The complete chloroplast genome sequence of Abies nephrolepis (Pinaceae: Abietoideae)

Complete chloroplast genome features and phylogenetic analysis of Abies ernestii var. salouenensis (Bordères and Gaussen) W. C. Cheng and L. K. Fu from southwest China

Abies ernestii var. salouenensis (Bordères & Gaussen) W. C. Cheng & L. K. Fu is endemic to southwest China, including the southeastern Tibetan Plateau and the northwestern Yunnan Province. The taxonomic relationships between A. ernestii var. salouenensis and two other closely related fir species (A. chensiensis Tiegh. and A. ernestii Rehd.) still need to be determined. Here, we report for the first time the whole chloroplast genome of A. ernestii var. salouenensis. Its genome is 121,759 bp long and is characterized by a circular structure with 68 peptide-encoding genes, 16 tRNAs, six ORFs, and four rRNAs. We also identified 70 microsatellite repeat sequences and 14 tandem repeat sequences in the chloroplast genome of A. ernestii var. salouenensis. Comparative genome analysis indicated considerable variation in ycf1 and ycf2. Phylogenetic analysis supported the monophyly of A. ernestii var. salouenensis, A. chensiensis Tiegh., and A. ernestii Rehd. The relationships among them should be surveyed using more samples at the species level. This study will facilitate taxonomic studies and the development of suitable chloroplast markers for fir species.

The complete chloroplast genome of Abies ernestii Rehder (Pinaceae) and its phylogenetic implications

Abies ernestii Rehder is endemic to the montane regions of Southwest China. Till now, phylogenetic relationships between A. ernestii and other closely related species remain unclear. In this study, we first characterized the complete chloroplast (cp) genome of A. ernestii. The whole cp genome was 121,841 bp in size, including one hundred and thirteen genes. Results of comparative cp genome revealed that only ycf1 and ycf2 was characterized by a considerable variation. Our phylogenetic analyses supported the monophyly of the genus Abies and revealed a clear separation between A. ernestii and A. chensiensis Tiegh. This study highlights the significance of using cp genomes to examine species boundaries among closely related fir species.

Molecular Structure and Phylogenetic Analyses of the Complete Chloroplast Genomes of Three Medicinal Plants Conioselinum vaginatum, Ligusticum sinense, and Ligusticum jeholense

Most plants of Ligusticum have an important medicinal and economic value with a long history, Ligusticum sinense and L. jeholense ("Gaoben") has long been used in traditional Chinese medicine for the treatment of carminative, dispelling cold, dehumidification, and analgesia. While in the market Conioselinum vaginatum (Xinjiang Gaoben) is substitution for Gaoben, and occupies a higher market share. These three Gaoben-related medicinal materials are similar in morphology, and are difficult to distinguish from each other by the commonly used DNA barcodes. The chloroplast genome has been widely used for molecular markers, evolutionary biology, and barcoding identification. In this study, the complete chloroplast genome sequences of C. vaginatum, L. sinense, and L. jeholense were reported. The results showed that the complete chloroplast genomes of these three species have typical quadripartite structures, which were comprised of 148,664, 148,539, and 148,497 bp. A total of 114 genes were identified, including 81 protein-coding genes (PCGs), 29 tRNA genes, and four rRNA genes. Our study indicated that highly variable region ycf2-trnL and accD-ycf4 that can be used as specific DNA barcodes to distinguish and identify C. vaginatum, L. sinense, and L. jeholense. In addition, phylogenetic study showed that C. vaginatum nested in Ligusticum and as a sister group of L. sinense and L. jeholense, which suggested these two genera are both in need of revision. This study offer valuable information for future research in the identification of Gaoben-related medicinal materials and will benefit for further phylogenetic study of Apiaceae.

The dynamic history of gymnosperm plastomes: Insights from structural characterization, comparative analysis, phylogenomics, and time divergence

Gymnosperms are among the most endangered groups of plant species; they include ginkgo, pines (Conifers I), cupressophytes (Conifers II), cycads, and gnetophytes. The relationships among the five extant gymnosperm groups remain equivocal. We analyzed 167 available gymnosperm plastomes and investigated their diversity and phylogeny. We found that plastome size, structure, and gene order were highly variable in the five gymnosperm groups, of which Parasitaxus usta (Vieill.) de Laub. and Macrozamia mountperriensis F.M.Bailey had the smallest and largest plastomes, respectively. The inverted repeats (IRs) of the five groups were shown to have evolved through distinctive evolutionary scenarios. The IRs have been lost in all conifers but retained in cycads and gnetophytes. A positive association between simple sequence repeat (SSR) abundance and plastome size was observed, and the SSRs with the most variation were found in Pinaceae. Furthermore, the number of repeats was negatively correlated with IR length; thus, the highest number of repeats was detected in Conifers I and II, in which the IRs had been lost. We constructed a phylogeny based on 29 shared genes from 167 plastomes. With the plastome tree and 13 calibrations, we estimated the tree height between present-day angiosperms and gymnosperms to be ∼380 million years ago (mya). The placement of Gnetales in the tree agreed with the Gnetales-other gymnosperms hypothesis. The divergence between Ginkgo and cycads was estimated as ∼284 mya; the crown age of the cycads was 251 mya. Our time-calibrated plastid-based phylogenomic tree provides a framework for comparative studies of gymnosperm evolution.

