Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide

Identification and characterization of a new species of Taxus - Taxus qinlingensis by multiple taxonomic methods

BACKGROUND

The taxonomy of Taxus Linn. remains controversial due to its continuous phenotypic variation and unstable topology, thus adversely affecting the formulation of scientific conservation strategies for this genus. Recently, a new ecotype, known as Qinling type, is mainly distributed in the Qinling Mountains and belongs to a monophyletic group. Here, we employed multiple methods including leaf phenotype comparison (leaf shapes and microstructure), DNA barcoding identification (ITS + trnL-trnF + rbcL), and niche analysis to ascertain the taxonomic status of the Qinling type.

RESULTS

Multiple comparisons revealed significant differences in the morphological characters (length, width, and length/width ratio) among the Qinling type and other Taxus species. Leaf anatomical analysis indicated that only the Qinling type and T. cuspidata had no papilla under the midvein or tannins in the epicuticle. Phylogenetic analysis of Taxus indicated that the Qinling type belonged to a monophyletic group. Moreover, the Qinling type had formed a relatively independent niche, it was mainly distributed around the Qinling Mountains, Ta-pa Mountains, and Taihang Mountains, situated at an elevation below 1500 m.

CONCLUSIONS

Four characters, namely leaf curvature, margin taper, papillation on midvein, and edges were put forward as primary indexes for distinguishing Taxus species. The ecotype Qingling type represented an independent evolutionary lineage and formed a unique ecological niche. Therefore, we suggested that the Qingling type should be treated as a novel species and named it Taxus qinlingensis Y. F. Wen & X. T. Wu, sp. nov.

Testing plastomes and nuclear ribosomal DNA sequences as the next-generation DNA barcodes for species identification and phylogenetic analysis in Acer

BACKGROUND

Acer is a taxonomically intractable and speciose genus that contains over 150 species. It is challenging to distinguish Acer species only by morphological method due to their abundant variations. Plastome and nuclear ribosomal DNA (nrDNA) sequences are recommended as powerful next-generation DNA barcodes for species discrimination. However, their efficacies were still poorly studied. The current study will evaluate the application of plastome and nrDNA in species identification and perform phylogenetic analyses for Acer.

RESULT

Based on a collection of 83 individuals representing 55 species (c. 55% of Chinese species) from 13 sections, our barcoding analyses demonstrated that plastomes exhibited the highest (90.47%) species discriminatory power among all plastid DNA markers, such as the standard plastid barcodes matK + rbcL + trnH-psbA (61.90%) and ycf1 (76.19%). And the nrDNA (80.95%) revealed higher species resolution than ITS (71.43%). Acer plastomes show abundant interspecific variations, however, species identification failure may be due to the incomplete lineage sorting (ILS) and chloroplast capture resulting from hybridization. We found that the usage of nrDNA contributed to identifying those species that were unidentified by plastomes, implying its capability to some extent to mitigate the impact of hybridization and ILS on species discrimination. However, combining plastome and nrDNA is not recommended given the cytonuclear conflict caused by potential hybridization. Our phylogenetic analysis covering 19 sections (95% sections of Acer) and 128 species (over 80% species of this genus) revealed pervasive inter- and intra-section cytonuclear discordances, hinting that hybridization has played an important role in the evolution of Acer.

CONCLUSION

Plastomes and nrDNA can significantly improve the species resolution in Acer. Our phylogenetic analysis uncovered the scope and depth of cytonuclear conflict in Acer, providing important insights into its evolution.

A leading-edge scenario in the phylogeography and evolutionary history of East Asian insular Taxus in Taiwan and the Philippines

The cool temperate origin of gymnosperm Taxus species in East Asia is specifically diverse and widespread. Certain lineages have managed to extend their distribution further south to subtropical and tropical islands such as Taiwan and the Philippines. To address questions including whether these insular lineages, recently identified as T. phytonii, have become genetically distinct from each other and from their continental relatives, and when and how they colonized their residing islands, we sampled over 11 populations, covering 179 Taxus individuals from Taiwan and the Philippines. Using four cpDNA and one nuclear marker, we showed in population genetic and genealogical analyses that the two insular lineages were genetically distinct from each other and also from other continental Taxus and that they represented each other's closest relative. Estimated with the coalescent-based multi-type tree (MTT) analyses, we inferred an origin of Taiwanese T. phytonii more ancient than 2.49 Mya and that of Philippine T. phytonii more ancient than 1.08 Mya. In addition, the divergence demographic history revealed by both MTT and isolation with migration (IM) analyses indicated the presence of recent post-split migrations from a continental taxon, T. mairei, to Taiwanese T. phytonii, as well as from Taiwanese T. phytonii to Philippine T. phytonii. Overall, this study suggests Taiwan as a stepping stone through which the temperate-origin yew trees can extend their distributions to tropical regions such as the Philippines.

Leaf variegation caused by plastome structural variation: an example from Dianella tasmanica

Variegated plants often exhibit plastomic heteroplasmy due to single-nucleotide mutations or small insertions/deletions in their albino sectors. Here, however, we identified a plastome structural variation in albino sectors of the variegated plant Dianella tasmanica (Asphodelaceae), a perennial herbaceous plant widely cultivated as an ornamental in tropical Asia. This structural variation, caused by intermolecular recombination mediated by an 11-bp inverted repeat flanking a 92-bp segment in the large single-copy region (LSC), generates a giant plastome (228 878 bp) with the largest inverted repeat of 105 226 bp and the smallest LSC of 92 bp known in land plants. It also generates an ~7-kb deletion on the boundary of the LSC, which eliminates three protein coding genes (psbA, matK, and rps16) and one tRNA gene (trnK). Albino sectors exhibit dramatic changes in expression of many plastid genes, including negligible expression of psbA, matK, and rps16, reduced expression of photosynthesis-related genes, and increased expression of genes related to the translational apparatus. Microscopic and ultrastructure observations showed that albino tissues were present in both green and albino sectors of the variegated individuals, and chloroplasts were poorly developed in the mesophyll cells of the albino tissues of the variegated individuals. These poorly developed chloroplasts likely carry the large and rearranged plastome, which is likely responsible for the loss of photosynthesis and albinism in the leaf margins. Considering that short repeats are relatively common in plant plastomes and that photosynthesis is not necessary for albino sectors, structural variation of this kind may not be rare in the plastomes of variegated plants.

Retrieving complete plastid genomes of endangered Guibourtia timber using hybridization capture for forensic identification and phylogenetic analysis

The high economic value and increased demand for timber have led to illegal logging and overexploitation, threatening wild populations. In this context, there is an urgent need to develop effective and accurate forensic tools for identifying endangered Guibourtia timber species to protect forest ecosystem resources and regulate their trade. In this study, a hybridization capture method was developed and applied to explore the feasibility of retrieving complete plastid genomes from Guibourtia sapwood and heartwood specimens stored in a xylarium (wood collection). We then carried out forensic identification and phylogenetic analyses of Guibourtia within the subfamily Detarioideae. This study is the first to successfully retrieve high-quality plastid genomes from xylarium specimens, with 76.95-99.97% coverage. The enrichment efficiency, sequence depth, and coverage of plastid genomes from sapwood were 16.73 times, 70.47 times and 1.14 times higher, respectively, than those from heartwood. Although the DNA capture efficiency of heartwood was lower than that of sapwood, the hybridization capture method used in this study is still suitable for heartwood DNA analysis. Based on the complete plastid genome, we identified six endangered or commonly traded Guibourtia woods at the species level. This technique also has the potential for geographical traceability, especially for Guibourtia demeusei and Guibourtia ehie. Meanwhile, Bayesian phylogenetic analysis suggested that these six Guibourtia species diverged from closely related species within the subfamily Detarioideae ca. 18 Ma during the Miocene. The DNA reference database established based on the xylarium specimens provides admissible evidence for diversity conservation and evolutionary analyses of endangered Guibourtia species.

