Comparative studies on species identification of Noctuoidea moths in two nature reserve conservation zones (Beijing, China) using DNA barcodes and thin-film biosensor chips

The complete chloroplast genome of Pluchea pteropoda Hemsl, a mangrove associate plant

Pluchea pteropoda Hemsl is a mangrove associate plant of Asteraceae with medicinal properties such as anti-inflammation and fever-relieving. Here, our study presented the complete chloroplast (cp) genome of Pluchea pteropoda Hemsl. The cp genome of P. pteropoda was 152,300 bp in length, including a large single copy (LSC) region of 84,127 bp, a small single copy (SSC) region of 18,093 bp and a pair of inverted repeats (IR) regions of 25,040 bp. A total of 111 unique genes were found, comprising 79 protein-coding genes, 28 tRNA genes, and 4 rRNA genes. The GC content of the cp genome was 37.5%. Phylogenetic analysis suggested that P. pteropoda nested in Pluchea clade, which was closely related to Ageratina adenophora and Senecio scandens. The work provides beneficial data for following researches on the genetic variation, species delimitation, phylogeny and classification of Pluchea genus.

The efficacy of DNA barcoding in the classification, genetic differentiation, and biodiversity assessment of benthic macroinvertebrates

Macroinvertebrates have been recognized as key ecological indicators of aquatic environment and are the most commonly used approaches for water quality assessment. However, species identification of macroinvertebrates (especially of aquatic insects) proves to be very difficult due to the lack of taxonomic expertise in some regions and can become time-consuming. In this study, we evaluated the feasibility of DNA barcoding for the classification of benthic macroinvertebrates and investigated the genetic differentiation in seven orders (Insecta: Ephemeroptera, Plecoptera, Trichoptera, Diptera, Hemiptera, Coleoptera, and Odonata) from four large transboundary rivers of northwest China and further explored its potential application to biodiversity assessment. A total of 1,144 COI sequences, belonging to 176 species, 112 genera, and 53 families were obtained and analyzed. The barcoding gap analysis showed that COI gene fragment yielded significant intra- and interspecific divergences and obvious barcoding gaps. NJ phylogenetic trees showed that all species group into monophyletic species clusters whether from the same population or not, except two species (Polypedilum. laetum and Polypedilum. bullum). The distance-based (ABGD) and tree-based (PTP and MPTP) methods were utilized for grouping specimens into Operational Taxonomic Units (OTUs) and delimiting species. The ABGD, PTP, and MPTP analysis were divided into 177 (p = .0599), 197, and 195 OTUs, respectively. The BIN analysis generated 186 different BINs. Overall, our study showed that DNA barcoding offers an effective framework for macroinvertebrate species identification and sheds new light on the biodiversity assessment of local macroinvertebrates. Also, the construction of DNA barcode reference library of benthic macroinvertebrates in Eurasian transboundary rivers provides a solid backup for bioassessment studies of freshwater habitats using modern high-throughput technologies in the near future.

Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae

Avicennia marina (family Acanthaceae) is a halotolerant woody shrub that grows wildly and cultivated in the coastal regions. Despite its importance, the species suffers from lack of genomic datasets to improve its taxonomy and phylogenetic placement across the related species. Here, we have aimed to sequence the plastid genome of A. marina and its comparison with related species in family Acanthaceae. Detailed next-generation sequencing and analysis showed a complete chloroplast genome of 150,279 bp, comprising 38.6% GC. Genome architecture is quadripartite revealing large single copy (82,522 bp), small single copy (17,523 bp), and pair of inverted repeats (25,117 bp). Furthermore, the genome contains 132 different genes, including 87 protein-coding genes, 8 rRNA, 37 tRNA genes, and 126 simple sequence repeats (122 mononucleotide, 2 dinucleotides, and 2 trinucleotides). Interestingly, about 25 forward, 15 reversed and 14 palindromic repeats were also found in the A. marina. High degree synteny was observed in the pairwise alignment with related genomes. The chloroplast genome comparative assessment showed a high degree of sequence similarity in coding regions and varying divergence in the intergenic spacers among ten Acanthaceae species. The pairwise distance showed that A. marina exhibited the highest divergence (0.084) with Justicia flava and showed lowest divergence with Aphelandra knappiae (0.059). Current genomic datasets are a valuable resource for investigating the population and evolutionary genetics of family Acanthaceae members' specifically A. marina and related species.