Phylogenetic origin of two Japanese Torreya taxa found in two regions with strongly contrasting snow depth

The Japanese archipelago exhibits a notable difference in snow depth in winter, deep snow on the Sea of Japan side and low snow cover on the Pacific Ocean side. This contrasting pattern has shaped the distribution of infraspecific taxon pairs in a range of woody plants, with taxa found on the Sea of Japan side typically exhibiting a stunted shrub form with multiple decumbent stems. The phylogenetic origin of these taxon pairs is unknown, i.e., whether the two taxa diverged from the same species or if they have different origins. This study aimed to reveal the phylogenetic origin of two varieties of Torreya nucifera (Taxaceae); var. nucifera is a tree found on the Pacific Ocean side, whereas var. radicans is a shrub found on the Sea of Japan side. We examined the phylogenetic relationships of the two varieties and worldwide Torreya taxa using whole chloroplast genomes, chloroplast DNA fragments, and the nuclear ribosomal internal transcribed spacer (ITS). The whole chloroplast genome phylogeny indicated that T. nucifera var. radicans was a sister taxon to Chinese T. grandis, rather than to var. nucifera. In contrast, the nuclear ITS phylogeny indicated that while several haplotypes of T. nucifera var. radicans were closely related to T. grandis, most haplotypes of T. nucifera var. radicans formed a single clade with those of var. nucifera. This implies that the homogenization of the ITS has occurred between the two taxa, while taxon-specific chloroplast DNA haplotypes were retained. These discordant phylogenies suggested that the two taxa have different phylogenetic origins, but have an intricate evolutionary history, involving inter-taxa hybridization and gene flow, possibly when their distributions were confined to sympatric refugia. Given the genetic evidence and distinct difference in growth form, we propose that T. nucifera var. radicans should be taxonomically treated as a distinct species, T. fruticosa.

Complete chloroplast genome of Zingiber mioga by de novo sequencing

Zingiber mioga (Thunb.) Rosc. (Zingiber mioga) is an important edible species, which also has important medical and natural pigment value. This article is firstly reported the Zingiber mioga's chloroplast genomes which detect by de novo sequencing. The results showed that the length sequence of Zingiber mioga's chloroplast genome was 163,541 bp, and the length of LSC, SSC, and two IR regions was 88,035, 15,886, and 29,810 bp, respectively. Zingiber mioga's chloroplast genome was encoded 135 genes involving 10 rRNA, 38 tRNA, and 87 protein-coding genes. After phylogenetic and cluster analysis, the Zingiber were closest approach to Zingiber mioga, followed by Kaempferia, Curcuma, Hedychium, and Roscoea.

Molecular delimitation of European leafy liverworts of the genus Calypogeia based on plastid super-barcodes

BACKGROUND

Molecular research revealed that some of the European Calypogeia species described on the basis of morphological criteria are genetically heterogeneous and, in fact, are species complexes. DNA barcoding is already commonly used for correct identification of difficult to determine species, to disclose cryptic species, or detecting new taxa. Among liverworts, some DNA fragments, recommend as universal plant DNA barcodes, cause problems in amplification. Super-barcoding based on genomic data, makes new opportunities in a species identification.

RESULTS

On the basis of 22 individuals, representing 10 Calypogeia species, plastid genome was tested as a super-barcode. It is not effective in 100%, nonetheless its success of species discrimination (95.45%) is still conspicuous. It is not excluded that the above outcome may have been upset by cryptic speciation in C. suecica, as our results indicate. Having the sequences of entire plastomes of European Calypogeia species, we also discovered that the ndhB and ndhH genes and the trnT-trnL spacer identify species in 100%.

CONCLUSIONS

This study shows that even if a super-barcoding is not effective in 100%, this method does not close the door to a traditional single- or multi-locus barcoding. Moreover, it avoids many complication resulting from the need to amplify selected DNA fragments. It seems that a good solution for species discrimination is a development of so-called "specific barcodes" for a given taxonomic group, based on plastome data.

