs with a length greater than or equal to 8 bp. Here, we analyzed the distribution and the type of SSRs contained in C. tomentella and C. saxicola cp genomes. A total of 172 SSRs were identified in the whole C. tomentella cp genome (take MHJ1 as an example), including 100 mono-, 34 di-, and one compound nucleotide SSRs. Among all SSR types, A and T were the most commonly used bases and 116 SSRs in the C. tomentella cp genome had A, T, or AT repeat units (Table 3 and S3). For C. saxicola, 170 SSRs (take YHL2 as an example) were categorized as 96 mono-, 36 di-, six tri- and six compound nucleotide SSRs, including 115 SSRs with A, T, or AT repeat units (Table 3 and S3).

Table 3

Interspersed repeat sequences and tandem repeat sequences of *C. saxicola* and *C. tomentella*
Species	Voucher No.	SSR		Interspersed repeat sequences
Species	Voucher No.	Total	Mono SSR	total	T	F	P
Corydalis tomentella	MHJ1	172	100	111	61	39	11
Corydalis tomentella	MHJ2	174	102	112	62	39	11
Corydalis saxicola	YHL1	171	96	132	82	23	27
Corydalis saxicola	YHL2	170	96	133	83	26	24
T: tandem repeats, F: Forward repeats and P: palindromic repeats.

In addition to SSRs, forward repeats (F) and palindromic repeats (P) are also called interspersed repeat sequences (length ≥ 30 bp). In the C. tomentella cp genome, there were 112 interspersed repeat sequences, comprised of 64 tandem repeats, 39 forward repeats, and 11 palindromic repeats (Table 3). A total of 132 long repeats were present in C. saxicola cp genome, comprised of 82 tandem repeats, 23 forward repeats, and 27 palindromic repeats (Table 3). Comparing the cp genomes of the two species, the C. saxicola genome had a greater total number of repeats than the C. tomentella cp genome, and the cp genome repeat content in both species was significantly higher than that of most species.

IR contraction and expansion

IR regions are the most conserved regions in the plant plastome, contraction and expansion at their borders are regarded as the major causes of size variation [18–19]. We selected four phylogenetically close species (Papaver rhoeas, Papaver orientale, Papaver somniferum, and Coreanomecon hylomeconoides) and two model species (N. tabacum and Arabidopsis thaliana) as references for cp genome structure comparisons. Figure 3 displays the detailed information about the boundaries between IR/SSC and IR/LSC in the eight species.

Except for C. tomentella and C. saxicola, the IRb/SSC boundaries were generally positioned in the coding region of the ycf1 gene, resulting in duplication of the 3′ end of this gene. This duplication also produced a variably sized pseudogene ycf1 at the IRa/SSC border. The length of the ycf1 pseudogene varied from 916 bp to 1,200 bp. However, the ycf1 genes in C. tomentella and C. saxicola cp genomes have been transferred to the SSC region to become a single copy gene. Except for C. tomentella, C. saxicola and N. tabacum, the LSC/IRb borders of other species were located within the rps19 coding region. Correspondingly, a 3’-truncated rps19 pseudogene with a length of 74 bp to 113 bp was located at the IRb/LSC border. In the C. tomentella cp genome, the LSC/IRb border was located in the rpl2 coding region. Additionally, in C. tomentella and C. saxicola cp genomes, the IRa/SSC boundaries were positioned in the ndhA coding region, and trnN was situated in the IRa and IRb regions, away from the LSC/IRa and IRb/LSC borders. The trnH gene was present in LSC regions, away from the IRb/LSC border.

Comparative genomic analysis and genome sequence divergence

VISTA software was used to make multiple comparisons of the C. tomentella and C. saxicola cp genome sequences, and results show that intra-specific variation was small but there were still some inter-specific differences (Fig. 4). The coding and non-coding regions of C. saxicola samples were conserved, while the coding regions of C. tomentella samples were conserved but there were differences in several consecutive intergenic regions of rps12-clpP, clpP-psbB, and petB-psbH. Comparing C. tomentella and C. saxicola, the most highly divergent regions mainly was observed in coding regions and intergenic regions, including rpl20, rrn23s, trnH-GUG, trnN-GUU, rps12-clpP, clpP-psbB, petB-psbH, and ycf1-ndhL. On the basis of morphological features and cluster analysis of DNA barcodes, it was found that the two species are closely related and difficult to identify accurately. The cp genome differences between the two species have potential for use as molecular markers for species authentication.