The Complete Mitochondrial Genome of Paeonia lactiflora Pall. (Saxifragales: Paeoniaceae): Evidence of Gene Transfer from Chloroplast to Mitochondrial Genome

Paeonia lactiflora (P. lactiflora), a perennial plant renowned for its medicinal roots, provides a unique case for studying the phylogenetic relationships of species based on organelle genomes, as well as the transference of DNA across organelle genomes. In order to investigate this matter, we sequenced and characterized the mitochondrial genome (mitogenome) of P. lactiflora. Similar to the chloroplast genome (cpgenome), the mitogenome of P. lactiflora extends across 181,688 base pairs (bp). Its unique quadripartite structure results from a pair of extensive inverted repeats, each measuring 25,680 bp in length. The annotated mitogenome includes 27 protein-coding genes, 37 tRNAs, 8 rRNAs, and two pseudogenes (rpl5, rpl16). Phylogenetic analysis was performed to identify phylogenetic trees consistent with Paeonia species phylogeny in the APG Ⅳ system. Moreover, a total of 12 MTPT events were identified and 32 RNA editing sites were detected during mitogenome analysis of P. lactiflora. Our research successfully compiled and annotated the mitogenome of P. lactiflora. The study provides valuable insights regarding the taxonomic classification and molecular evolution within the Paeoniaceae family.

The low level of plastome differentiation observed in some lineages of Poales hinders molecular species identification

Chloroplast genomes are a source of information successfully used in various fields of plant genetics, including molecular species identification. However, recent studies indicate an extremely low level of interspecific variability in the plastomes of some taxonomic groups of plants, including the genus Stipa L., which is a representative of the grass family. In this study we aimed to analyze the level of chloroplast genome diversity within particular genera as well as the effectiveness of identifying plant species in the Poaceae family and the other representatives of Poales order. Analysis of complete plastid genome alignments created for 96 genera comprising 793 species and 1707 specimens obtained from the GenBank database allowed defining and categorizing molecular diagnostic characters distinguishing the analyzed species from the other representatives of the genus. The results also demonstrate which species do not have any species-specific mutations, thereby they cannot be identified on the basis of differences between the complete chloroplast genomes. Our research showed a huge diversity of the analyzed species in terms of the number of molecular diagnostic characters and indicated which genera pose a particular challenge in terms of molecular species identification. The results show that a very low level of genetic diversity between plastomes is not uncommon in Poales. This is the first extensive research on super-barcoding that tests this method on a large data set and illustrates its effectiveness against the background of phylogenetic relationships.

Multiple paternally inherited chloroplast capture events associated with Taxus speciation in the Hengduan Mountains

Mountainous regions provide a multitude of habitats and opportunities for complex speciation scenarios. Hybridization leading to chloroplast capture, which can be revealed by incongruent phylogenetic trees, is one possible outcome. Four allopatric Taxus lineages (three species and an undescribed lineage) from the Hengduan Mountains, southwest China, exhibit conflicting phylogenetic relationships between nuclear and chloroplast phylogenies. Here, we use multi-omic data at the population level to investigate their historical speciation processes. Population genomic analysis based on ddRAD-seq data revealed limited contemporary inter-specific gene flow involving only populations located close to another species. In a historical context, chloroplast and nuclear data (transcriptome) consistently showed conflicting phylogenetic relationships for T. florinii and the Emei type lineage. ILS and chloroplast recombination were excluded as possible causes, and transcriptome and ddRAD-seq data revealed an absence of the mosaic nuclear genomes that characterize hybrid origin scenarios. Therefore, T. florinii appears to have originated when a lineage of T. florinii captured the T. chinensis plastid type, whereas plastid introgression in the opposite direction generated the Emei Type. All four species have distinct ecological niche based on community investigations and ecological niche analyses. We propose that the origins of both species represent very rare examples of chloroplast capture events despite the paternal cpDNA inheritance of gymnosperms. Specifically, allopatrically and/or ecologically diverged parental species experienced a rare secondary contact, subsequent hybridization and reciprocal chloroplast capture, generating two new lineages, each of which acquired a unique ecological niche. These events might have been triggered by orogenic activities of the Hengduan Mountains and an intensification of the Asian monsoon in the late Miocene, and may represent a scenario more common in these mountains than presently known.

Comprehensive Comparative Analyses of Aspidistra Chloroplast Genomes: Insights into Interspecific Plastid Diversity and Phylogeny

Limestone karsts are renowned for extremely high species richness and endemism. Aspidistra (Asparagaceae) is among the highly diversified genera distributed in karst areas, making it an ideal group for studying the evolutionary mechanisms of karst plants. The taxonomy and identification of Aspidistra species are mainly based on their specialized and diverse floral structures. Aspidistra plants have inconspicuous flowers, and the similarity in vegetative morphology often leads to difficulties in species discrimination. Chloroplast genomes possess variable genetic information and offer the potential for interspecies identification. However, as yet there is little information about the interspecific diversity and evolution of the plastid genomes of Aspidistra. In this study, we reported chloroplast (cp) genomes of seven Aspidistra species (A. crassifila, A. dolichanthera, A. erecta, A. longgangensis, A. minutiflora, A. nankunshanensis, and A. retusa). These seven highly-conserved plastid genomes all have a typical quartile structure and include a total of 113 unique genes, comprising 79 protein-coding genes, 4 rRNA genes and 30 tRNA genes. Additionally, we conducted a comprehensive comparative analysis of Aspidistra cp genomes. We identified eight divergent hotspot regions (trnC-GCA-petN, trnE-UUC-psbD, accD-psaI, petA-psbJ, rpl20-rps12, rpl36-rps8, ccsA-ndhD and rps15-ycf1) that serve as potential molecular markers. Our newly generated Aspidistra plastomes enrich the resources of plastid genomes of karst plants, and an investigation into the plastome diversity offers novel perspectives on the taxonomy, phylogeny and evolution of Aspidistra species.

Plastid phylogenomics and species discrimination in the "Chinese" clade of Roscoea (Zingiberaceae)

Roscoea is an alpine or subalpine genus from the pan-tropical family Zingiberaceae, which consists of two disjunct groups in geography, namely the "Chinese" clade and the "Himalayan" clade. Despite extensive research on the genus, Roscoea species remain poorly defined and relationships between these species are not well resolved. In this study, we used plastid genomes of nine species and one variety to resolve phylogenetic relationships within the "Chinese" clade of Roscoea and as DNA super barcodes for species discrimination. We found that Roscoea plastid genomes ranged in length from 163,063 to 163,796 bp, and encoded 113 genes, including 79 protein-coding genes, 30 tRNA genes, four rRNA genes. In addition, expansion and contraction of the IR regions showed obvious infraspecific conservatism and interspecific differentiation. Plastid phylogenomics revealed that species belonging to the "Chinese" clade of Roscoea can be divided into four distinct subclades. Furthermore, our analysis supported the independence of R. cautleoides var. pubescens, the recovery of Roscoea pubescens Z.Y. Zhu, and a close relationship between R. humeana and R. cautloides. When we used the plastid genome as a super barcode, we found that it possessed strong discriminatory power (90%) with high support values. Intergenic regions provided similar resolution, which was much better than that of protein-coding regions, hypervariable regions, and DNA universal barcodes. However, plastid genomes could not completely resolve Roscoea phylogeny or definitively discriminate species. These limitations are likely related to the complex history of Roscoea speciation, poorly defined species within the genus, and the maternal inheritance of plastid genomes.

Phylogenetic Relationships and Next-Generation Barcodes in the Genus Torreya Reveal a High Proportion of Misidentified Cultivated Plants

Accurate species identification is key to conservation and phylogenetic inference. Living plant collections from botanical gardens/arboretum are important resources for the purpose of scientific research, but the proportion of cultivated plant misidentification are un-tested using DNA barcodes. Here, we assembled the next-generation barcode (complete plastid genome and complete nrDNA cistron) and mitochondrial genes from genome skimming data of Torreya species with multiple accessions for each species to test the species discrimination and the misidentification proportion of cultivated plants used in Torreya studies. A total of 38 accessions were included for analyses, representing all nine recognized species of genus Torreya. The plastid phylogeny showed that all 21 wild samples formed species-specific clades, except T. jiulongshanensis. Disregarding this putative hybrid, seven recognized species sampled here were successfully discriminated by the plastid genome. Only the T. nucifera accessions grouped into two grades. The species identification rate of the nrDNA cistron was 62.5%. The Skmer analysis based on nuclear reads from genome skims showed promise for species identification with seven species discriminated. The proportion of misidentified cultivated plants from arboreta/botanical gardens was relatively high with four accessions (23.5%) representing three species. Interspecific relationships within Torreya were fully resolved with maximum support by plastomes, where Torreya jackii was on the earliest diverging branch, though sister to T. grandis in the nrDNA cistron tree, suggesting that this is likely a hybrid species between T. grandis and an extinct Torreya ancestor lineage. The findings here provide quantitative insights into the usage of cultivated samples for phylogenetic study.

