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

Yi, Dong‐Keun; Choi, Kyung; Joo, Minjung; Yang, Jong Cheol; Mustafina, F. U.; Han, Jun-Soo; Son, Dong Chan; Chang, Kyung‐Il; Shin, Chang Ho; Lee, You-Mi

doi:10.1016/j.japb.2016.03.014

Cited by 18 publications

(20 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Similarly, in our studies on Calypogeia, the ycf genes: ycf1, ycf2, ycf66 were in the top five of the most variable coding regions, what predisposes them to be a potential DNA barcodes. In the past few years, it is more and more often reported about the usefulness of the ycf1 and ycf2 genes in the identification of plant species [29,61,62,63]. Especially two regions of the ycf1 gene: ycf1a and ycf1b are highly variable and can serve as an effective barcode for land plants.…”

Section: Hot-spots and Dna Barcodingmentioning

confidence: 99%

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

Ślipiko

Myszczyński

Buczkowska

et al. 2020

Preprint

View full text Add to dashboard Cite

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.

show abstract

Section: Hot-spots and Dna Barcodingmentioning

confidence: 99%

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

Ślipiko

Myszczyński

Buczkowska

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Previous investigations of bioactive compound extraction processes usually aimed solely at one part of the plants such as leaves or bark, which suggested their applicability but often lacked widespread adoption. Different plant parts show variable cell structures, including the thickness and strength of the cell wall.Abies nephrolepis, belonging to the family Pinaceae, is an important perennial timber arbor that is mainly distributed in the highlands of Northeast Asia, although distributions in Europe, North and Middle America and North Africa have also been mentioned [3]. A. nephrolepis trees have been widely planted in the Lesser Xingan Mountains (Heilongjiang, China) and Xiaowutai Mountain (Shanxi, China) regions, bringing remarkable economic benefits for those farmers [4,5]; additionally, the extra value of nonvolatile compounds and essential oils from this plant has received attention among academic circles.…”

mentioning

confidence: 99%

“…Abies nephrolepis, belonging to the family Pinaceae, is an important perennial timber arbor that is mainly distributed in the highlands of Northeast Asia, although distributions in Europe, North and Middle America and North Africa have also been mentioned [3]. A. nephrolepis trees have been widely planted in the Lesser Xingan Mountains (Heilongjiang, China) and Xiaowutai Mountain (Shanxi, China) regions, bringing remarkable economic benefits for those farmers [4,5]; additionally, the extra value of nonvolatile compounds and essential oils from this plant has received attention among academic circles.…”

mentioning

confidence: 99%

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

et al. 2020

View full text Add to dashboard Cite

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.

show abstract

“…Most plant genomes have 66-82 protein-coding genes, 29-32 genes encoding tRNAs, and four genes encoding rRNAs, With the exception of nonphotosynthetic parasitic plants, gene composition, sequence, content, and orientation are highly conserved among seed plants (Jansen & Ruhlman, 2012). However, structural modifications such as loss of IR domains or entire genes and gene rearrangement have been reported in gymnosperms such as conifers (Lin et al, 2010;Wu et al, 2011;Wu & Chaw, 2014;Yi et al, 2016). The first complete sequences of Pinus cpDNA were reported in Pinus thunbergii Parl., with 4 rRNA genes and 32 tRNA genes, and the most striking feature is the loss of all 11 functional genes (ndh genes) for in subunits of a putative NADH dehydrogenase that are found in the chloroplast genomes of angliosperms and a bryophyte (Wakasugi et al, 1994).…”

Section: Introductionmentioning

confidence: 99%

“…In particular, species that are difficult to differentiate morphologically can be distinguished using molecular markers. The complete chloroplast genome can be rapidly sequenced at a relatively low cost (Yi et al, 2016). Also, PCR restriction fragment length polymorphism (RFLP) analysis, also known as cleaved amplified polymorphic sequence (CAPS), is widely used to detect intra-and interspecies variation (Rasmussen, 2012).…”

Section: Introductionmentioning

confidence: 99%

Untitled

Supplemental Information 1: Pinus Densiflora Chloroplast Genome File

View full text Add to dashboard Cite

Background: Identifying and characterizing genetic variation can clarify the molecular basis of biological phenomena in plants. In particular, related or morphologically similar species can be distinguished by molecular markers. Pinus densiflora Siebold & Zucc. is a species that is distributed in the Korean peninsula, the Japanese archipelago, and China's Shandong and Manchu Provinces and has long been harvested for timber. However, it is difficult to distinguish P. densiflora from Pinus sylvestris L. both morphologically and phylogenetically. The complete chloroplast genome of P. densiflora has not yet been reported. In this study, we sequenced the P. densiflora chloroplast genome in order to identify the molecular markers that can be used to distinguish this species from P. sylvestris. Methods: Genomic DNA was extracted from P. densiflora samples obtained from the clone bank of the National Forest Seed Variety Center and was sequenced on an Ion Torrent platform. Filtered sequences were assembled with P. sylvestris sequences used as a reference and gene annotation was performed. The chloroplast genome sequences of the two species were aligned and the number and location of forward, reverse, complement and palindromic matches were determined. Single nucleotide polymorphisms (SNPs) and insertion/deletion mutations (Indels) were identified and analyzed by PCR. Results: The P. densiflora chloroplast genome consisted of circular double-stranded DNA with 119,835 bp compared to 119,758 bp for P. sylvestris. Between the two Pinus chloroplast genomes, we identified 73 SNPs and 171 Indels; two gene regions with amplification products ≤ 300 bp (rpoC1 and trnM-trnV) were validated as molecular markers. Discussion: PCR restriction fragment length polymorphism analysis revealed differences between P. sylvestris and P. densiflora at the molecular level. These differences can be used to distinguish between these two species, which is not possible by microscopy-based morphological examination.

show abstract

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

Cited by 18 publications

References 33 publications

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

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

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

Untitled

Contact Info

Product

Resources

About