Comparisons with the N. tabacum outgroup and Papaveraceae family plants P. rhoeas, P. orientale, P. somniferum, and C. hylomeconoides showed that C. tomentella and C. saxicola cp genomes have distinct cp genome structures. The differences included genome size, number of genes, and genome structure (Fig. 5). First, the C. tomentella and C. saxicola cp genome sizes (189.1-190.2 kb) were larger than those of N. tabacum (155.9 kb) and P. somniferum (152.9 kb). Second, the length of intergenic regions in C. tomentella and C. saxicola cp genomes were longer than those in N. tabacum and P. somniferum, as seen, for example, in the lengths of intergenic regions for psal/rpl32 (7 kb) in the IR region and rps12/clpP (5 kb) in the LSC region. Third, C. tomentella and C. saxicola cp genome structures were significantly different from those of the other six species, including large-scale gene replication, movement, reversal, and changes in the number and arrangement of genes. Fourth, C. tomentella and C. saxicola IR regions were highly dilated (41.9–42.5 kb). The ndhF, ndhD, ndhL, ndhG, ndhE, psaC, ccsA, trnL-UAG and rpl32 genes, usually located in the SSC region, migrated to the IR regions to become double-copy genes (Fig. 1). A few rpl19 and rpl2 genes migrated from the IR region to the LSC region. In particular, in C. tomentella and C. saxicola, there is a large fragment (containing rpl23, trnL-CAU, ycf2, ycf15, and trnL-CAA) that moved within the IR region. Gene migration increased the length of the IR region and decreased the length of the SSC region. Fifth, the LSC region was highly conserved, but the accD gene was lost and the position of the rbcL gene changed substantially. In short, both the coding and non-coding regions of C. tomentella and C. saxicola cp genomes differ greatly from those of other Papaveraceae and tobacco.

Phylogenetic analysis of Papaveraceae

With C. chinensis and N. tabacum as outgroups, common protein coding sequences from 13 cp genome sequences were extracted from C. saxicola, C. tomentella, and six Papaveraceae species (P. somniferum: NC029434, P. orientale: NC037832, P. rhoeas: MF943221, Coreanomecon hymenoides: NC031446, Macleaya microcarpa: NC039623, and Meconopsis racemosa: MH394401 NC039625) to build a Maximum Likelihood (ML) phylogenetic tree (Fig. 6). The ML tree has high bootstrap values at each node, indicating a highly credible tree. In this ML tree, the Papaveraceae family is monophyletic, and all samples from Papaveraceae are clustered in a clade. In Papaveraceae, the samples from the genus Papaver (P. somniferum, P. orientale, and P. rhoeas) are clustered in a clade; the samples from Corydalis (Corydalis saxicola and Corydalis tomentella) are clustered in a clade; the samples from Meconopsis (M. racemosa) are clustered in a clade; and C. hymenoides and M. microcarpa are clustered in a clade. Except for Coreanomecon and Macleaya genera, which had only one sample, species in the same genera are clustered into one branch, consistent with previous classification of Papaveraceae genera. At the species level, the C. saxicola and C. tomentella samples are clustered into separate branches, indicating that the cp genome clustering analysis could effectively distinguish them, while these two closely related species were not monophyletic in the Phylogenetic analysis based on short sequence DNA barcodes. At the same time, C. saxicola and C. tomentella are clustered in a clade in the ML phylogenetic tree that is distant from other Papaveraceae genera. On one hand, this shows that C. saxicola and C. tomentella, both from Sect. Thalictrifoliae in Corydalis, have a close genetic relationship. On the other hand, it also shows that Corydalis has a relatively distant genetic relationship with the other Papaveraceae genera included in this study.

