Plastome phylogenomic and biogeographic study on Thuja (Cupressaceae)

doi:10.21203/rs.2.13750/v1

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Plastome phylogenomic and biogeographic study on Thuja (Cupressaceae)

https://doi.org/10.21203/rs.2.13750/v1

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Background: Investigating the biogeographical disjunction of East Asia and North America flora is the key to understanding the formation and dynamic biodiversity in the Northern Hemisphere. The small Cupressaceae genus Thuja, comprising five species, exhibits a typical disjunct distribution in East Asia and North America. Owing to the obscure relationships, the biogeographical history of the genus remains controversial. Here, complete plastomes were employed to investigate the plastome evolution, phylogenetic relationships and biogeographic history of Thuja.

Results: All plastomes of Thuja share the same gene contents arranged in the same order. The loss of an IR was evident in all Thuja plastomes, and the B-arrangement as previously recognized was detected. Phylogenomic analyses resolved two sister pairs, T. standishii-T. koraiensis and T. occidentalis-T. sutchuenensis, with T. plicata sister to T. occidentails-T. sutchuenensis. Molecular dating and biogeographic result suggest the diversification of Thuja occurred in the Middle Miocene, and the ancestral area of extant species was located in northern East Asia. Incorporating the fossil record, we inferred that Thuja likely originated from the high-latitude areas of North America in the Paleocene with a second diversification center in northern East Asia.

Conclusions: The dispersal events attributed to the Bering Land Bridge in the Miocene and subsequent vicariance events accompanying climate cooling may have shaped the current geographic distributions of Thuja. Given most lineages of gymnosperm, including Thuja, have encountered massive extinction resulted from climatic oscillations, we here advocate that the potential effect of extinction should be re-evaluated in exploring the evolutionary history of gymnosperms.

Evolutionary Biology

Evolutionary Developmental Biology

Thuja

Plastome phylogenomic

Biogeography

Eastern Asia–North America disjunction

Diversification

Extinction

Understanding the differences and connections of biogeographic distribution patterns between the flora of the Northern Hemisphere, especially the flora of East Asia and North America, has been of great interest to systematists and biogeographers since the last century [1–8]. Multiple studies suggest that the geological activities and climatic oscillation in the Cenozoic, especially in the Late Tertiary and Quaternary, have been responsible for plant biogeographic patterns of intercontinental disjunction [9–12]. In addition, two intercontinental land bridges, the Bering and the North Atlantic Land Bridges, have also played vital roles in the formation and dynamic floristic disjunctions due to their connectivity at different time points [4, 5, 8, 10]. Previous studies have shown that in angiosperm lineages, the prevalent pattern is origination in east Asia followed by migration to North America [13–16], while the opposite case, species originating in North America and then migrating to East Asia, has also been reported in some gymnosperms [17–20]. Given that gymnosperms originated much earlier than angiosperms, they have been proposed as an ideal system for understanding the deep biogeographical patterns, in particular those of an intercontinental nature.

Thuja is a small genus of Cupressaceae comprising five species: T. plicata Donn ex D. Don, T. occidentalis L., T. koraiensis Nakai, T. standishii (Gordon) Carrière and T. sutchuenensis Franch [21, 22]. Species of Thuja are discontinuously distributed across East Asia and North America. Species T. plicata and T. occidentalis are distributed in western and eastern North America respectively, whereas T. koraiensis, T. standishii and T. sutchuenensis are endemic to East Asia with quite restricted distributions [23, 24].