Genomic evidence of prevalent hybridization throughout the evolutionary history of the fig-wasp pollination mutualism

Ficus (figs) and their agaonid wasp pollinators present an ecologically important mutualism that also provides a rich comparative system for studying functional co-diversification throughout its coevolutionary history (~75 million years). We obtained entire nuclear, mitochondrial, and chloroplast genomes for 15 species representing all major clades of Ficus. Multiple analyses of these genomic data suggest that hybridization events have occurred throughout Ficus evolutionary history. Furthermore, cophylogenetic reconciliation analyses detect significant incongruence among all nuclear, chloroplast, and mitochondrial-based phylogenies, none of which correspond with any published phylogenies of the associated pollinator wasps. These findings are most consistent with frequent host-switching by the pollinators, leading to fig hybridization, even between distantly related clades. Here, we suggest that these pollinator host-switches and fig hybridization events are a dominant feature of fig/wasp coevolutionary history, and by generating novel genomic combinations in the figs have likely contributed to the remarkable diversity exhibited by this mutualism.

Complete chloroplast genome sequence of Punica granatum ‘Nana’ (Lythraceae) and phylogenetic analysis

Pomegranate (Punica granatum L.) is of great significance both as a fruit tree and an ornamental plant. Hereon, we sequenced and characterized the complete chloroplast genome of Punica granatum ‘Nana’ and performed phylogenetic analysis concerning related species. It turned out that the length of chloroplast genome sequence reached 158,639 bp and exhibited a four-conjoined structure, i.e., a large single copy region (LSC, 89,022 bp), a small single copy region (SSC, 18,685 bp) and twain inverted repeat regions (IRa and IRb, 25,466 bp). 112 unique genes were identified, consisting of 78 protein-coding genes, four ribosomal RNA (rRNA) genes and 30 transfer RNA (tRNA) genes. The result of phylogenetic analysis based on Neighbor-joining (NJ) method was consistent with that of Bayesian inference (BI), which strongly supported that Punica granatum ‘Nana’ was close to its original species Punica granatum and they together had a close relationship with Heimia myrtifolia within Lythraceae.

Development and characterization of 16 novel microsatellite markers by Transcriptome sequencing for Angelica dahurica and test for cross-species amplification

BACKGROUND

Angelica dahurica (Apiaceae) is an important herb in traditional Chinese medicine. Because of its important medicinal and economic values, its wild resources were over-exploited and increasingly reduced. Meanwhile, the diversity of cultivars of A. dahurica has decreased as a result of long-term artificial cultivation. However, there are no population genetics studies of natural A. dahurica reported yet, especially for using microsatellite markers (SSRs) to investigate population genetics of the species.

RESULTS

Sixteen polymorphic EST-SSR loci were isolated from A. dahurica with transcriptome sequencing technology (RNA-Seq). The number of alleles varied from 2 to 15 per polymorphic locus over populations with the observed and expected heterozygosities ranging from 0.000 to 1.000 and from 0.000 to 0.829, respectively. Significant deviations from Hardy-Weinberg equilibrium were observed at 8 loci. Tests of linkage disequilibrium showed 11 informative locus pairs were significant across all populations. Cross-species amplification showed that 14 out of 16 SSR loci have the transferability in cultivar-A. dahurica cv. 'Hangbaizhi' and A. decursiva.

CONCLUSIONS

The 16 newly developed loci microsatellite primers with RNA-Seq will be useful for further investigating population genetics of A. dahurica, cultivars and other members of this genus.

The complete chloroplast genome sequence of an alpine wildflower, Philadelphus calvescens (Rehd.) S. M. Hwang (Saxifragaceae)

Philadelphus calvescens, belonging to the family Saxifragaceae, is a beautiful shrub with white fragrant flowers which is widely distributed in southwest China. In this study, we sequenced the complete chloroplast (cp) genome of P. calvescens to investigate its phylogenetic relationship in Saxifragaceae. Total length of the cpDNA genome was 157,237 bp, consisting of a large single copy (LSC) region of 86,481 bp, a small single copy (SSC) region of 18,728 bp, and a pair of inverted repeat regions (IRs, 26,014 bp). The genome contained 114 genes, namely 79 protein-coding genes, 31 tRNA genes, and 4 rRNA. The overall GC content was 37.8%. Phylogenetic analysis suggested that Philadelphus was closely related to Deutzia. The present study was the first report on complete cp genome of Philadelphus so it could afford important genetic information for further researches on the genus and related genera.