Comparative study on chloroplast genomes of three Hansenia forbesii varieties (Apiaceae)

To find the gene hypervariable regions of three varieties of Hansenia forbesii H. Boissieu and determine their phylogenetic relationship, the chloroplast (cp) genome of these three varieties were firstly sequencing by the Illumina hiseq platform. In this study, we assembled the complete cp genome sequences of Hansenia forbesii LQ (156,954 bp), H. forbesii QX (157,181 bp), H. forbesii WQ (156,975 bp). They all contained 84 protein-coding genes, 37 tRNAs, and 8 rRNAs. The hypervariable regions between three cp genomes were atpF-atpH, petD, and rps15-ycf1. Phylogenetic analysis showed that H. forbesii LQ and H. forbesii WQ were closely related, followed by H. forbesii QX. This study showed that the three varieties of H. forbesii could be identified by the complete cp genome and specific DNA barcode (trnC-GCA-petN) and provided a new idea for germplasm identification of similar cultivated varieties.

Comparative plastome genomics, taxonomic delimitation and evolutionary divergences of Tetraena hamiensis var. qatarensis and Tetraena simplex (Zygophyllaceae)

The Zygophyllum and Tetraena genera are intriguingly important ecologically and medicinally. Based on morphological characteristics, T. hamiensis var. qatarensis, and T. simplex were transferred from Zygophyllum to Tetraena with the least genomic datasets available. Hence, we sequenced the T. hamiensis and T. simplex and performed in-depth comparative genomics, phylogenetic analysis, and estimated time divergences. The complete plastomes ranged between 106,720 and 106,446 bp-typically smaller than angiosperms plastomes. The plastome circular genomes are divided into large single-copy regions (~ 80,964 bp), small single-copy regions (~ 17,416 bp), and two inverted repeats regions (~ 4170 bp) in both Tetraena species. An unusual shrinkage of IR regions 16-24 kb was identified. This resulted in the loss of 16 genes, including 11 ndh genes which encode the NADH dehydrogenase subunits, and a significant size reduction of Tetraena plastomes compared to other angiosperms. The inter-species variations and similarities were identified using genome-wide comparisons. Phylogenetic trees generated by analyzing the whole plastomes, protein-coding genes, matK, rbcL, and cssA genes exhibited identical topologies, indicating that both species are sisters to the genus Tetraena and may not belong to Zygophyllum. Similarly, based on the entire plastome and proteins coding genes datasets, the time divergence of Zygophyllum and Tetraena was 36.6 Ma and 34.4 Ma, respectively. Tetraena stem ages were 31.7 and 18.2 Ma based on full plastome and protein-coding genes. The current study presents the plastome as a distinguishing and identification feature among the closely related Tetraena and Zygophyllum species. It can be potentially used as a universal super-barcode for identifying plants.

Complete chloroplast genome and phylogenetic analysis of Anemone shikokiana

BACKGROUND

Anemone shikokiana (Makino) Makino, disjunctly distributed in Shandong Peninsula of China and Shikoku Island of Japan, is a rare and endangered species. To provide genetic information and understand its phylogeny, we conducted research on the chloroplast (cp) genome of A. shikokiana.

METHODS AND RESULTS

The complete cp genome sequence of A. shikokiana was constructed in this study. The results showed that the cp genome of A. shikokiana has a typical quadripartite cyclic with a total length of 159,286 bp. In total, 111 unique genes were identified, including 78 protein-coding genes, 29 tRNA-coding genes and 4 rRNA-coding genes. A total of 37 long repeat sequences and 67 microsatellites were found in this cp genome. The cp genome of A. shikokiana was compared with eleven other Anemone cp genomes available from the Genbank database. We found some variations among the different genomes, especially in the LSC and SSC regions, and identified some regions as potential molecular markers such as ycf1, ndhE, ndhD, ndhF-trnL, ndhA and ndhF. The results of phylogenetic analysis suggested that A. narcissiflora was the closest relative of A. shikokiana.

CONCLUSIONS

The results filled the gap of cp genome sequence information of A. shikokiana, laying the foundation to explore the evolutionary relationships of A. shikokiana in future studies. It provided a valuable genetic resource for the molecular identification and phylogenetic study of Anemone.

Testing complete plastomes and nuclear ribosomal DNA sequences for species identification in a taxonomically difficult bamboo genus Fargesia

Fargesia, the largest genus within the temperate bamboo tribe Arundinarieae, has more than 90 species mainly distributed in the mountains of Southwest China. The Fargesia bamboos are important components of the subalpine forest ecosystems that provide food and habitat for many endangered animals, including the giant panda. However, species-level identification of Fargesia is difficult. Moreover, the rapid radiation and slow molecular evolutionary rate of Fargesia pose a significant challenge to using DNA barcoding with standard plant barcodes (rbcL, matK, and ITS) in bamboos. With progress in the sequencing technologies, complete plastid genomes (plastomes) and nuclear ribosomal DNA (nrDNA) sequences have been proposed as organelle barcodes for species identification; however, these have not been tested in bamboos. We collected 196 individuals representing 62 species of Fargesia to comprehensively evaluate the discriminatory power of plastomes and nrDNA sequences compared to standard barcodes. Our analysis indicates that complete plastomes have substantially higher discriminatory power (28.6%) than standard barcodes (5.7%), whereas nrDNA sequences show a moderate improvement (65.4%) compared to ITS (47.2%). We also found that nuclear markers performed better than plastid markers, and ITS alone had higher discriminatory power than complete plastomes. The study also demonstrated that plastomes and nrDNA sequences can contribute to intrageneric phylogenetic resolution in Fargesia. However, neither of these sequences were able to discriminate all the sampled species, and therefore, more nuclear markers need to be identified.

Morphological Characteristics and Comparative Chloroplast Genome Analyses between Red and White Flower Phenotypes of Pyracantha fortuneana (Maxim.) Li (Rosaceae), with Implications for Taxonomy and Phylogeny

Pyracantha fortuneana (Maxim.) Li (Rosaceae), commonly known as Chinese firethorn, is an evergreen shrub with high nutritional, medicinal, and horticultural importance. This species typically has white flowers, but a rare red flower phenotype has been found in very few wild populations in western Hubei, China, showing great ornamental potential. In this study, the complete chloroplast genome of the red flower phenotype of P. fortuneana was reported for the first time, using high-throughput sequencing technology. The complete chloroplast genome was 160,361 bp in length and showed a typical quadripartite structure with a pair of inverted repeat (IR) regions (26,350 bp) separated by a large single-copy (LSC) region (88,316 bp) and a small single-copy (SSC) region (19,345 bp). A total of 131 functional genes were annotated in this chloroplast genome, including 86 protein-coding genes (PCGs), eight rRNA genes, and 37 tRNA genes. Comparative chloroplast genome analyses revealed that high genome similarity existed not only between red and white flower phenotypes of P. fortuneana, but also among Pyracantha species. No evidence for positive selection was found in any PCG, suggesting the evolutionary conservation of Pyracantha chloroplast genomes. Furthermore, four mutational hotspots (trnG-trnR-atpA, psbZ-trnG-trnfM-rps14, ycf3-trnS-rps4, and ndhF-rpl32) with π > 0.004 were identified as potential molecular markers for Pyracantha species. Phylogenomic analysis strongly supported that the red flower phenotype of P. fortuneana was nested within the common white flower phenotype. Based on both morphological and molecular evidence, we suggest that the red flower phenotype of P. fortuneana could be considered as a new forma. Overall, the availability of these genetic resources will not only offer valuable information for further studies on molecular taxonomy, phylogeny, and population genetics of Pyracantha species but also could be used as potential genetic resources for Chinese firethorn breeding.