The biogeographic history of Thuja remains controversial due mainly to the ambiguous relationships among species, despite several phylogenetic studies having been conducted [23–25]. Early phylogenies of Thuja, including both extant and fossil species, inferred that T. sutchuenensis may have arisen from an ancestor similar to the fossil species T. polaris and represents the basal clade of Thuja [25]. Molecular evidence from nrDNA ITS sequences of Thuja suggested that T. standishii and T. sutchuenensis were sister and they together formed a clade with T. occidentalis, while T. koraiensis and T. plicata formed another clade. Based on the ITS tree, an eastern Asia origin and two dispersals to North America were inferred for Thuja [23]. Later, a phylogenetic study using five cpDNA regions (rpl16, AtpI-rpoC1, trnS-trnfM, trnS-trnG, trnT-trnF),, nrDNA ITS and two low-copy nuclear genes (LEAFY, 4CL) showed high topological discordance between chloroplast and nuclear gene trees, with discordance even occurring between the different nuclear gene trees [24]. In that study, the sister relationship of T. sutchuenensis-T. standishii was supported by both chloroplast and nuclear genes, whereas the sister relationship of T. koraiensis-T. plicata was supported in the 4CL, nrDNA ITS and combined nuclear gene trees. Biogeographic analysis based on the 4CL tree showed that the most recent common ancestor (MRCA) of Thuja likely had a wide distribution in East Asia and North America [24]. Additionally, comparisons with living species and species known only in the fossil records showed that Thuja likely first appeared at high latitudes of North America before the Paleocene and spread to eastern Asia in the Miocene [26]. Owing to the relatively incompatible hypotheses proposed previously, the evolutionary history of Thuja still needs further investigation.

Phylogenomic approaches, which generate large amounts of DNA sequence data throughout the genome, have become increasingly essential for reconstructing entangled phylogenetic relationships among gymnosperms [27–29]. However, because of the extremely large genome sizes in gymnosperms [19, 30, 31], phylogenomic studies based on the nuclear genome still presents significant challenges, most notably in expense and annotation. In contrast, plastomes, which exhibit a high copy number per cell and a much smaller size, have been successfully implemented in the phylogeny of gymnosperms such as in the Pinaceae [32, 33] and Cupressaceae [34, 35]. Furthermore, the structural variations in plastomes are phylogenetically informative characters themselves, for instance, the conifers (which Thuja belongs to) are characterized by lacking canonical inverted repeats (IRs) and containing lineage-specific repeated tRNA genes [36–41]. Given the fundamental role of plastomes in understanding gymnosperm evolution, studies within each family/genus of conifers are insufficient to date.

In the present study, we newly sequenced three plastomes of Thuja. Including two previously reported plastomes [40, 42], we aim to (i) understand the plastome evolution of Thuja; and (ii) reconcile the phylogenetic relationships within this small genus; and (iii) investigate the biogeographical history of Thuja. Additionally, rich molecular markers will be obtained as genetic resources for future research.

Plastome assembly, structure, and gene content

After de novo and reference-guided assembly, we obtained three plastome sequences without gaps. The plastome features of all Thuja species are presented in Table 1. The size of Thuja plastomes range from 130,505 bp in T. standishii to 131,118 bp in T. occidentalis. A total of 116 genes are identified including 82 protein-coding genes, 4 ribosomal RNAs and 30 transfer RNAs (Fig. 1). Among the 116 unique genes, there are 15 genes that contain one intron (seven tRNA genes and eight protein-coding genes) and three protein-coding genes containing two introns (rps12 and ycf3).. Two tRNA genes, trnI-CAU and trnQ-UUG, have two copies (Table 2). Similar to other conifers, all species of Thuja are found to lack the Inverted Repeat (IR) regions, thereby differing from the conventional quadripartite structure typical of angiosperm plastomes (Fig. 1). In addition, a 36-kb inversion is detected in all Thuja plastomes, resulting in an isomeric plastome with the same B-arrangement as previously recognized. This inversion segment is precisely flanked by the duplicates of the trnQ-UUG gene (Figs. 1, S1).

Repetitive sequences

We characterized SSRs without setting a minimum satellite length constraint, thus, abundant molecular markers were obtained. The numbers and types of SSRs are quite similar in all plastomes, with the total number ranging from 700 in T. koraiensis to 723 in T. standishii (Fig. 2a). The proportion for each type of SSRs are shown (Fig. 2b). A total of 117 tandem repeats are detected in all five plastomes, with the number ranging from 20 in T. sutchuenensis to 26 in T. standishii. Among the 117 tandem repeats, 82 of them are located in intergenic regions (IGR) and 35 of them are in coding regions (CDS) (Fig. 2c). The detailed information of SSRs and tandem repeats are provided in Appendix (Table S2-S11).

Phylogenetic analyses

After trimming of poorly aligned fragments, the final alignment contained 82-genes for 34-taxa consisting of 67,044 bp. ML and BI analyses yielded identical tree topologies (Fig. 3; BS value and PP are depicted in one tree). All nodes included in our phylogeny obtained robust support. The sister relationship between Thuja and Thujopsis is supported with 100% bootstrap support and 1.0 posterior probability. Two clades are resolved within Thuja in the present phylogenetic analyses. T. plicata is sister to the clade formed by T. sutchuenensis and T. occidentalis, they together are sister to the T. standishii and T. koraiensis alliance.