The first complete chloroplast genome sequence of the medicinal plant Bletilla formosana (Orchidaceae)

Bletilla formosana is a medicinal plant commonly used in southwest of China. In this study, we sequenced the complete chloroplast (cp) genome sequence of B. formosana to investigate its phylogenetic relationship in the family Orchidaceae. The chloroplast genome of B. formosana was 159,112 bp in length with 37.3% overall GC content, including a large single-copy (LSC) region of 86,838 bp, a small single-copy (SSC) region of 18,672 bp and a pair of inverted repeats (IRs) of 26,801 bp. The cp genome contained 116 genes, including 83 protein-coding genes, 29 tRNA genes, and 4 rRNA genes. The phylogenetic analysis indicated the genus Bletilla was closely related to Platanthera.

Complete chloroplast genome of Panax japonicus var. major (Burkill) C. Y. Wu & K. M. Feng (Araliaceae) and phylogenetic analysis

Panax japonicus var. major (Araliaceae) is an important medicinal plant, whose rhizomes have pharmacological activities such as protection of cardiovascular and cerebrovascular system, central nervous system and so on. In this study, we sequenced complete chloroplast (cp) genome sequence of P. japonicus var. major so as to explore phylogenetic relationship between this species and related species. The results showed that complete cp genome of P. japonicus var. major was 156,402 bp in length, consisting of a large single copy (LSC) region of 86,187 bp, a small single copy (SSC) region of 18,007 bp, and two inverted repeat regions (IRa and IRb) of 26,104 bp. In total, 114 genes were annotated, comprising of 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis indicated that P. japonicus var. major was closely related to its original variety, P. japonicus var. japonicus; meanwhile, Panax was a monophyletic group with high support value and it had a close relationship with Aralia in Araliaceae.

Complete chloroplast genome sequences of two species used for Tibetan medicines, Meconopsis punicea vig. and M. henrici vig. (Papaveraceae)

Meconopsis Vig. is a genus possessing important medicinal and ornamental values in the Papaveraceae. Many species in this genus are commonly used in traditional Tibetan medicines over thousands of years. In this study, we sequenced complete chloroplast (cp) genome sequences of two species, namely Meconopsis punicea and M. henrici to investigate their phylogenetic relationships in Papaveraceae. Total lengths of the chloroplast genomes were 153,281 bp and 153,388 bp, respectively. Both of the two genomes had typical quadripartite structure, LSC region (83,999 bp and 83,698 bp) and SSC region (17,730 bp and 17,822 bp) were separated by a pair of IRs (25,776 bp and 26,107 bp), respectively. Moreover, they were composed of 112 genes, including 78 protein coding genes, 30 tRNA genes, three rRNA genes and one pseudogene. Phylogenetic analysis based on complete chloroplast genomes showed that M. henrici had closer relationship with M. racenosa than M. punicea; meanwhile, Meconopsis was closely related to Papaver in Papaveraceae.

Characterization of the complete chloroplast genome of Ajuga forrestii (Lamiaceae), a medicinal plant in southwest of China

Ajuga forrestii is a medicinal plant commonly used in southwest of China. In this study, we sequenced the complete chloroplast (cp) genome sequence of A. forrestii to investigate its phylogenetic relationship in the family Lamiaceae. The chloroplast genome of A. forrestii was 150,492 bp in length with 38.3% overall GC content, including a large single copy (LSC) region of 82,148 bp, a small single copy (SSC) region of 17,160 bp and a pair of inverted repeats (IRs) of 25,592 bp. The cp genome contained 112 genes, including 79 protein coding genes, 29 tRNA genes, and 4 rRNA genes. The phylogenetic analysis indicated Ajuga was closely related to Scutellaria.