Plastid phylogenomics uncovers multiple species in Medicago truncatula (Fabaceae) germplasm accessions

Medicago truncatula is a model legume that has been extensively investigated in diverse subdisciplines of plant science. Medicago littoralis can interbreed with M. truncatula and M. italica; these three closely related species form a clade, i.e. TLI clade. Genetic studies have indicated that M. truncatula accessions are heterogeneous but their taxonomic identities have not been verified. To elucidate the phylogenetic position of diverse M. truncatula accessions within the genus, we assembled 54 plastid genomes (plastomes) using publicly available next-generation sequencing data and conducted phylogenetic analyses using maximum likelihood. Five accessions showed high levels of plastid DNA polymorphism. Three of these highly polymorphic accessions contained sequences from both M. truncatula and M. littoralis. Phylogenetic analyses of sequences placed some accessions closer to distantly related species suggesting misidentification of source material. Most accessions were placed within the TLI clade and maximally supported the interrelationships of three subclades. Two Medicago accessions were placed within a M. italica subclade of the TLI clade. Plastomes with a 45-kb (rpl20-ycf1) inversion were placed within the M. littoralis subclade. Our results suggest that the M. truncatula accession genome pool represents more than one species due to possible mistaken identities and gene flow among closely related species.

Comprehensive Comparative Analysis and Development of Molecular Markers for Dianthus Species Based on Complete Chloroplast Genome Sequences

Dianthus spp. is a genus with high economic and ornamental value in the Caryophyllaceae, which include the famous fresh-cut carnation and the traditional Chinese herbal medicine, D. superbus. Despite the Dianthus species being seen everywhere in our daily lives, its genome information and phylogenetic relationships remain elusive. Thus, we performed the assembly and annotation of chloroplast genomes for 12 individuals from seven Dianthus species. On this basis, we carried out the first comprehensive and systematic analysis of the chloroplast genome sequence characteristics and the phylogenetic evolution of Dianthus. The chloroplast genome of 12 Dianthus individuals ranged from 149,192 bp to 149,800 bp, containing 124 to 126 functional genes. Sequence repetition analysis showed the number of simple sequence repeats (SSRs) ranged from 75 to 80, tandem repeats ranged from 23 to 41, and pair-dispersed repeats ranged from 28 to 43. Next, we calculated the synonymous nucleotide substitution rates (Ks) of all 76 protein coding genes to obtain the evolution rate of these coding genes in Dianthus species; rpl22 showed the highest Ks (0.0471), which suggested that it evolved the swiftest. By reconstructing the phylogenetic relationships within Dianthus and other species of Caryophyllales, 16 Dianthus individuals (12 individuals reported in this study and four individuals downloaded from NCBI) were divided into two strongly supported sister clades (Clade A and Clade B). The Clade A contained five species, namely D. caryophyllus, D. barbatus, D. gratianopolitanus, and two cultivars (‘HY’ and ‘WC’). The Clade B included four species, in which D. superbus was a sister branch with D. chinensis, D. longicalyx, and F1 ‘87M’ (the hybrid offspring F1 from D. chinensis and ‘HY’). Further, based on sequence divergence analysis and hypervariable region analysis, we selected several regions that had more divergent sequences, to develop DNA markers. Additionally, we found that one DNA marker can be used to differentiate Clade A and Clade B in Dianthus. Taken together, our results provide useful information for our understanding of Dianthus classification and chloroplast genome evolution.

DNA barcoding: an efficient technology to authenticate plant species of traditional Chinese medicine and recent advances

Traditional Chinese medicine (TCM) plays an important role in the global traditional health systems. However, adulterated and counterfeit TCM is on the rise. DNA barcoding is an effective, rapid, and accurate technique for identifying plant species. In this study, we collected manuscripts on DNA barcoding published in the last decade and summarized the use of this technique in identifying 50 common Chinese herbs listed in the Chinese pharmacopoeia. Based on the dataset of the major seven DNA barcodes of plants in the NCBI database, the strengths and limitations of the barcodes and their derivative barcoding technology, including single-locus barcode, multi-locus barcoding, super-barcoding, meta-barcoding, and mini-barcoding, were illustrated. In addition, the advances in DNA barcoding, particularly identifying plant species for TCM using machine learning technology, are also reviewed. Finally, the selection process of an ideal DNA barcoding technique for accurate identification of a given TCM plant species was also outlined.

Molecular Identification of African Nymphaea Species (Water Lily) Based on ITS, trnT-trnF and rpl16

The genus Nymphaea L. (water lily) is the most diverse genus in the family Nymphaeaceae, with more than 50 species worldwide, including 11 species distributed in Africa. The complex and variable morphology of Nymphaea makes it extremely difficult to accurately identify species based on morphological characteristics alone. DNA barcoding has the potential to identify species accurately. In this study, 158 Nymphaea populations from seven African countries were collected for species identification by ITS, trnT-trnF and rpl16. Additionally, the three candidate DNA barcodes were evaluated for genetic distance and barcoding gap. Based on the comprehensive analysis of sequence similarity, genetic distance method and phylogenetic tree, a total of 137 populations of seven Nymphaea species from African were well-identified, including N. lotus, N. petersiana, N. zenkeri, N. nouchali var. caerulea, N. micrantha and N. guineensis. ITS has more obvious advantages over trnT-trnF, rpl16 and trnT-trnF+rpl16 in the intraspecific and interspecific variation differences and barcoding gap and can identify most species. trnT-trnF and rpl16 can identify some species that cannot be identified by ITS. The results showed that it is more appropriate to apply the combination of ITS and trnT-trnF (or rpl16) as the DNA barcoding of Nymphaea. Additionally, this study further enriches the DNA barcoding database of Nymphaea and provides a reference basis for studying taxonomy, phylogenetics and evolutionary origin of Nymphaea.

Comparative Analysis of Bacillariophyceae Chloroplast Genomes Uncovers Extensive Genome Rearrangements Associated with Speciation

The Bacillariophyceae is a species-rich, ecologically significant class of Bacillariophyta. Despite their critical importance in marine ecosystems as primary producers and in the development of harmful algal blooms (HABs), taxonomic research on Bacillariophyceae species has been hindered because of their limited morphological features, plasticity of morphologies, and the low resolution of common molecular markers. Hence molecular markers with improved resolution are urgently needed. Organelle genomes, which can be constructed efficiently with the recent development of high throughput DNA sequencing technologies and the advancement of bioinformatics tools, have been proposed as super barcodes for their higher resolution for distinguishing different species and intra-species genomic variations. In this study, we tested the value of full-length chloroplast genomes (cpDNAs) as super barcodes for distinguishing diatom species, by constructing cpDNAs of 11 strains of the class Bacillariophyceae, including Nitzschia ovalis, Nitzschia traheaformis, Cylindrotheca spp., Psammodictyon constrictum, Bacillaria paxillifer, two strains of Haslea tsukamotoi, Haslea avium, Navicula arenaria, and Pleurosigma sp. Comparative analysis of cpDNAs revealed that cpDNAs were not only adequate for resolving different species, but also for enabling recognition of high levels of genome rearrangements between cpDNAs of different species, especially for species of the genera Nitzschia, Cylindrotheca, Navicula and Haslea. Additionally, comparative analysis suggested that the positioning of species in the genus Haslea should be transferred to the genus Navicula. Chloroplast genome-based evolutionary analysis suggested that the Bacillariophyceae species first appeared during the Cretaceous period and the diversity of species rose after the mass extinction about 65 Mya. This study highlighted the value of cpDNAs in research on the biodiversity and evolution of Bacillariophyceae species, and, with the construction of more cpDNAs representing additional genera, deeper insight into the biodiversity and evolutionary relationships of Bacillariophyceae species will be gained.