High variability of genome size and the expansion of IRs

C. saxicola and C. tomentella cp genomes are among the largest cp genomes due to expansion of IR regions. Most angiosperms cp genomes are highly conserved, typically 115–165 kb in size and possessing a quadripartite structure with two IR regions (IRa and IRb) separating the LSC region and the SSC region the LSC region [19]. The sizes of C. saxicola and C. tomentella cp genomes are larger than those of most flowering plants, such as N. tabacum [20–22], 30–40 kb larger than those reported genomes in Papaveriaceae, such as P. somniferum [23] and C. hymenoides [24]. Distinctions between different cp genomes mainly result from the variability of the length and direction of IR regions [25]. In terms of length, IR regions of the genus Taxodium (T. distichum, T. mucronatum and T. ascendens) contracted to about 282 bp [26], while IR regions were entirely absent in Pisum sativum and Cryptomeria japonica [27–28]. In contrast, the length of Pelargonium hortorum IR regions expanded to 76 kb [25]. Numerous studies have shown that IR region lengths are the main factor influencing cp genome size [29]. In our study, IR region lengths for the two newly sequenced species were 41,955 bp to 42,350 bp, which significantly increased their cp genome sizes over that of other Papaveraceae species. Genes normally located in the SSC region, such as ndhC, ndhD, ndhE, ndhF, ndhG, ndhL, rpl32 and trnL-UAG, have moved to IR regions, contributing to the expanded size of C. saxicola and C. tomentella IRs.

Gene inversions, duplications, and deletions

Inversions usually serve as useful phylogenetic markers [30–32]. An up to 9 kb inversion containing five genes (rpl23, ycf2, ycf15, trnL-CAU and trnL-CAA) was found in the IR regions of C. tomentella and C. saxicola cp genomes. Relatively large inversions have emerged in some other flowering plants. The 22.8 kb inversion is present in all Asteraceae, except Barnadesioideae [32–33], the 36 kb and 78 kb inversions have been detected in core genistoid legumes and Fabaceae subtribe Phaseolinae, respectively [34–35]. These distinctive inversions serve as phylogenetic markers. The inversion in C. tomentella and C. saxicola is quite distinct from other sequenced Papaveraceae species. To determine if it can be used as a phylogenetic marker of genus Corydalis, more species will need to be sequenced. In some plants, the large inversions have been found to be associated with short inverted repeats in cp genome [26, 30, 36–37]. In Geraniaceae, Campanulaceae and some Fabaceae species, a mass of short inverted repeats have been found to be present at their inversion endpoints [29–30]. However, we didn't detect large numbers of short inverted repeats emerged in inversion endpoints in C. tomentella and C. saxicola.

Several NDH (NADH dehydrogenase-like) genes (ndhD, ndhE, ndhF, ndhG, ndhL) are duplicated in the C. tomentella and C. saxicola cp genomes, which could provide an explanation for their robust adaptability to harsh environments. Large-scale duplication of cp genes tends to occur only in highly rearranged genomes and can be explained by repeated expansion and contraction of IRs [38–39]. In this study, genes that are normally located in the SSC region (ndhD, ndhE, ndhF, ndhG, ndhL, psaC, rpl32, ccsA and trnL-UAG) have migrated to IRs resulting in IR expansion and gene duplication. We found that most of these duplicated genes belong to the NDH complex. Because of plastid NDH genes are dispensable under optimal growth conditions, which have been lost in a number of autotrophic and heterotrophic lineages, although they are widely retained across land plants [29, 37–39]. For example, plastid NDH genes have been partially lost or pseudogenized in parasitic plants, such as several orchids and Petrosavia (Petrosaviaceae), and autotrophs plants, such as Najas (Hydrocharitaceae) and Erodium (Geraniaceae) [38], even they have been completely lost in Selaginella tamariscina [40]. Conversely, it is rare for NDH genes to undergo large-scale duplication and augmentation, and the effects of the increased genes resulting from gene duplication on plant growth and development have rarely been discussed in previous research. The NDH complex participates in photosystem I (PSI) cyclic electron flow (CEF), chlororespiration. NDH-dependent CEF provides additional pH change and ATP for CO₂ assimilation and alleviates oxidative stress caused by stromal over-reduction under stress conditions [38–39]. The non-photochemical quenching ability of NDH deficient mutants decreased under mild drought [43]. NDH deficient mutants grow slowly at low humidity [42]. Under strong light, tobacco ndhB mutants were more susceptible to photobleaching [43]. Under heat stress conditions, NDH-mediated cyclic and chlororespiratory electron transport are accelerated, mitigating photo-oxidative damage and inhibition of CO2 assimilation caused by high temperature [44]. C. tomentella and C. saxicola mainly grow in dry cracks of limestone, a unique environment with little available soil and water [45] (Fig. 1). So they have long been subjected to extreme environmental conditions, such as high temperature, drought, and low light. In view of NDH gene functions in plant defense against various environmental stresses, the doubling of NDH genes those results from IR expansion could lead to overexpression of these doubled genes, which would be helpful for adaptation to harsh environmental conditions. The special structure of the C. tomentella and C. saxicola cp genomes provides a clue that could explain their robust adaptation to harsh environments.