The complete chloroplast genome sequence of Ficus hirta (Moraceae)

The dry root (Radix Fici Hirtae) of Ficus hirta has been used as a traditional herbal medicine in Ling nan regions of China for a long time. As its large market demand, the wild resources of F. hirta have sharply reduced. It is necessary to conduct the study of conservation genetics. However, there is still lack of complete genome information for the research on evolutionary biology, population genetics and phylogeography of this species. Here, we sequenced the complete chloroplast (CP) genome of F. hirta using Next Generation Sequencing technology (NGS). The CP genome of F. hirta is 160,374 bp in length, which contains a large single-copy (LSC) region of 88,446 bp, a small sing-copy (SSC) region of 18,134 bp, and two inverted repeat (IRa and IRb) regions of 26,897 bp. A total of 130 genes were successfully annotated containing 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Phylogenetic analysis support genus Ficus is monophyletic and F. hirta is closely related to F. carica within this genus.

The complete plastome genome and its inference on the phylogenetic position of Bletilla formosana (Orchidaceae)

Bletilla formosana is a traditional Chinese medicinal herb and recently threatened by overexploitation owing to the increasing demand. In present study, we sequenced and assembled the complete chloroplast (cp) genomes of this species. The plastome genome is a typical quadripartite circle molecule with the total lenth of 158,968 bp and overall GC content of 37.3%. We predicted 104 genes in the cp genome, including 80 protein coding gens, 20 tRNA and 4 rRNA. Phylogenetic analysis shows that B. formosana is sister to B. striata.

Characterisation of the complete chloroplast genome of Gentiana delavayi Franch. (gentianaceae), a medicinal plant in southwest of China

Gentiana delavayi is a medicinal plant commonly used in southwest of China. In this study, we sequenced the complete chloroplast (cp) genome sequence of G. delavayi to investigate its phylogenetic relationship in the family Gentianaceae. The chloroplast genome of G. delavayi was 151,569 bp in length with 37.8% overall GC content, including a large single copy (LSC) region of 81,177 bp, a small single copy (SSC) region of 16,921 bp and a pair of inverted repeats (IRs) of 25,471 bp. The cp genome contained 114 genes, including 78 protein coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic analysis indicated G. delavayi was closely related to G. stipitata.

The complete chloroplast genome sequence of the medicinal plant Salvia yunnanensis C. H. Wright. (Lamiaceae)

Salvia yunnanensis is a medicinal plant commonly used in the southwest of China. In this study, we sequenced the complete chloroplast (cp) genome sequence of S. yunnanensis to investigate its phylogenetic relationship in the family Lamiaceae. The total length of the cp genome was 151,338 bp, with 38.0% overall GC content and exhibited typical quadripartite structure, a pair of IRs (inverted repeats) of 25,578 bp each were separated by a small single-copy (SSC) region of 17,564 bp and a large single-copy (LSC) region of 82,618 bp. The cp genome contained 114 genes, including 80 protein coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic analysis indicated S. yunnanensis was closely related to S. miltiorrhiza, which afforded a scientific evidence that S. yunnanensis could be used as original species of Radix et Rhizoma Saliviae Miltiorrhizae (Danshen).

The complete chloroplast genome sequence of the medicinal plant Paeonia delavayi Franchet. (Paeoniaceae)

Paeonia delavayi is a medicinal plant commonly used in southwest of China. In this study, we sequenced the complete chloroplast (cp) genome sequence of P. delavayi to investigate its phylogenetic relationship in the family Paeoniaceae. The chloroplast genome of P. delavayi was 152,872 bp in length with 38.4% overall GC content, including a large single copy (LSC) region of 84,523 bp, a small single copy (SSC) region of 17,053 bp and a pair of inverted repeats (IRs) of 25,646 bp. The cp genome contained 105 genes, including 75 protein coding genes, 27 tRNA genes, and 4 rRNA genes. The phylogenetic analysis indicated P. delavayi was closely related to P. ludlowii.

The complete chloroplast genome sequence of Eriobotrya fragrans

Eriobotrya fragrans Champion ex Bentham is a potential medicinal plant of the genus Eriobotrya Lindl in the family Rosaceae. To better determine its phylogenetic location with respect to the other Rosaceae species, the complete chloroplast genome of E. fragrans was sequenced. The whole E. fragrans chloroplast genome is 159,286 bp in length, consisting of a pair of inverted repeat (IR) regions of 26,343 bp, one large single-copy (LSC) region of 87,301 bp, and one small single-copy (SSC) region of 19,299 bp. The overall GC content of the whole chloroplast genome is 36.7%. Further, phylogenetic analysis using maximum likelihood with TVM + F+R2 model strongly supports the relationship: sisterhood of E. fragrans and E. japonica, followed by three species of Pyrus L.