Comparative Analyses of 35 Complete Chloroplast Genomes from the Genus Dalbergia (Fabaceae) and the Identification of DNA Barcodes for Tracking Illegal Logging and Counterfeit Rosewood

The genus Dalbergia contains more than 200 species, several of which are trees that produce traditional medicines and extremely high-value timber commonly referred to as rosewood. Due to the rarity of these species in the wild, the high value of the timber, and a growing international illicit trade, CITES (Convention on International Trade in Endangered Species of Wild Fauna and Flora) has listed the entire genus in appendix II and the species Dalbergia nigra in appendix I because species in this genus are considered at risk of extinction. Given this, and the fact that species or even genus level determination is nearly impossible from cut timber morphology, alternative molecular methods are needed to identify and track intercepted rosewood. To better identify rosewood using molecular methods, we sequenced and assembled eight chloroplast genomes including D. nigra as well as conducted comparative analyses with all other available chloroplast genomes in Dalbergia and closely related lineages. From these analyses, numerous repeats including simple sequence repeats (SSR) and conserved nucleotide polymorphisms unique to subclades within the genus were detected. From phylogenetic analysis based on the CDS from 77 chloroplast genes, the groups Siam rosewood and scented rosewood resolved as monophyletic, supporting the morphological traits used to delimit these species. In addition, several instances of paraphyly and polyphyly resulting from mismatches between taxonomic determinations and phylogenetic tree topology were identified. Ultimately, the highly variable regions in the chloroplast genomes will provide useful plastid markers for further studies regarding the identification, phylogeny, and population genetics of Dalbergia species, including those frequently intercepted in illegal trade.

Genome Skimming Contributes to Clarifying Species Limits in Paris Section Axiparis (Melanthiaceae)

Paris L. section Axiparis H. Li (Melanthiaceae) is a taxonomically perplexing taxon with considerable confusion regarding species delimitation. Based on the analyses of morphology and geographic distribution of each species currently recognized in the taxon, we propose a revision scheme that reduces the number of species in P. sect. Axiparis from nine to two. To verify this taxonomic proposal, we employed a genome skimming approach to recover the plastid genomes (plastomes) and nuclear ribosomal DNA (nrDNA) regions of 51 individual plants across the nine described species of P. sect. Axiparis by sampling multiple accessions per species. The species boundaries within P. sect. Axiparis were explored using phylogenetic inference and three different sequence-based species delimitation methods (ABGD, mPTP, and SDP). The mutually reinforcing results indicate that there are two species-level taxonomic units in P. sect. Axiparis (Paris forrestii s.l. and P. vaniotii s.l.) that exhibit morphological uniqueness, non-overlapping distribution, genetic distinctiveness, and potential reproductive isolation, providing strong support to the proposed species delimitation scheme. This study confirms that previous morphology-based taxonomy overemphasized intraspecific and minor morphological differences to delineate species boundaries, therefore resulting in an overestimation of the true species diversity of P. sect. Axiparis. The findings clarify species limits and will facilitate robust taxonomic revision in P. sect. Axiparis.

DNA Barcoding and Phylogenomic Analysis of the Genus Fritillaria in China Based on Complete Chloroplast Genomes

The Fritillaria is an extremely complicated genus in taxonomy and phylogeny, which contains numerous medicinal species in China. Both traditional characteristic-based taxonomy and universal DNA barcodes (ITS, trnH-psbA, and rbcL) are difficult to effectively identify the species. Here, we generated a large dataset of chloroplast genomes from multiple accessions per species of Fritillaria to evaluate their effectiveness in species discrimination. Moreover, phylogeny of species in China was explored based on the complete chloroplast genomes, and then divergence times of each node were estimated. The results showed that all 21 species in Fritillaria here (including two suspicious species) could be correctly discriminated using cpDNA genomes except F. cirrhosa, which suggested that DNA super-barcode could greatly enhance species discriminatory resolution for complicated genera. Furthermore, four regions (ycf1, matK-trnG-GCC, rpoC1, and matK) gained remarkably higher resolution than that of other plastid regions, but only matK might be suitable to identify Fritillaria species in consideration of its lengths. Phylogenomic analysis showed that the subgenus Fritillaria in China was divided into four major clades with obvious geographic structure. Among them, Clade I, mainly distributed in southwest China, was a young and complicated group. Moreover, according to the analysis, taxonomic treatments of the two suspicious species, namely "F. omeiensis" and "F. hupehensis" in Flora of China (2000) are questionable and might need further revision. Molecular dating revealed that both origin and divergence of subgenus Fritillaria, as well as its four major clades, were significantly associated with geological and climatic fluctuations during the Middle to Late Miocene. This study would enrich case studies of DNA super-barcode and provide new insights on speciation, lineage diversification, and biogeography of the Fritillaria in China.

Testing the Complete Plastome for Species Discrimination, Cryptic Species Discovery and Phylogenetic Resolution in Cephalotaxus (Cephalotaxaceae)

Species of Cephalotaxus have great economic and ecological values. However, the taxonomy and interspecific phylogenetic relationships within the genus have been controversial and remained not fully resolved until now. To date, no study examined the efficiency of the complete plastome as super-barcode across Cephalotaxus species with multiple samples per taxon. In this study, we have evaluated the complete plastome in species discrimination and phylogenetic resolution in Cephalotaxus by including 32 individuals of all eight recognized species and five varieties following Farjon's classification (2010) with multiple samples per taxon. Our results indicated that not all species recognized in recent taxonomic revisions of Cephalotaxus could be distinguished and not all were monophyletic. Based on the plastome phylogeny, a new taxonomic classification for the genus comprising nine species and two varieties, including a cryptic species, was proposed. The phylogeny also resolved all interspecific relationships. Compared to the plastome based classification, standard DNA barcodes, alone or in combination, only recognized a maximum of seven out of the nine species. Moreover, two highly variable single loci, ycf1 and rps16, each alone achieved full species discrimination. With the moderate length of 1079 bp, rps16 is proposed as a specific barcode to discriminate Cephalotaxus species. The super-barcodes and specific barcode candidates will aid in the identification of endangered Cephalotaxus species, and to help focus conservation measures.

Comparative Analysis of Chloroplast Genomes of Seven Chaetoceros Species Revealed Variation Hotspots and Speciation Time

Chaetoceros is a species-rich diatom genus with broad distribution and plays an important role in global carbon cycle and aquatic ecosystems. However, genomic information of Chaetoceros species is limited, hindering advanced researches on Chaetoceros biodiversity and their differential impact on ecology. In this study, we constructed full-length chloroplast genomes (cpDNAs) for seven Chaetoceros species, including C. costatus, C. curvisetus, C. laevisporus, C. muelleri, C. pseudo-curvisetus, C. socialis, and C. tenuissimus. All of these cpDNAs displayed a typical quadripartite structure with conserved genome arrangement and specific divergence. The sizes of these cpDNAs were similar, ranging from 116,421 to 119,034 bp in size, and these cpDNAs also displayed similar GC content, ranging from 30.26 to 32.10%. Despite extensive synteny conservation, discrete regions showed high variations. Divergence time estimation revealed that the common ancestor of Chaetoceros species, which formed a monophyletic clade at approximately 58 million years ago (Mya), split from Acanthoceras zachariasii at about 70 Mya. The availability of cpDNAs of multiple Chaetoceros species provided valuable reference sequences for studying evolutionary relationship among Chaetoceros species, as well as between Chaetoceros species and other diatom species.

Reference-based assembly of chloroplast genome from leaf transcriptome data of Pterocarpus santalinus

Chloroplast genome sequencing is an essential tool to understand genome evolution and phylogenetic relationship. The available methods for constructing chloroplast genome include chloroplast enrichment followed by long overlapping PCR or extraction and assembly of chloroplast-specific reads from whole-genome datasets. In the present study, we propose an alternate strategy of extraction and assembly of chloroplast-specific reads from leaf transcriptome data of Pterocarpus santalinus using bowtie2 aligner program. The assembled genome was compared with the published chloroplast genome of P. santalinus for genome size, number of predicted genes, microsatellite repeat motifs, and nucleotide repeats. A near-complete chloroplast genome was assembled from the transcriptome reads. The proposed method requires less computational time and know-how, limited virtual memory, and is cost-effective when compared to whole-genome sequencing. Assembly of Cp genome from transcriptome data will enhance the resolution of phylogenetic studies through comparative plastome analysis, facilitate accurate species/genotype discrimination and accelerate the development of transplastomic plants with enhanced biotic and abiotic tolerance.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02943-0.

Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron

Standard plant DNA barcodes based on 2-3 plastid regions, and nrDNA ITS show variable levels of resolution, and fail to discriminate among species in many plant groups. Genome skimming to recover complete plastid genome sequences and nrDNA arrays has been proposed as a solution to address these resolution limitations. However, few studies have empirically tested what gains are achieved in practice. Of particular interest is whether adding substantially more plastid and nrDNA characters will lead to an increase in discriminatory power, or whether the resolution limitations of standard plant barcodes are fundamentally due to plastid genomes and nrDNA not tracking species boundaries. To address this, we used genome skimming to recover near-complete plastid genomes and nuclear ribosomal DNA from Rhododendron species and compared discrimination success with standard plant barcodes. We sampled 218 individuals representing 145 species of this species-rich and taxonomically difficult genus, focusing on the global biodiversity hotspots of the Himalaya-Hengduan Mountains. Only 33% of species were distinguished using ITS+matK+rbcL+trnH-psbA. In contrast, 55% of species were distinguished using plastid genome and nrDNA sequences. The vast majority of this increase is due to the additional plastid characters. Thus, despite previous studies showing an asymptote in discrimination success beyond 3-4 plastid regions, these results show that a demonstrable increase in discriminatory power is possible with extensive plastid genome data. However, despite these gains, many species remain unresolved, and these results also reinforce the need to access multiple unlinked nuclear loci to obtain transformative gains in species discrimination in plants.

Unprecedented Intraindividual Structural Heteroplasmy in Eleocharis (Cyperaceae, Poales) Plastomes

Plastid genomes (plastomes) of land plants have a conserved quadripartite structure in a gene-dense unit genome consisting of a large inverted repeat that separates two single copy regions. Recently, alternative plastome structures were suggested in Geraniaceae and in some conifers and Medicago the coexistence of inversion isomers has been noted. In this study, plastome sequences of two Cyperaceae, Eleocharis dulcis (water chestnut) and Eleocharis cellulosa (gulf coast spikerush), were completed. Unlike the conserved plastomes in basal groups of Poales, these Eleocharis plastomes have remarkably divergent features, including large plastome sizes, high rates of sequence rearrangements, low GC content and gene density, gene duplications and losses, and increased repetitive DNA sequences. A novel finding among these features was the unprecedented level of heteroplasmy with the presence of multiple plastome structural types within a single individual. Illumina paired-end assemblies combined with PacBio single-molecule real-time sequencing, long-range polymerase chain reaction, and Sanger sequencing data identified at least four different plastome structural types in both Eleocharis species. PacBio long read data suggested that one of the four E. dulcis plastome types predominates.

Plastome-based phylogeny improves community phylogenetics of subtropical forests in China

Phylogenetic trees have been extensively used in community ecology. However, how the phylogeny construction affects ecological inferences is poorly understood. In this study, we constructed three different types of phylogenetic trees (a synthetic-tree generated using V.PhyloMaker, a barcode-tree generated using rbcL+matK+trnH-psbA, and a plastome-tree generated from plastid genomes) that represented an increasing level of phylogenetic resolution among 580 woody plant species from six forest dynamic plots in subtropical evergreen broadleaved forests of China. We then evaluated the performance of each phylogeny in estimations of community phylogenetic structure, turnover and phylogenetic signal in functional traits. As expected, the plastome-tree was most resolved and most supported for relationships among species. For local phylogenetic structure, the three trees showed consistent results with Faith's PD and MPD; however, only the synthetic-tree produced significant clustering patterns using MNTD for some plots. For phylogenetic turnover, contrasting results between the molecular trees and the synthetic-tree occurred only with nearest neighbor distance. The barcode-tree agreed more with the plastome-tree than the synthetic-tree for both phylogenetic structure and turnover. For functional traits, both the barcode-tree and plastome-tree detected phylogenetic signal in maximum height, but only the plastome-tree detected signal in leaf width. This is the first study that uses plastid genomes in large-scale community phylogenetics. Our results highlight the improvement of plastome-trees over barcode-trees and synthetic-trees for the analyses studied here. Our results also point to the possibility of type I and II errors in estimation of phylogenetic structure and turnover and detection of phylogenetic signal when using synthetic-trees.

Highly degenerate plastomes in two hemiparasitic dwarf mistletoes: Arceuthobium chinense and A. pini (Viscaceae)

The leafless and endophytic habitat may significantly relax the selection pressure on photosynthesis, and plastid transcription and translation, causing the loss/pseudogenization of several essential plastid-encoding genes in dwarf mistletoes. Dwarf mistletoes (Arceuthobium spp., Viscaceae) are the most destructive plant parasites to numerous conifer species worldwide. In this study, the plastid genomes (plastomes) of Arceuthobium chinense Lecomte and A. pini Hawksworth and Wiens were sequenced and characterized. Although dwarf mistletoes are hemiparasites capable of photosynthesis, their plastomes were highly degenerated, as indicated by the smallest plastome size, the lowest GC content, and relatively very few intact genes among the Santalales hemiparasites. Unexpectedly, several essential housekeeping genes (rpoA, rpoB, rpoC1, and rpoC2) and some core photosynthetic genes (psbZ and petL), as well as the rpl33 gene, that is indispensable for plants under stress conditions, were deleted or pseudogenized in the Arceuthobium plastomes. Our data suggest that the leafless and endophytic habit, which heavily relies on the coniferous hosts for nutrients and carbon requirement, may largely relax the selection pressure on photosynthesis, as well as plastid transcription and translation, thus resulting in the loss/pseudogenization of such essential plastid-encoding genes in dwarf mistletoes. Therefore, the higher level of plastome degradation in Arceuthobium species than other Santalales hemiparasites is likely correlated with the evolution of leafless and endophytic habit. A higher degree of plastome degradation in Arceuthobium. These findings provide new insights into the plastome degeneration associated with parasitism in Santalales and deepen our understanding of the biology of dwarf mistletoes.

Plastome phylogenomics of Cephalotaxus (Cephalotaxaceae) and allied genera

BACKGROUND AND AIMS

Cephalotaxus is a paleo-endemic genus in East Asia that consists of about 7-9 conifer species. Despite its great economic and ecological importance, the relationships between Cephalotaxus and related genera, as well as the interspecific relationships within Cephalotaxus, have long been controversial, resulting in contrasting taxonomic proposals in delimitation of Cephalotaxaceae and Taxaceae. Based on plastome data, this study aims to reconstruct a robust phylogeny to infer the systematic placement and the evolutionary history of Cephalotaxus.

METHODS

A total of 11 plastomes, representing all species currently recognized in Cephalotaxus and two Torreya species, were sequenced and assembled. Combining these with previously published plastomes, we reconstructed a phylogeny of Cephalotaxaceae and Taxaceae with nearly full taxonomic sampling. Under a phylogenetic framework and molecular dating, the diversification history of Cephalotaxus and allied genera was explored.

KEY RESULTS

Phylogenetic analyses of 81 plastid protein-coding genes recovered robust relationships between Cephalotaxus and related genera, as well as providing a well-supported resolution of interspecific relationships within Cephalotaxus, Taxus, Torreya and Amentotaxus. Divergence time estimation indicated that most extant species of these genera are relatively young, although fossil and other molecular evidence consistently show that these genera are ancient plant lineages.

CONCLUSIONS

Our results justify the taxonomic proposal that recognizes Cephalotaxaceae as a monotypic family, and contribute to a clear-cut delineation between Cephalotaxaceae and Taxaceae. Given that extant species of Cephalotaxus are derived from recent divergence events associated with the establishment of monsoonal climates in East Asia and Pleistocene climatic fluctuations, they are not evolutionary relics.

The complete chloroplast genome sequence of Anemone reflexa (Ranunculaceae)

The complete chloroplast genome sequence of Anemone reflexa exhibited a typical quadripartite structure with two inverted repeats (IRa and IRb) of 31,260 bp, a large single-copy region (LSC) of 80,767 bp, and a small single-copy region (SSC) of 17,623 bp. The chloroplast genome encoded a set of 133 genes, comprised of 89 protein coding genes, 36 tRNA genes and 8 rRNA genes. Phylogenetic analysis suggested that A. reflexa was closely related to A. raddeana. The complete chloroplast genome sequence of A. reflexa will provide valuable genetic resources for molecular identification and phylogenetic analysis of Anemone.