The accD gene was absent in C. saxicola and C. tomentella cp genomes. Usually, gene content is highly conserved among photosynthetic angiosperm cp genomes [29, 46], but in a very few plants, for example, legumes and Circaeasteraceae [40, 47], a number of genes have been lost or pseudogenized. The loss of accD in the cp genome is mirrored in other plant taxa, such as grasses, Circaeasteraceae and Oleaceae [29, 30, 37]. The accD gene encodes an acetyl-CoA carboxylase subunit and is an important regulator of carbon flow entering the fatty acid biosynthesis pathway [48]. It is known to be essential for leaf development in angiosperms [49–50]. Recent research has shown that the accD gene present in the plastome of most angiosperms is functional [48, 50]. Furthermore, several studies have shown that the accD gene has been transferred into the nucleus, and the proteins it encodes are transported from the nucleus to the chloroplast to function in the form of a transfer peptide [37–48, 50–51]. Whether the C. tomentella and C. saxicola accD genes have been lost or transferred to the nucleus, the effects on development are currently unknown.

Papaveraceae phylogenetic relationships and potential application of cp genomics in Corydalis

By exhibiting high species identification power that accurately distinguished two closely related species (C. saxicola and C. tomentella), cp genomes have demonstrated a great potential for use as a super-barcode to discriminate Corydalis species. Genus Corydalis, is considered to be one of the most taxonomically complex taxa [13]. It is extremely difficult to depend on morphological characteristics for Corydalis species identification. Single-locus DNA barcodes lack adequate variation in closely related taxa. Researches using short sequence gene fragments and DNA barcodes showed that both nuclear genome (ITS/ITS2) sequence and cp genome (matK/rbcL/rps16) sequence produced unsatisfactory taxonomic identifications within Corydalis [14, 45, 52]. Cp genomes, exhibiting many advantages, including a moderate size and an appropriate frequency of nucleotide substitutions that can provide sufficient mutation sites [29], have been successfully used in the identification of various taxa, such as genera Epimedium [10] Fritillaria [53], Epipremnum [54], and Papaver [55]. In this study, C. saxicola and C. tomentella, two closely related species from Section Thalictrifoliae in Corydalis, are clustered into two branches in the phylogenetic tree, which indicates they could be accurately distinguished by cp genome analysis. While, these two affinities were not monophyletic in the phylogenetic analysis based on short sequences of DNA barcodes and couldn't been effectively distinguished. Recent barcoding studies have placed a greater emphasis on the use of whole-cp genome sequences, which are now more readily available as a consequence of improving sequencing technologies [3]. The demonstrated use of cp genomics in Corydalis species identification suggests that it has a great potential for taxonomic identification of this genus.

The cp genomics also efficiently identified Papaveraceae genera. The evolution rates of coding and non-coding regions are significantly different in cp genomes, enabling cp genome use for systematic analysis of different phylogenetic ranks [7]. Genus Corydalis belongs to Papaveraceae Fumarioideae (Corydaleae) and the phylogenetic relationships between this genus and its relatives remain controversial [13]. Recent studies have tended to treat genus Corydalis and closely related genera as an independent Fumariaceae family because the morphological characteristics of this family constitute a unique evolutionary series [15–16, 56–58]. In this study, a Papaveriaceae phylogenetic tree, built using common protein coding sequences, shows that each genera is clustered into one branch. However, Corydalis species are clustered into a distinct clade that is quite distant from other Papaveriaceae genera. Combined with the substantial differences in cp genome structures between Corydalis and other Papaveriaceae genera, these results provide preliminary molecular evidence that supports classifying Corydalis as a separate Fumariaceae family. However, because there were few species included in this study, it will be necessary to analyze additional representative species in further studies.