Plastome sequences help to improve the systematic position of trinerved Lindera species in the family Lauraceae

Lindera is a genus (c. 100 spp.) of trees belonging to the “core Laureae” group in the family Lauraceae. It is often confused with Litsea, and the systematics of the genus is unclear. Here, total 10 complete plastomes from nine trinerved Lindera species and another species Lindera obtusiloba (sect. Palminerviae Meissn.) were sequenced. Nine highly variable regions, trnH-GUG/psbA, psbM/trnD-GUC, petA/psbL, ndhF, trnL-UAG/ndhD, and ycf1, were identified among the 10 Lindera species. In addition, a total of 1,836 mutation events including six micro-inversions, 156 indels, and 1,674 substitutions, were also summarized. Comparing our sequences with other available plastomes in the “core Laureae,” we put forward that six hypervariable loci, trnH-GUG/psbA, ndhF, ndhF/rpl32, trl32/trnL-UAG, ndhD, and ycf1, could potentially be used as plastid barcode candidates for species identification. Further phylogenetic analyses were conducted using 49 complete Lauraceae plastomes. The results supported a close relationship among trinerved Lindera species and suggested an improved trinerved group comprising species of trinerved Lindera species and Iteadaphne caudate.

The complete chloroplast genome sequence of Onosma paniculatum Bur. et Franch. (Boraginaceae), a medicinal plant in Yunnan and its adjacent regions

Onosma paniculatum is a medicinal plant commonly used in Yunnan and its adjacent regions, China. In the present study, we sequenced the complete chloroplast (cp) genome sequence of O. paniculatum to investigate the phylogenetic relationship in the Tubiflorae. The total length of the chloroplast genome was 151,198 bp, with 37.4% overall GC content and exhibited typical quadripartite structure, a pair of IRs (inverted repeats) of 25,889 bp was separated by a small single copy (SSC) region of 17,274 bp and a large single copy (LSC) region of 82,146 bp. The cp genome was composed of 113 genes, including 79 protein coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic analysis indicated that Boraginaceae was closely related to Convolvulaceae and Solanaceae in Tubiflorae.

The plastid genome of a spice plants Cinnamomum glanduliferum in Tibet (Lauraceae)

Cinnamomum glanduliferum (Wall) Meissn is a commercially important timber tree and wild spice plants of the genus Cinnamomum Trew in the family Lauraceae. To determine its phylogenetic location with respect to the other Cinnamomum species, the complete plastid genome of C. glanduliferum was sequenced. The whole plastome is 152,715 bp in length, consisting of a pair of inverted repeat (IR) regions of 20,114 bp, one large single copy (LSC) region of 93,617 bp, and one small single copy (SSC) region of 18,870 bp. The overall GC content of the whole plastome is 39.1%. Further, maximum likelihood phylogenetic analyse was conducted using 13 complete plastomes of the Lauraceae, which support close relationship between C. glanduliferum and C. bodinieri.

Characterization of the complete plastome of medicinal plant Saururus chinensis (Saururaceae)

Saururus chinensis is an important medicinal plant in Southeast Asia. Here, we determined the first complete plastome of S. chinensis using high throughput Illumina sequencing technology. The S. chinensis plastome is 161,494 bp in length and presents a typical quadripartite structure consisting of one large single-copy region (LSC, 88,863 bp), one small single-copy region (SSC, 18,679 bp), and a pair of inverted repeat regions (IRs, 26,976 bp each). The phylogenetic analysis robustly supports that S. chinensis is sister to the group including the Saruma henryi, Asarum sieboldii, Piper kadsura, Piper cenocladum.

Complete plastome of Houttuynia cordata (Saururaceae), a medicinal and edible plant

The complete plastome of Houttuynia cordata, an important medicinal and edible plant, was identified and sequenced in this study. The circular plastome is 160,217 bp in length and consists of a pair of inverted repeats (IRs 26,854 bp each), which is separated by a large single-copy region (LSC, 88,189 bp) and a small single-copy region (SSC, 18,320 bp). It encodes 132 genes, of which 114 are unique genes (80 protein-coding genes, 30 tRNAs, and 4 rRNAs). The phylogenetic analysis strongly reveals the sister group between H. cordata and the clade including Piper kadsura, Piper cenocladum, Saruma henryi, and Asarum sieboldii.