Divergence time estimation

The BEAST analysis based on 82 protein-coding regions, yielded effective sample sizes that were well above 200 for all parameters, indicating adequate sampling of the posterior distribution. The MRCA of Thuja and Thujopsis was dated to 62.7 Ma (95% highest posterior density (HPD), 59.69–67.69 Ma). The divergence time among species of Thuja was estimated to be 16.33 Ma (95% HPD, 8.46–26.85 Ma). The time of MRCAs of the two recognized sister pairs, T. standishii-T. koraiensis and T. occidentails-T. sutchuenensis, were approximately 11.61 Ma (95% HPD, 4.55–21.23 Ma) and 6.95 Ma (95% HPD, 2.05–14.29 Ma), respectively. The split time between T. plicata and T. sutchuenensis-T. occidentalis was estimated to be 10.94 Ma (95% HPD, 4.47–16.19 Ma).

Biogeographic result of Thuja

Model tests in the BioGeoBEARS package suggested that DEC +J is the better-performing model than the DEC model (AICc values: DEC +J = 30.2, DEC = 33.85, p = 0.0002). The DEC +J analysis showed the distribution area of Thuja is most likely to be northern East Asia (approx. 0.46), or less likely western North America (approx. 0.18) and northern East Asia/western North America (approx. 0.10). This may indicate that the MRCA of extant Thuja had a wide distribution in East Asia and North America. In addition, six dispersal and three vicariance events were identified within Thuja.

Characterizations of Thuja plastomes

Prior to this study, only two Thuja species had sequenced plastomes available [40, 42]. In the present study, we incorporated three newly sequenced plastomes with two previously reported ones, which provided the opportunity to illustrate plastome evolution, as well as identify valuable molecular markers. All plastomes of Thuja possess 116 unique genes arranged in the same order, including 82 protein coding genes, 30 tRNA genes, and 4 rRNA genes, with trnI-CAU and trnQ-UUG having two copies. Previous studies have commonly reported that the plastomes of conifers are usually characterized by the loss of an IR [36–44], which is different from the typical quadripartite structure shared by most angiosperm plastomes [45]. As expected, the loss of an IR was evident in all Thuja plastomes.

Previously, repeated tRNA genes in direct or inverted copies have been commonly discovered in conifer plastomes [37–40, 44]. For instance, the duplicated gene trnI-CAU was discovered in Pinaceae [33, 37], trnQ-UUG genehad two copies in Cupressophytes [38], the duplicated trnQ-UUG and trnI-CAU genes were reported in Taxus [46] and Cryptomeria [47], and three duplicated tRNA genes, trnI-CAU, trnQ-UUG, and trnN-GUU, were found in Torreya [44]. Consistent with previous studies, we detected two repeated tRNA genes, trnI-CAU and trnQ-UUG, existing inall Thuja plastomes. As proposed previously [37, 41, 44], these types of repeated tRNA genes in direct or inverted copies are possibly the result of the incomplete loss of IR regions.

The isomeric plastomes triggered by repeated trnQ-UUG gene (i.e. the trnQ-IR arrangements) have been discovered in Cephalotaxus (Cephalotaxaceae; [38]) and Cupressoideae species (Cupressaceae; [39, 40]). Guo et al. [39] recognized two types of isomeric plastome arrangements, namely the A-arrangement and B-arrangement, by comparative and southern blot analyses in Juniperus. Later, another two new types, C- and D-arrangements, were discovered by Qu et al. [40] in Calocedrus. Both studies suggested that the trnQ-IR may have promoted homologous recombination activity and is responsible for the presence of different isomeric forms. In our study, all Thuja plastomes contain the B-arrangement (Fig. 1, S1), which may support the hypothesis of Qu et al. [40] that the B-arrangement predominates in cuppressophyte plastomes. Interestingly, we found that the relict species of Thujopsis, who is the sister to Thuja, exhibits the A-arrangement, indicating the plastome rearrangement may have occurred multiple times during cupressophyte evolution. From all the evidence above, we could infer that the existence of isomeric plastomes might be a diagnostic feature in cupressophytes.