Materials, DNA extraction and sequencing

Plant materials were provided by the Chongqing Institute of Medicinal Plant Cultivation and identified by researcher Zhengyu Liu as C. tomentella Franch. and C. saxicola Bununting. We collected young leaves from selected plants that were vigorous, healthy, and disease-free. These leaves were wiped with 70% alcohol and repeatedly washed with sterile water before genomic DNA extraction. Total DNA was extracted using a Tiangen plant genomic DNA extraction kit, and the DNA quality and concentration were detected using 1% agarose electrophoresis and a Nanodrop2000. Qualified total DNA was sent to Shanghai Biotech for sequencing with the Illumina HiSeq4000 platform.

Genome assembly and annotation

Referring to the method of Li et al. [4], cp genomes were assembled on a Linux system using BLAST+, capturereads.py, soapdenovo-127mer, and SSPACE-Basic-v2.0.pl software [4, 55]. The completed genomes were annotated using CPGAVAS2 [59], and the results were modified for starter and terminator revisions by Apollo software [60]. CPGAVAS2 software was used to convert revised GFF3 format annotation results into a sqn format for NCBI submission. Sequin software was used to check and correct unsatisfactory comments in the sqn file, and the corrected results were submitted to the NCBI database [4]. Physical maps of the cp genomes were drawn by GenomeDRAW [61] using a GB format file exported from the sqn file by sequin software.

Genome structure analyses and genome comparison

GC content was analyzed using Mega 6.0 software [55, 62]. The distribution of codon usage was investigated using CodonW software with the RSCU ratio [55, 63]. MISA software (http://pgrc.ipk

-gatersleben.de/misa/) was used to detect simple sequence repeats (SSRs) [64]. Parameters were set as follows: no less than 8 single-base repeat units; no less than 4 units with 2, 3 bases in one unit; and no less than 3 units with 4, 5, 6 bases in one unit [65]. Tandem Repeats Finder v4.0.4 software [66] was used to detect tandem repeat sequences, and the default parameter was set to 2–7 -7 -80- 10 -50- 500-f-d-m [4]. REPuter software (http://bibiserv.techfak.uni-bielefeld.de/reputer) was used to detect scattered repeating sequences (> 30 bp) using the parameter: hamming distance = 3 [4, 67]. VISTA software was used to compare multiple cp genomes [68].

Phylogenetic analysis

A total of 15 cp whole genome sequences were used in cluster analysis. Thirteen genomes were from Papaveraceae (four Corydalis genomes, five Papaver genomes, two Meconopsis genomes, one Macleaya, and one Coreanomecon genome), and Coptis chinensis and Nicotiana tabacum genomes were included as outgroups. Of the Papaveraceae genomes, four genomes were newly sequenced in this study, and nine genomes were downloaded from the NCBI database. Common protein coding sequences were extracted from the cp genome sequences [4], and multiple global alignments of the protein coding sequences was performed using the Clustalw module in MEGA6.06 software [62]. The maximum-likelihood tree (ML) was constructed on the basis of the alignments of common protein sequences and full-length cp genome sequences by MEGA6.06 software [62].