The complete plastome of Gymnotheca chinensis (Saururaceae) and its phylogenetic analysis

The complete plastome of Gymnotheca chinensis, an important medicinal herb, was firstly elucidated and analyzed in this study. The plastome is 161,621 bp in size, which comprises of one large single-copy (LSC) region and one small single-copy (SSC) region of 89,291 bp and 18,592 bp, respectively, separated by a pair of IR regions of 26,869 bp each. It encodes a total of 132 genes, including 87 protein-coding genes, 37 tRNA, and 8 rRNA. The phylogeny robustly supports that G. chinensis is sister to the clade including Piper kadsura, Piper cenocladum, Saruma henryi, Asarum sieboldii.

Characterization of the whole plastome of Dipentodon Sinicus (Dipentodontaceae)

In this study, we sequenced and assembled the whole plastome of Dipentodon sinicus. The plastome was 158,020 bp in length and consisted of a pair of inverted repeat regions (IRs, 26,551 bp), a large single-copy region (LSC, 86,624 bp) and a small single-copy region (SSC, 18,294 bp). It encoded 114 unique genes (80 protein-coding genes, 30 tRNA genes and 4 rRNA genes). Phylogenetic analysis showed that Dipentodon sinicus was sister to Tapiscia sinensis.

Characterization of the complete chloroplast genome of Boschniakia himalaica J. D. Hooker & Thomson (Orobanchaceae), a medicinal species in southwest China

Boschniakia himalaica is a medicinal plant in southwest China. In this study, we sequenced complete chloroplast (cp) genome of B. himalaica to investigate its phylogenetic relationship in Orobanchaceae. The chloroplast genome was 106,466 bp in length with 37.3% overall GC content, including a large single copy (LSC) region of 49,606 bp, a small single copy (SSC) region of 5572 bp, and a pair of inverted repeats (IRs) of 25,644 bp. The cp genome contained 84 genes, including 50 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic analysis indicated B. himalaica was closely related to Cistanche deserticola.

Characterization of the complete chloroplast genome of Scutellaria amoena C. H. Wright (Lamiaceae), a medicinal plant in southwest China

Scutellaria amoena is a frequently-used medicinal plant in Southwerst China. In this study, we sequenced the complete chloroplast (cp) genome sequence of S. amoena C. H. Wright to investigate its phylogenetic relationship in the family Lamiaceae. The chloroplast genome of S. amoena was 151, 569 bp in length with 38.4% overall GC content, including a large single copy (LSC) region of 83,739 bp, a small single copy (SSC) region of 17,326 bp and a pair of inverted repeats (IRs) of 25,252 bp. The cp genome contained 112 genes, including 79 protein-coding genes, 29 tRNA genes, and 4 rRNA genes. The phylogenetic analysis indicated S. amoena was closely related to S. baicalensis that is used as original species of Scutellariae Radix.

Complete plastome of the medicinally important plant, Alstonia scholaris (Apocynaceae)

Alstonia scholaris is an evergreen tropical tree with significant medicinal values. To better understand its genetic and genomic profiles, we sequenced and assembled the completed plastome of A. scholaris. The plastome is 154,699 bp in length, consisting of a large (LSC, 85,364 bp) and a small single-copy region (SSC, 18,027 bp), which are separated by a pair of inverted repeat regions (IRs, 25,654 bp). It possesses 116 unique genes (82 protein-coding genes, 30 tRNAs, and 4 rRNAs). Phylogenetic analysis suggests that A. scholaris is sister to the clade including remaining Apocynaceae species.

The complete chloroplast genome of Ophiopogon japonicus, an ornamental and medicinal plant

Ophiopogon japonicus, extensively distributed in East Asia, is widely used in landscaping, the tuber of which also play a vital role in Oriental Medicine. Here, we reported the complete chloroplast genome which exhibited a typical quadripartite structure, 156,679 bp in length with 37.7% overall GC content, including 131 protein-coding genes, 37 transfer RNA genes, eight ribosomal RNA genes, and one pseudogene. Phylogenetic analysis suggested that O. japonicus has a close relationship to Liriope spicata.