Tight association of genome rearrangements with gene expression in conifer plastomes

BACKGROUND

Our understanding of plastid transcriptomes is limited to a few model plants whose plastid genomes (plastomes) have a highly conserved gene order. Consequently, little is known about how gene expression changes in response to genomic rearrangements in plastids. This is particularly important in the highly rearranged conifer plastomes.

RESULTS

We sequenced and reported the plastomes and plastid transcriptomes of six conifer species, representing all six extant families. Strand-specific RNAseq data show a nearly full transcription of both plastomic strands and detect C-to-U RNA-editing sites at both sense and antisense transcripts. We demonstrate that the expression of plastid coding genes is strongly functionally dependent among conifer species. However, the strength of this association declines as the number of plastomic rearrangements increases. This finding indicates that plastomic rearrangement influences gene expression.

CONCLUSIONS

Our data provide the first line of evidence that plastomic rearrangements not only complicate the plastomic architecture but also drive the dynamics of plastid transcriptomes in conifers.

Comparative plastid genomics of four Pilea (Urticaceae) species: insight into interspecific plastid genome diversity in Pilea

BACKGROUND

Pilea is a genus of perennial herbs from the family Urticaceae, and some species are used as courtyard ornamentals or for medicinal purposes. At present, there is no information about the plastid genome of Pilea, which limits our understanding of this genus. Here, we report 4 plastid genomes of Pilea taxa (Pilea mollis, Pilea glauca 'Greizy', Pilea peperomioides and Pilea serpyllacea 'Globosa') and performed comprehensive comparative analysis.

RESULTS

The four plastid genomes all have a typical quartile structure. The lengths of the plastid genomes ranged from 150,398 bp to 152,327 bp, and each genome contained 113 unique genes, including 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Comparative analysis showed a rather high level of sequence divergence in the four genomes. Moreover, eight hypervariable regions were identified (petN-psbM, psbZ-trnG-GCC, trnT-UGU-trnL-UAA, accD-psbI, ndhF-rpl32, rpl32-trnL-UAG, ndhA-intron and ycf1), which are proposed for use as DNA barcode regions. Phylogenetic relationships based on the plastid genomes of 23 species of 14 genera of Urticaceae resulted in the placement of Pilea in the middle and lower part of the phylogenetic tree, with 100% bootstrap support within Urticaceae.

CONCLUSION

Our results enrich the resources concerning plastid genomes. Comparative plastome analysis provides insight into the interspecific diversity of the plastid genome of Pilea. The identified hypervariable regions could be used for developing molecular markers applicable in various research areas.

High Sequence Divergence but Limited Architectural Rearrangements in Organelle Genomes of Cyanophora (Glaucophyta) Species

Cyanophora is the glaucophyte model taxon. Following the sequencing of the nuclear genome of C. paradoxa, studies based on single organelle and nuclear molecular markers revealed previously unrecognized species diversity within this glaucophyte genus. Here, we present the complete plastid (ptDNA) and mitochondrial (mtDNA) genomes of C. kugrensii, C. sudae, and C. biloba. The respective sizes and coding capacities of both ptDNAs and mtDNAs are conserved among Cyanophora species with only minor differences due to specific gene duplications. Organelle phylogenomic analyses consistently recover the species C. kugrensii and C. paradoxa as a clade and C. sudae and C. biloba as a separate group. The phylogenetic affiliations of the four Cyanophora species are consistent with architectural similarities shared at the organelle genomic level. Genetic distance estimations from both organelle sequences are also consistent with phylogenetic and architecture evidence. Comparative analyses confirm that the Cyanophora mitochondrial genes accumulate substitutions at 3-fold higher rates than plastid counterparts, suggesting that mtDNA markers are more appropriate to investigate glaucophyte diversity and evolutionary events that occur at a population level. The study of complete organelle genomes is becoming the standard for species delimitation and is particularly relevant to study cryptic diversity in microbial groups.

Genome skimming and exploration of DNA barcodes for Taiwan endemic cypresses

Cypresses are characterized by their longevity and valuable timber. In Taiwan, two endemic cypress species, Chamaecyparis formosensis and C. obtusa var. formosana, are threatened by prevalent illegal logging. A DNA barcode system is urgently needed for reforestation and conservation of these two cypresses. In this study, both plastomes and 35S rDNAs from 16, 10, and 6 individuals of C. formosensis, C. obtusa var. formosana, and C. obtusa var. obtusa were sequenced, respectively. We show that the loss of plastid trnT-GGU readily distinguishes C. formosensis from its congeneric species. We demonstrate that entire sequences of plastomes or 35S rDNAs are capable of correctly identifying cypress species and varieties, suggesting that they are effective super-barcodes. We also discover three short hypervariable loci (i.e., 3′ETS, ITS1, and trnH-psbA) that are promising barcodes for identifying cypress species and varieties. Moreover, nine species-specific indels of > 100 bp were detected in the cypress plastomes. These indels, together with the three aforementioned short barcodes, constitute an alternative and powerful barcode system crucial for identifying specimens that are fragmentary or contain degraded/poor DNA. Our sequenced data and barcode systems not only enrich the genetic reference for cypresses, but also contribute to future reforestation, conservation, and forensic investigations.

Repeated intercontinental migrations and recurring hybridizations characterise the evolutionary history of yew (Taxus L.)

The genus Taxus (Taxaceae) consists of 16 genetically well-defined lineages that are predominantly distributed across the Northern hemisphere. We investigated its biogeographic origin and evolutionary history by sampling 13 chloroplast gene sequences, the nuclear internal transcribed spacers (ITS) and NEEDLY sequences for all 16 lineages. We applied Maximum Parsimony and Bayesian Inference analyses to infer their phylogenetic relationships, time-calibrated phylogenies using BEAST and inferred the ancestral area of occupancy with BioGeoBEARS. We found strong evidence for the hybrid origin of three lineages and dated these events to a rather narrow time window of 6.8-4.9 million years ago (Mya). The dated phylogenies inferred an Upper Cretaceous origin of the genus, with the extant lineages diversifying in North America much later during the Oligocene/early Miocene. Repeated migrations via the Bering land bridge to Eurasia and back were further inferred, with the return to North America as a possible result of vicariance. The diversification in Eurasia (from ~8 Mya onwards) coincided with the orogeny of the Hengduan Mountains, the intensification of the East Asian summer monsoon and the occupancy of ecological niches by lineages that experienced secondary contacts and hybridizations in the Hengduan Mountains and Qinling Mountain, especially around the Sichuan basin. We provide a hypothesis for the evolution of extant lineages of Taxus, a genus with an old and complex evolutionary history. The study highlights that the history of complex species can be unravelled with a careful dissection of phylogenetic signals.

The utility of DNA barcodes to confirm the identification of palm collections in botanical gardens

The palm family (Arecaceae) is of high ecological and economic value, yet identification in the family remains a challenge for both taxonomists and horticulturalists. The family consists of approximately 2600 species across 181 genera and DNA barcoding may be a useful tool for species identification within the group. However, there have been few systematic evaluations of DNA barcodes for the palm family. In the present study, five DNA barcodes (rbcL, matK, trnH-psbA, ITS, ITS2) were evaluated for species identification ability across 669 samples representing 314 species and 100 genera in the Arecaceae, employing four analytical methods. The ITS gene region was found to not be a suitable barcode for the palm family, due in part, to low recovery rates and paralogous gene copies. Among the four analyses used, species resolution for ITS2 was much higher than that achieved with the plastid barcodes alone (rbcL, matK, trnH-psbA), and the barcode combination ITS2 + matK + rbcL gave the highest resolution among all single barcodes and their combinations, followed by ITS2 + matK. Among 669 palm samples analyzed, 110 samples (16.3%) were found to be misidentified. The 2992 DNA barcode sequences generated in this study greatly enriches the existing identification toolbox available to plant taxonomists that are interested in researching genetic relationships among palm taxa as well as for horticulturalists that need to confirm palm collections for botanical garden curation and horticultural applications. Our results indicate that the use of the ITS2 DNA barcode gene region provides a useful and cost-effective tool to confirm the identity of taxa in the Palm family.