In this study, we sequenced and characterized four complete cp genomes for C. tomentella and C. saxicola from Papaveraceae. Comparisons of these cp genomes indicated high similarity. In comparisons of these cp genomes with those from other Papaveraceae species, C. tomentella and C. saxicola cp genomes exhibited large variations in genome sizes, genome structures, gene content and gene arrangements. C. saxicola and C. tomentella have large cp genome sizes of 189,029 bp to 190,247 bp, which are the results of IR expansion to sizes as large as 42,350 bp. Genes (ndhF, ndhD, ndhL, ndhG, ndhE, psaC, ccsA, rpl32 and trnL-UAG genes) normally located in the SSC region have migrated to IRs resulting in IR expansion and gene duplication. Duplication of the NDH genes may contribute to C. saxicola and C. tomentella adaptation to harsh environments. An up to 9 kb inversion containing five genes (rpl23, ycf2, ycf15, trnl-CAU and trnL-CAA) was found in IR regions. In addition, accD was found to have been deleted. The ycf1 gene has shifted from the IR/SSC border to the SSC region as a single copy. In its place, ndhA and rpl2 were located at the IR/SSC border and as partial genes (pseudogenes) in other IR regions. Phylogenetic analysis showed that genus Corydalis is quite distantly related to the other Papaveraceae genera. Thus, these cp genome characteristics provide preliminary molecular evidence that supports recent suggestion to create a separate Fumariaceae family. Our results provide a useful resource for classification and identification of this taxonomically complicated genus, and will be valuable for understanding Papaveraceae evolutionary relationships.

cp: chloroplast; IR: inverted repeat; NCBI: National Center for Biotechnology Information; LSC: large single-copy region; SSC: small single-copy region; IR: inverted repeats; RSCU: relative synonymous codon usage; PSI: photosystem I; CEF: cyclic electron flow; T: tandem repeats; F: forward repeats; P: palindromic repeats; ML: Maximum Likelihood; NDH: NADH dehydrogenase-like; ML: maximum-likelihood; SSR: simple sequence repeats.

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Availability of data and materials

The collection of plant material was complied with institutional and national guidelines. The field of the study was conducted in accordance with local legislation. Four plastomes sequenced in this study have been deposited in the National Center for Biotechnology Information (NCBI) genome database (https://www.ncbi.nlm.nih.gov/) (Accession numbers: see Table 1). All sequences used in phylogenetic analysis of Papaveraceae are available from NCBI (Accession numbers: see the “Phylogenetic analysis of Papaveraceae” in Result section).

Competing interests

The authors declare no conflict of interest.

Funding

This research was funded by National Natural Science Foundation of China (81874339); National Science and Technology Major Project for "Significant New Drugs Development" (2019ZX09201005-006-003); Science and Technology Project of Traditional Chinese Medicine in Chongqing (ZY201702143) and 2019 Basic Scientific Research Project of Chongqing (19KF10-2012). The funders did not play any roles in the design of the study, collection, analysis and interpretation of the relevant data, and writing the manuscript.

Author’s Contributions

Conceptualization: S.J.-Y. and R.F.-M.; Formal analysis: L.Y.(Li), Z.W. and X.Z-C.; Funding acquisition: S.J.-Y.; Software: W.L.-Q., L.Y.(Li), X.Z-C. and G.H-J.; Validation: G.R.-R; Writing-original draft: R.F.-M. and Z.W.; Writing-review & editing: W.L.-Q., L.Y. and S.J.-Y. All co‐authors approved the manuscript before submission. All authors have read and agreed to the published version of the manuscript.

Acknowledgments

We are grateful to Jianguo Zhou and Yuanyao Xin for support and troubleshooting.

Authors' information

¹Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China. ²Chongqing Institute of Medicinal Plant Cultivation, Research and Utilization on Characteristic Biological Resources of Sichuan and Chongqing Co‐construction Lab, Chinese Medicine Breeding and Evaluation Engineering Technology Research Center of Chongqing, Chongqing 400010, China. ³College of Pharmacy, Heze University, Heze 274015, Shandong Province, China. ⁴Wuhu Institute of Technology, Wuhu 241000, Anhui Province, China. ⁵Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China

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Highly variable chloroplast genome from two endangered Papaveraceae lithophytes Corydalis saxicola and C. tomentella

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Abstract

Figures

Background

Results

Organization and features of tomentella and saxicola genomes

Codon usage bias, SSRs analysis, and repeat sequences

IR contraction and expansion

Comparative genomic analysis and genome sequence divergence

Phylogenetic analysis of Papaveraceae

Discussion

High variability of genome size and the expansion of IRs

Gene inversions, duplications, and deletions

Papaveraceae phylogenetic relationships and potential application of cp genomics in Corydalis

Methods

Materials, DNA extraction and sequencing

Genome assembly and annotation

Genome structure analyses and genome comparison

Phylogenetic analysis

Conclusions

Abbreviations

Declarations

References

Supplementary Files

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