Phylogenetic relationships and evolutionary history of Thuja

The whole plastome sequence data used in our study yielded well-supported relationships among Cupressaceae, as well as within Thuja. Our phylogenomic analysis suggested that species form East Asian and North American are not monophyletic, respectively. Inconsistent with previous studies [23, 24], our result supports two sister pairs, T. standishii-T. koraiensis and T. occidentalis-T. sutchuenensis (Fig. 3). We consider this discrepancy most likely results from the different types of markers used in previous phylogenetic inference compared to ours. The closely related affinity of T. standishii-T. koraiensis can be reflected from geographic distribution, with T. koraiensis distributed in the Changbai Mountains of northeastern China and the Korean Peninsula, and T. standishii native to Japan [24]. These sister species were resolved as the early-diverging clade of Thuja, and originated in the Middle Miocene, which corresponds with the fossil records of T. nipponica found in both Akita County (NE Honshu), and in the Sikhote-Alin area of Far Eastern Russia during the Miocene [26]. The younger aged sister pair, T. occidentalis-T. sutchuenensis, display an intercontinental disjunction. Thuja sutchuenensis was once listed as an extinct species in the wild by IUCN-SSC but was rediscovered in 1999 in Chengkou, Chongqing in the southwest of China [21, 24]. In the late Pliocene, the fossil record of T. sutchuenensis was discovered in Shanxi Province, in northwest China. Dating to the late Pliocene to Pleistocene, the northern Greenland cone bearing material of T. occidentalis has been characterized [26]. From both paleobotanical and our phylogenomic evidence, we can hypothesize that the ancestor of T. occidentalis and T. sutchuenensis had a widespread distribution in the high-latitude areas of the Northern Hemisphere, but that climate cooling in the Late Tertiary and Quaternary created a barrier separating populations on either side of the ocean. The barrier further facilitated the allopatric speciation of Thuja.

Prior to this study, two relatively incompatible standpoints have been proposed for explaining the biogeographic process of Thuja. Li and Xiang [23] suggested an eastern Asia origin for Thuja based on ITS sequences. While, the multiple-genes evidence provided by [24] indicated the reticulate evolution occurred in Thuja, and they inferred that Thuja could have originated from the high-latitude areas of North America, although only the 4CL gene was used. Comparative analyses using fossils suggest that Thuja probably first appeared at high latitudes of North America in or before the Paleocene and arrived in eastern Asia in the Miocene [24, 26]. According to the present study, the diversification of Thuja was dated to approximately the Middle Miocene and the ancestral area was located in northern East Asia, indicating a second diversification center of Thuja in northern East Asia. In the Middle Miocene, the Bering Land Bridge and the warm climate may have facilitated long distance dispersals from East Asia to North America. Subsequently, climate cooling and drying after the Miocene, acting as vicariance driver, forced a southward migration of Thuja and restricted species in their current distributions.

Previous studies of gymnosperm radiations have mostly inferred Oligocene-age crown groups [11, 18, 48–51], as is the case in cycads [51], Pinaceae [11], and Cupressaceae [18], indicating relatively recent diversifications occurred in gymnosperms. The extinction following ancient origination may contribute to the young ages of most living gymnosperm clades. In conifer lineages, the evidence for widespread extinction and range shrinkage has been extensively reported. For example, Sequoioideae and Taxodioideae had a widespread distribution in the Northern Hemisphere in the Cretaceous and Early Tertiary, with Sequoioideae also found in Australia, but now are restricted to southern North America and East Asia [52]. Torreya were widely distributed in the Northern Hemisphere during the Cretaceous but now are restricted to East Asia and North America [44, 53]. Other examples include the genera Chamaecyparis [54], Austrocedrus [55], and Calocedrus [56] having wider distributions in the past. Fossils of Thuja have been widely found in sediments of Paleocene to Pleistocene age in the Northern Hemisphere from 36.8°N to 86.3°N [26, 57], reflecting an early widespread distribution of Thuja. Climatic oscillations and glaciation in the Quaternary have reportedly eliminated many plant groups from Europe [4, 53]; this phenomenon is apparently applicable to the whole Northern Hemisphere flora, which have largely been influenced by recent extinction. We speculate that the discrepancy between geographic distributions and phylogenetic relationships of Thuja could be attributed extinction, which can be difficult to trace. Therefore, in the intercontinental disjunction context, we advocate that the potential effect of extinction should be re-evaluated in the East Asia and North America floras, in particular, for the ancient rare gymnosperms.