Characteristics and Mutational Hotspots of Plastomes in Debregeasia (Urticaceae)

Debregeasia is an economically important genus of the nettle family (Urticaceae). Previous systematic studies based on morphology, or using up to four plastome regions, have not satisfactorily resolved relationships within the genus. Here, we report 25 new plastomes for Urticaceae, including 12 plastomes from five Debregeasia species and 13 plastomes from other genera. Together with the one published plastome for Debregeasia, we analyzed plastome structure and character, identified mutation hotspots and loci under selection, and constructed phylogenies. The plastomes of Debregeasia were found to be very conservative, with a size from 155,743 bp to 156,065 bp, and no structural variation. Eleven mutation hotspots were identified, including three (rpoB-trnC-GCA, trnT-GGU-psbD and ycf1) that are highly variable both within Debregeasia and among genera; these show high potential value for future DNA barcoding, population genetics and phylogenetic reconstruction. Selection pressure analysis revealed nine genes (clpP, ndhF, petB, psbA, psbK, rbcL, rpl23, ycf2, and ycf1) that may experience positive selection. Phylogenomic analyses results suggest that Debregeasia was monophyletic, and closest to Boehmeria among genera examined. Within Debregeasia, D. longifolia was sister to D. saeneb, whereas D. elliptica, D. orientalis with D. squamata formed the other subclade. This study enriches organelle genome resources for Urticaceae, and highlights the utility of plastome data for detecting mutation hotspots for evolutionary and systematic analysis.

Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in China

BACKGROUND

Calligonum (Polygonaceae) is distributed from southern Europe through northern Africa to central Asia, and is typically found in arid, desert regions. Previous studies have revealed that standard DNA barcodes fail to discriminate Calligonum species. In this study, the complete plastid genomes (plastome) for 32 accessions of 21 Calligonum species is sequenced to not only generate the first complete plastome sequence for the genus Calligonum but to also 1) Assess the ability of the complete plastome sequence to discern species within the group, and 2) screen the plastome sequence for a cost-effective DNA barcode that can be used in future studies to resolve taxonomic relationships within the group.

RESULTS

The whole plastomes of Calligonum species possess a typical quadripartite structure. The size of the Calligonum plastome is approximately 161 kilobase pairs (kbp), and encodes 113 genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Based on ML phylogenetic tree analyses, the complete plastome has higher species identification (78%) than combinations of standard DNA barcodes (rbcL + matK + nrITS, 56%). Five newly screened gene regions (ndhF, trnS-G, trnC-petN, ndhF-rpl32, rpl32-trnL) had high species resolution, where ndhF and trnS-G were able to distinguish the highest proportion of Calligonum species (56%).

CONCLUSIONS

The entire plastid genome was the most effective barcode for the genus Calligonum, although other gene regions showed great potential as taxon-specific barcodes for species identification in Calligonum.

Microfluidic Enrichment Barcoding (MEBarcoding): a new method for high throughput plant DNA barcoding

DNA barcoding is a valuable tool to support species identification with broad applications from traditional taxonomy, ecology, forensics, food analysis, and environmental science. We introduce Microfluidic Enrichment Barcoding (MEBarcoding) for plant DNA Barcoding, a cost-effective method for high-throughput DNA barcoding. MEBarcoding uses the Fluidigm Access Array to simultaneously amplify targeted regions for 48 DNA samples and hundreds of PCR primer pairs (producing up to 23,040 PCR products) during a single thermal cycling protocol. As a proof of concept, we developed a microfluidic PCR workflow using the Fluidigm Access Array and Illumina MiSeq. We tested 96 samples for each of the four primary DNA barcode loci in plants: rbcL, matK, trnH-psbA, and ITS. This workflow was used to build a reference library for 78 families and 96 genera from all major plant lineages - many currently lacking in public databases. Our results show that this technique is an efficient alternative to traditional PCR and Sanger sequencing to generate large amounts of plant DNA barcodes and build more comprehensive barcode databases.

Comparison of the abilities of universal, super, and specific DNA barcodes to discriminate among the original species of Fritillariae cirrhosae bulbus and its adulterants

Fritillariae cirrhosae bulbus is a famous type of traditional Chinese medicine used for cough relief and eliminating phlegm. The medicine originates from dried bulbs of five species and one variety of Fritillaria. Recently, immature bulbs from other congeneric species, such as F. ussuriensis, have been sold as adulterants of Fritillariae cirrhosae bulbus in medicine markets owing to the high price and limited availability of the genuine medicine. However, it is difficult to accurately identify the bulbs from different original species of Fritillariae cirrhosae bulbus and its adulterants based on traditional methods, although such medicines have different prices and treatment efficacies. The present study adopted DNA barcoding to identify these different species and compared the discriminatory power of super, universal, and specific barcodes in Fritillaria. The results revealed that the super-barcode had strong discriminatory power (87.5%). Among universal barcodes, matK provided the best species resolution (87.5%), followed by ITS (62.5%), rbcL (62.5%), and trnH-psbA (25%). The combination of these four universal barcodes provided the highest discriminatory power (87.5%), which was equivalent to that of the super-barcode. Two plastid genes, ycf1 and psbM-psbD, had much better discriminatory power (both 87.5%) than did other plastid barcodes, and were suggested as potential specific barcodes for identifying Fritillaria species. Phylogenetic analyses indicated that F. cirrhosa was not a "good" species that was composed of multiple lineages, which might have affected the evaluation of the discriminatory ability. This study revealed that the complete plastid genome, as super barcode, was an efficient and reliable tool for identifying the original species of Fritillariae cirrhosae bulbus and its adulterants.

Comparative Genomic Analysis Reveals the Mechanism Driving the Diversification of Plastomic Structure in Taxaceae Species

Inverted repeat (IR) regions in the plastomes from land plants induce homologous recombination, generating isomeric plastomes. While the plastomes of Taxaceae species often lose one of the IR regions, considerable isomeric plastomes were created in Taxaceae species with a hitherto unclarified mechanism. To investigate the detailed mechanism underpinning the IR-independent genesis of plastomic diversity, we sequenced four Taxaceae plastomes, including Taxus cuspidata Siebold & Zuccarini, Taxus fauna Nan Li & R. R. Mill, and two individuals of Taxus wallichiana Zuccarini. Then we compared these structures with those of previously reported Taxaceae plastomes. Our analysis identified four distinct plastome forms that originated from the rearrangements of two IR-flanking inverted fragments. The presence of isomeric plastomes was then verified in T. cuspidata individuals. Both rearrangement analyses and phylogenetic results indicated that Taxaceae were separated into two clades, one including Taxus and Pseudotaxus and another formed by Amentotaxus and Torreya. Our reconstructed scenario suggests that the minimum number of inversion events required for the transformation of the plastome of Cephalotaxus oliveri Masters into the diversified Taxaceae plastomes ranged from three to six. To sum up, our study reveals a distinct pattern and the mechanism driving the structural diversification of Taxaceae plastomes, which will advance our understanding of the maintenance of plastomic diversity and complexity in conifers.

Species Identification of Oaks (Quercus L., Fagaceae) from Gene to Genome

Species identification of oaks (Quercus) is always a challenge because many species exhibit variable phenotypes that overlap with other species. Oaks are notorious for interspecific hybridization and introgression, and complex speciation patterns involving incomplete lineage sorting. Therefore, accurately identifying Quercus species barcodes has been unsuccessful. In this study, we used chloroplast genome sequence data to identify molecular markers for oak species identification. Using next generation sequencing methods, we sequenced 14 chloroplast genomes of Quercus species in this study and added 10 additional chloroplast genome sequences from GenBank to develop a DNA barcode for oaks. Chloroplast genome sequence divergence was low. We identified four mutation hotspots as candidate Quercus DNA barcodes; two intergenic regions (matK-trnK-rps16 and trnR-atpA) were located in the large single copy region, and two coding regions (ndhF and ycf1b) were located in the small single copy region. The standard plant DNA barcode (rbcL and matK) had lower variability than that of the newly identified markers. Our data provide complete chloroplast genome sequences that improve the phylogenetic resolution and species level discrimination of Quercus. This study demonstrates that the complete chloroplast genome can substantially increase species discriminatory power and resolve phylogenetic relationships in plants.