Comparative analysis of the complete chloroplast genome among Prunus mume, P. armeniaca, and P. salicina

Prunus mume Sieb. et Zucc., P. armeniaca L., and P. salicina L. are economically important fruit trees in temperate regions. These species are taxonomically perplexing because of shared interspecific morphological traits and variation, which are mainly attributed to hybridization. The chloroplast is cytoplasmically inherited and often used for evolutionary studies. We sequenced the complete chloroplast genomes of P. mume, P. armeniaca, and P. salicina using Illumina sequencing followed by de novo assembly. The three chloroplast genomes exhibit a typical quadripartite structure with conserved genome arrangement, structure, and moderate divergence. The lengths of the genomes are 157,815, 157,797, and 157,916 bp, respectively. The length of the large single-copy region (LSC) region is 86,113, 86,283, and 86,122 bp, and the length of the SSC region is 18,916, 18,734, and 19,028 bp; the IR region is 26,393, 26,390, and 26,383 bp, respectively. Each of the three chloroplast genomes encodes 133 genes, including 94 protein-coding, 31 tRNA, and eight rRNA genes. Differential gene analysis for the three species revealed that trnY-ATA is a unique gene in P. armeniaca; in contrast, the gene trnI-TAT is only present in P. mume and P. salicina, though the position of the gene in these chloroplast genomes differs. Further comparative analysis of the complete chloroplast genome sequences revealed that the ORF genes and the sequences of linked regions rps16 and atpA, atpH and atpI, trnc-GCA and psbD, ycf3 and atpB, and rpL32 and ndhD are significantly different and may be used as molecular markers in taxonomic studies. Phylogenetic evolution analysis of the three species suggests that P. mume has a closer genetic relationship to P. armeniaca than to P. salicina.

The complete chloroplast genome of Calanthe arcuata, an endemic terrestrial orchid in China

Calanthe arcuata is an endemic terrestrial orchid in China with high value of ornament and breeding. Here, we reported the first complete chloroplast genome of this plant in this research. The circular genome is 158,735 bp in length and includes large single-copy (LSC) region of 87,348 bp, small single-copy (SSC) region of 18,489 bp, and a pair of invert repeats (IR) regions of 26,449 bp. It contains 136 genes, including 88 protein-coding (PCG), 38 transfer RNA (tRNA), and eight ribosomal RNA (rRNA) gene. The phylogenetic analysis indicated that C. arcuata is the sister to C. davidii and C. triplicata.

Complete chloroplast genome of a Chinese endemic species Corydalis trisecta Franch. (Papaveraceae)

Corydalis trisecta Franch. is an endemic plant found in China. In this study, we presented the first complete chloroplast genome of C. trisecta, which was assembled and characterized based on Illumina pair-end sequencing data. The complete chloroplast genome was 161,410 bp in length, with a GC content of 41.4% in total. Its structure contained a large single copy (LSC) region of 89,127 bp and a small single copy (SSC) region of 16,993 bp, which were separated by a pair of extremely inverted repeats (IRs) of 27,645 bp each, with GC content 39.8, 87.2, and 45.2%, respectively. The phylogenetic analysis indicated that C. triscta was sister to Lamprocapons spectabilis in Papaveraceae.

The plastid genome sequence of Neocinnamomum delavayi (Lec.) Liou

Neocinnamomum delavayi (Lec.) Liou is a kind of medicinal plants belonging to the genus Neocinnamomum H. Liu, but is often confused with N. mekongense (Hand.-Mazz.) Kosterm. Here, the complete plastid sequence of the N. delavayi was determined. The length of the plastid genome is 150,584 bp with overall AT content of 61%. It exhibited a typical quadripartite structure comprising a large single copy region (LSC) of 91,887 bp, a small single copy region (SSC) of 18,443 bp, and a pair of inverted repeat regions (IRs) of 20,262 bp each. Maximum likelihood phylogenetic analysis with GTR + F+R2 model was performed using eighteen complete plastomes of the Lauraceae, which strongly supports the relationships: sisterhood of the N. delavayi and a clade containing N. mekongense and N. lecomtei Liou.