The complete plastomes of Thuja have provided new insight into its plastome evolution, phylogenetic relationships and evolutionary history. Phylogenomic analyses based on plastome sequences yielded robust relationships within Thuja. Incorporating paleobotanical evidence, we speculated a North America origination and a northern East Asia diversification of Thuja. The current geographic distributions of Thuja was likely shaped by dispersal events attributed to the Bering Land Bridge in the Miocene and subsequent vicariance events accompanying climate cooling. We further inferred that the potential effect of extinction has had profound influence on the biogeographical history of Thuja.

Taxon sampling, chloroplast DNA isolation, and high-throughput sequencing

The fresh leaves of Thuja sutchuenensis, T. occidentalis and T. koraiensis were collected from Wuhan Botanical Garden, Chinses Academy of Sciences; Atlantic Botanical Garden, USA; and Chang-bai-shan Mts. National Reserve, Jilin, China, respectively. Total DNA was extracted using a modified CTAB protocol [58]. The purified DNA were used to construct an Illumina Nextera XT library (Illumina, San Diego, CA, USA) following the manufacturer’s instructions. DNA sequencing was performed on an Illumina MiSeq platform with paired-end 300 bp reads using V3 chemistry at Kunming Institute of Botany, China.

Plastome assembly, annotation, and comparative analyses

After sequencing, Illumina data were filtered using NGS QC Tool Kit (Patel and Jain 2012) by removing adapter sequences and low-quality reads with a Q-value ≤ 20. The remaining high-quality reads were assembled into contigs with a minimum length of 1000 bp using SPAdes v.3.7.1 [59]. The complete plastome of T. standishii (GenBank: KX832627.1) was used as a reference for contig assembling [35]. Raw reads were then mapped against the resulting single contig to ensure no gaps remained. The assembled plastomes were annotated using Dual Organellar Genome Annotator (DOGMA) [60], with manual correction of gene start and stop codons. The tRNA genes were identified with tRNAscan-SE [61]. Graphical maps of the circular plastomes were visualized with OGDRAW [62].

To estimate locally collinear blocks (LCBs) among the examined plastomes, we performed whole genome alignment by using progressiveMauve implemented in Mauve v2.3.1 [63] with default parameters. Simple sequence repeats (SSRs) were identified using Phobos v.3.3.12 (http://www.rub.de/ecoevo/cm/cm_phobos.htm). The default settings in the perfect search function were used by setting a repeat unit size ranging from one to ten without setting a minimum satellite length constraint. Tandem repeats were identified with Tandem Repeats Finder (TRF) [64] with default parameter settings. The tandem repeat lengths were 20 bp or more with the minimum alignment score and maximum period size set as 50 and 500 (respectively), and the identity of repeats was set to 90%.

Phylogenetic analyses

All coding sequence (CDS) of all 82 protein-coding genes were extracted from the five plastomes of Thuja, 27 other Cupressaceae species, and two species of Taxaceae (Taxus baccata and Cephalotaxus sinensis) that were used as outgroups [52]. The accession number and voucher information for each species are provided (Table S1).The 82 genes from the 34 taxa were concatenated in PhyloSuite v.1.1.14 [65] and aligned using MAFFT v.7.22 [66] under ‘—auto’ strategy and codon alignment mode. Ambiguously aligned fragments of the alignment were removed using Gblocks [67] with the following parameter settings: minimum number of sequences for a conserved/flank position (17/17), maximum number of contiguous non-conserved positions (8), minimum length of a block (10), allowed gap positions (all).

Both maximum-likelihood (ML) and Bayesian inference (BI) were conducted. ML analysis was performed in RAxML v.8.2.10 [68] under the general time-reversible (GTR) substitution model and the gamma model of rate heterogeneity. Bootstrap support was estimated with 1000 bootstrap replicates. BI analysis was executed in MrBayes v.3.2.3 [69] with the same model as ML analysis (GTR + G). Two runs were conducted in parallel with four Markov chains (one cold and three heated), with each running for 2,000,000 generations from a random tree and sampled every 200 generations. The average standard deviation of split frequencies (<0.01) was used for checking convergence. After discarding the first 25% of the trees as burn-in, the remaining trees were used to construct majority-rule consensus trees and calculate the posterior probability (PP). The final trees were viewed using FigTree v.1.4.2 [70].