Ultrasound-Assisted Extraction of Taxifolin, Diosmin, and Quercetin from Abies nephrolepis (Trautv.) Maxim: Kinetic and Thermodynamic Characteristics

Extraction behaviors of the 3 flavonoids taxifolin, diosmin, and quercetin have been investigated in Abies nephrolepis leaves and bark. The following operation parameters—ethanol volume fraction, liquid–solid ratio, temperature, ultrasound irradiation power and time, and ultrasound frequency—were varied to study their effect on the yield of the 3 flavonoids during extraction. The results showed that a low extraction efficiency occurred at 293.15 K due to slow kinetics, while the situation was significantly improved at 333.15 K. The kinetic data for the extraction yields of the 3 flavonoids achieved good fits by the first-order kinetic model. From the thermodynamic analysis results, we realized that the ultrasound-assisted extraction of taxifolin, diosmin, and quercetin from the leaves and bark of A. nephrolepis was a spontaneous and endothermic process in which the disorder increased (ΔG⁰ < 0, ΔH⁰ > 0, and ΔS⁰ > 0). According to the response surface methodology (RSM) analysis, under the optimal operation conditions (ethanol concentration of 50%, liquid–solid ratio of 20 mL/g, frequency of 45 kHz, extraction time of 39.25 min, ultrasound irradiation power of 160 W and temperature of 332.19 K), the total yield of the 3 flavonoids were 100.93 ± 4.01 mg/g from the leaves of A. nephrolepis (with 31.03 ± 1.51 mg/g, 0.31 ± 0.01 mg/g, 69.59 ± 2.57 mg/g for taxifolin, diosmin, and quercetin, respectively), and under the optimal operation conditions (ethanol concentration of 50%, liquid–solid ratio of 20 mL/g, frequency of 45 kHz, extraction time of 36.80 min, ultrasound irradiation power of 150 W and temperature of 328.78 K), 16.05 mg/g ± 0.38 mg/g were obtained from the bark of A. nephrolepis (with 1.44 ± 0.05 mg/g, 0.47 ± 0.01 mg/g, 14.14 ± 0.38 mg/g for taxifolin, diosmin, and quercetin, respectively), which were close to the prediction values.

The complete chloroplast genome sequence of Abies chensiensis (Pinaceae: Abietoideae), an endangered species endemic to China

Chloroplast (cp) genome sequences became a widely used tool for evolutionary and phylogenetic studies in plants. Abies chensiensis (Pinaceae: Abietoideae) is an endangered species endemic to China. To understand its evolutionary characteristics, the complete chloroplast genome of the A. chensiensis has been reconstructed from the whole-genome Illumina sequencing data. The circular genome is 121,784 bp in length and without a typical quadripartite structure due to the loss of IR region. The total GC content of whole genome sequence is 38.3%. The chloroplast genome encodes 109 genes, including 75 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Among them, 35 genes involved in photosynthesis, while 58 genes involved in self-replication. The Maximum-Likelihood phylogenetic analysis showed a strong sister relationship with A. nephrolepis and A. koreana in Abietoideae. Our findings provide fundamental information for further evolutionary and phylogenetic researches of Abietoideae.

The extraordinary variation of the organellar genomes of the Aneura pinguis revealed advanced cryptic speciation of the early land plants

Aneura pinguis is known as a species complex with several morphologically indiscernible species, which are often reproductively isolated from each other and show distinguishable genetic differences. Genetic dissimilarity of cryptic species may be detected by genomes comparison. This study presents the first complete sequences of chloroplast and mitochondrial genomes of six cryptic species of A. pinguis complex: A. pinguis A, B, C, E, F, J. These genomes have been compared to each other in order to reconstruct phylogenetic relationships and to gain better understanding of the evolutionary process of cryptic speciation in this complex. The chloroplast genome with the nucleotide diversity 0.05111 and 1537 indels is by far more variable than mitogenome with π value 0.00233 and number of indels 1526. Tests of selection evidenced that on about 36% of chloroplast genes and on 10% of mitochondrial genes of A. pinguis acts positive selection. It suggests an advanced speciation of species. The phylogenetic analyses based on genomes show that A. pinguis is differentiated and forms three distinct clades. Moreover, on the cpDNA trees, Aneura mirabilis is nested among the cryptic species of A. pinguis. This indicates that the A. pinguis cryptic species do not derive directly from one common ancestor.

Application of a simplified method of chloroplast enrichment to small amounts of tissue for chloroplast genome sequencing

PREMISE OF THE STUDY

High-throughput sequencing of genomic DNA can recover complete chloroplast genome sequences, but the sequence data are usually dominated by sequences from nuclear/mitochondrial genomes. To overcome this deficiency, a simple enrichment method for chloroplast DNA from small amounts of plant tissue was tested for eight plant species including a gymnosperm and various angiosperms.

METHODS

Chloroplasts were enriched using a high-salt isolation buffer without any step gradient procedures, and enriched chloroplast DNA was sequenced by multiplexed high-throughput sequencing.

RESULTS

Using this simple method, significant enrichment of chloroplast DNA-derived reads was attained, allowing deep sequencing of chloroplast genomes. As an example, the chloroplast genome of the conifer Callitris sulcata was assembled, from which polymorphic microsatellite loci were isolated successfully.

DISCUSSION

This chloroplast enrichment method from small amounts of plant tissue will be particularly useful for studies that use sequencers with relatively small throughput and that cannot use large amounts of tissue (e.g., for endangered species).