The complete chloroplast genome sequence of the medicinal plant Nicandra physalodes (Linn.) Gaertn. (Solanaceae)

Nicandra physalodes is an alien plant in southern China, possessing important medicinal values. In this study, we sequenced complete chloroplast (cp) genome sequence of N. physalodes and investigated its phylogenetic relationship in the family Solanaceae. The total length of the chloroplast genome was 156,729 bp, with 37.8% overall GC content and exhibited typical quadripartite structure, a pair of IRs (inverted repeats) of 25,529 bp was separated by a small single copy (SSC) region of 18,560 bp and a large single copy (LSC) region of 87,111 bp. The cp genome contained 113 genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis indicated N. physalodes was closely related to Datura stramonium.

The complete chloroplast genome sequence of the medicinal plant Colquhounia coccinea var. mollis (Lamiaceae)

Colquhounia coccinea var. mollis is a medicinal plant commonly used in Dali area of southwest China. In this study, we sequenced the complete chloroplast (cp) genome sequence of C. coccinea var. mollis to investigate its phylogenetic relationship in the family Lamiaceae. The total length of the chloroplast genome was 151,965 bp, with 38.4% overall GC content and exhibited typical quadripartite structure, a pair of IRs (inverted repeats) of 25,651 bp was separated by a small single copy (SSC) region of 17,498 bp and a large single copy (LSC) region of 83,165 bp. The cp genome contained 113 genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic analysis indicated C. coccinea var. mollis was closely related to Galeopsis tetrahit and Lamium galeobdolon.

The chloroplast genome of aromatic plants Cinnamomum burmanni (Lauraceae)

Cinnamomum burmanni (Nees et T. Nees) Blume is a valuable aromatic timber tree of the genus Cinnamomum Tree in the family Lauraceae. To better determine its phylogenetic location with respect to the other Cinnamomum species, the complete chloroplast genome of C. burmanni was sequenced. The total chloroplast genome size is 152,775 bp, consisting of a pair of inverted repeats (IRa/b) with a length of 20,092 bp separated by a large single-copy region (LSC) and a small single-copy region (SSC) which are 93,687 and 18,903 bp, respectively. The overall GC content of the cp genome is 39.1%. Further, maximum-likelihood phylogenetic analysis with K3Pu + F+I model was performed using eleven complete plastomes of the Lauraceae, which revealed that C. burmanni is closely related to C. verum.

The complete chloroplast genome sequence of the medicinal plant Paris polyphylla (Melanthiaceae)

Paris polyphylla is a medicinal plant commonly used in southwest of China. In this study, we sequenced the complete chloroplast (cp) genome sequence of P. polyphylla to investigate its phylogenetic relationship in the genus Paris. The chloroplast genome of P. polyphylla was 163,533 bp in length with 37.1% overall GC content, including a large single copy (LSC) region of 84,272 bp, a small single copy (SSC) region of 12,899 bp and a pair of inverted repeats (IRs) of 33,181 bp. The cp genome contained 114 genes, including 79 protein coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic analysis indicated P. polyphylla was closely related to P. marmorata.

Origin of angiosperms and the puzzle of the Jurassic gap

Angiosperms are by far the most species-rich clade of land plants, but their origin and early evolutionary history remain poorly understood. We reconstructed angiosperm phylogeny based on 80 genes from 2,881 plastid genomes representing 85% of extant families and all orders. With a well-resolved plastid tree and 62 fossil calibrations, we dated the origin of the crown angiosperms to the Upper Triassic, with major angiosperm radiations occurring in the Jurassic and Lower Cretaceous. This estimated crown age is substantially earlier than that of unequivocal angiosperm fossils, and the difference is here termed the 'Jurassic angiosperm gap'. Our time-calibrated plastid phylogenomic tree provides a highly relevant framework for future comparative studies of flowering plant evolution.

Illumina midi-barcodes: quality proof and applications

DNA barcoding constitutes a supplemental genetically based characterization tool for the identification of species. Traditionally, the barcodes are generated with a length of 650 bp using standardized Sanger sequencing, but with the introduction of high-throughput sequencing (HTS) methods new opportunities for sequencing are available. To use HTS for barcode collection and identification, the amplification of shorter fragments is preferred. Reference DNA midi-barcodes of wild bees were produced using the Illumina MiSeq as well as the Sanger method. Although DNA midi-barcodes derived from Illumina were comparatively shorter (418 bp), their sequences were coherent to the morphological assignment of species. The Illumina barcodes proved to be effective and dealt better with some general limitations of DNA barcoding.