Divergence time estimation

Divergence times for Thuja were estimated using BEAST v.1.8.4 [71]. The molecular clock test was used by comparing the ML value with and without the molecular clock constraints under GTR model using MEGA X [72]. The null hypothesis of equal evolutionary rates throughout the tree (Relaxed Clock Log Normal) was rejected (with clock, lnL: –39638711.585; without clock, lnL: –157069.417; P<0). Thus, an uncorrelated log-normal relaxed-clock model with the Birth-Death process tree prior was implemented. The uncorrelated log-normal model allows uncertainty in the age of calibrations to be represented as prior distributions rather than as strict calibration/fixed points [71]. The Markov Chain Monte Carlo runs were set to 500 million generations with sampling every 5000 generations. Tracer v.1.7.1 [73] was used to assess the effective sample size (ESS > 200) of each parameter. After a burn-in of 25%, the maximum clade credibility (MCC) tree with median branch lengths and 95% highest posterior density (HPD) intervals on nodes was built using TreeAnnotator 2.1.3 [71].

According to the previous comprehensive biogeographic study of Cupressaceae [52], four calibration points, A: the crown age of Cupressaceae, B: the stem age of Thuja, C: the split time between Crytpmeria, Glyptostrobus and Taxodium, and D: the MRCA of Sequoia–Metasequoia, were constrained to the minimal age of 157.2 Ma, 58.5 Ma, 111 Ma, and 92.8 Ma, respectively. Since all calibration points are from fossil records, we modelled them as the lognormal distribution with a mean of 1.5, standard deviation of 0.5 and an offset (hard bound constraint) that equaled the minimum age of the calibrations.

Ancestral Area Reconstructions

To infer ancestral distribution ranges of living species of Thuja, we used the R package BioGeoBEARS (http://CRAN.Rproject.org/package = BioGeoBEARS), as implemented in program RASP v.4.0 [74]. A total of 10,000 random trees and one MCC tree generated by BEAST were used as input trees, which included only Thuja and its sister genus Thujopsis. We used the Dispersal-Extirpation-Cladogenesis (DEC) model [75], since it allows dispersal, extinction and cladogenesis as fundamental processes, accommodates differing dispersal probabilities among areas across different time periods, and can integrate branch lengths, divergence times and geological information. We compared the DEC model with the ‘+J’ suffix (i.e. DEC+J), which allow founder speciation events. According to current distributions, species of Thuja were assigned to four possible geographic areas: A: southwest of China, B: northern East Asia, C: western North America, and D: eastern North America. At most two areas were allowed for any node in any tree, as each sampled taxon is restricted to only one area. Influenced by extinction, the relict distribution of Thujopsis may be not representative [24], thus we labelled it as an ambiguous geographic area (ABCD). An among-area dispersal probability matrix, which was inferred from the connectivity of the Bering Land Bridge [10], was coded to define different dispersal probabilities in four time periods, 0–5, 5–30, 30–45, and 45–65.

AIC: Akaike Information Criterion; BI: Bayesian Inference; CDS: Protein-coding sequences; CTAB: Cetyl trimethylammonium bromide; DEC: Dispersal-Extirpation-Cladogenesis; GTR: General time reversible; IR: Inverted repeat; ITS: Internal transcribed spacer of ribosomal DNA; LSC: Large single copy; ML: Maximum Likelihood; NCBI: National Center for Biotechnology Information; PI: Parsimony-informative; rRNA: Ribosomal RNA; SSC: Small single copy; tRNA: Transfer RNA.

Ethics approval and consent to participate

Not applicable

Consent for publication

Not applicable

Availability of data and materials

The newly sequenced plastomes have been submitted to GenBank, accession numbers are provided in Table S1 (Appendix).

Funding

This work was supported by the Strategic Priority Research Program of Chinese Academy of Sciences (XDA20050203), the National Key R&D Program of China (2017YFC0505200), grants-in-aid from the Major Program of the National Natural Science Foundation of China (31590823) and NSFC fund (31070191, 31370223). The funding sources for this study had no role in the design of the study, collection of data, data analysis and interpretation, or in writing the manuscript.

Competing interests

The authors declare that they have no conflict of interest.

Authors’ contributions

HW and HS conceived and designed the study. KA, XZ and XQ performed de novo assembly, genome annotation, phylogenetic and other analyses. AM performed the experiments. KA and XZ, JBL and YS drafted the manuscript. All authors have read and approved the manuscript.

Acknowledgements

We thank Dr. Ron Determann of Atlantic Botanical Garden, USA, Dr. Xiaodong Li of Wuhan Botanical Garden and Mr. Haicheng Zhou of Chang-bai-shan Mts. National Reserve, China for providing materials.

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Table 1. Comparison of the plastomes within Thuja

Species	Size (bp)	Total number of genes	Ribosomal RNA	Transfer RNAs	Protein-coding genes	GC content (%)	Protein-coding genes (bp)	Ribosomal RNAs (bp)	Transfer RNAs (bp)
T. plicata	131,118	117	4	30	83	34.30	75,663	4,796	2,341
T. sutchuenensis	130,668	117	4	30	83	35.81	75,392	4,479	2,286
T. occidentalis	131,602	117	4	30	83	34.26	76,210	4,479	2,413
T. korainensis	130,273	117	4	30	83	34.30	74,271	4,478	2,475
T. standishii	130,505	117	4	30	83	34.24	75,333	4,874	2,413

Table 2. List of genes identified in the plastomes of Thuja

	Group of genes	Names of genes
Protein synthesis and	Ribosomal RNAs	rrn5, rrn4.5, rrn23, rrn16*
DNA replication	Transfer RNAs	trnH-GUG, trnI-CAU⁺, trnK–UUU, trnQ-UUG⁺, trnT-UGU, trnS-GGA, trnfM-CAU, trnG-GCC, trnS-UGA, trnT-GGU, trnE-UUC, trnY-GUA, trnD-GUC, trnC-GCA, trnR-UCU, trnG-UCC, trnS-GCU, trnL-UAA, trnF-GAA, trnN-GUU, trnR-ACG, trnA-UGC, trnI-GAU, trnV-GAC, trnL-CAA, trnW-CCA, trnP-UGG, trnV-UAC*, trnM-CAU, trnL-UAG
	small subunit	rps16, rps4, rps14, rps2, rps15, rps12**
	Ribosomal proteins large subunit	rpl32, rpl23, rpl2, rpl22, rpl16, rpl14, rpl36 , rpl33, rpl20,
	RNA polymerase	rpoB, rpoC1, rpoC2, rpoA*
Photosynthesis	Photosystem I	psaA, psaB, psaM, psaC, psaI, psaJ
	Photosystem II	psbA, psbD, psbZ, psbC, psbM, psbI, psbK, psbH, psbN, psbT, psbB, psbJ, psbL, psbF, psbE
	Cytochrome b6/f	petN, petD, petB, petA, petL, petG
	ATP synthase	atpI, atpH, atpF, atpA, atpB, atpE*
	NADH dehydrogenase	ndhD, ndhE, ndhG, ndhI, ndhA, ndhH, ndhF, ndhB, ndhJ, ndhK, ndhC,
	Large subunit of Rubisco	rbcL
Miscellaneous proteins	Subunit of Acetyl-CoA-carboxylase c-type cytochrome synthesis gene	accD, ccsA, cemA, clpP, infA, matK
Genes of unknown function	Hypothetical conserved coding frame	ycf3, ycf2, ycf4, ycf1

* Gene containing a single intron;

** Gene containing two introns.

⁺Gene having two copies.

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Plastome phylogenomic and biogeographic study on Thuja (Cupressaceae)

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Abstract

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Background

Results

Plastome assembly, structure, and gene content

Repetitive sequences

Phylogenetic analyses

Divergence time estimation

Biogeographic result of Thuja

Discussion

Characterizations of Thuja plastomes

Phylogenetic relationships and evolutionary history of Thuja

Conclusions

Methods

Taxon sampling, chloroplast DNA isolation, and high-throughput sequencing

Plastome assembly, annotation, and comparative analyses

Phylogenetic analyses

Divergence time estimation

Ancestral Area Reconstructions

List of abbreviations

Declarations

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Competing interests

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Acknowledgements

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