Identification of Pueraria spp. through DNA barcoding and comparative transcriptomics

High-integrity Pueraria montana var. lobata genome and population analysis revealed the genetic diversity of Pueraria genus

Pueraria montana var. lobata (P. lobata) is a traditional medicinal plant belonging to the Pueraria genus of Fabaceae family. Pueraria montana var. thomsonii (P. thomsonii) and Pueraria montana var. montana (P. montana) are its related species. However, evolutionary history of the Pueraria genus is still largely unknown. Here, a high-integrity, chromosome-level genome of P. lobata and an improved genome of P. thomsonii were reported. It found evidence for an ancient whole-genome triplication and a recent whole-genome duplication shared with Fabaceae in three Pueraria species. Population genomics of 121 Pueraria accessions demonstrated that P. lobata populations had substantially higher genetic diversity, and P. thomsonii was probably derived from P. lobata by domestication as a subspecies. Selection sweep analysis identified candidate genes in P. thomsonii populations associated with the synthesis of auxin and gibberellin, which potentially play a role in the expansion and starch accumulation of tubers in P. thomsonii. Overall, the findings provide new insights into the evolutionary and domestication history of the Pueraria genome and offer a valuable genomic resource for the genetic improvement of these species.

DNA Sequencing Technologies and DNA Barcoding

DNA barcodes are short, standardized DNA segments that geneticists can use to identify all living taxa. On the other hand, DNA barcoding identifies species by analyzing these specific regions against a DNA barcode reference library. In its initial years, DNA barcodes sequenced by Sanger's method were extensively used by taxonomists for the characterization and identification of species. But in recent years, DNA barcoding by next-generation sequencing (NGS) has found broader applications, such as quality control, biomonitoring of protected species, and biodiversity assessment. Technological advancements have also paved the way to metabarcoding, which has enabled massive parallel sequ.encing of complex bulk samples using high-throughput sequencing techniques. In future, DNA barcoding along with high-throughput techniques will show stupendous progress in taxonomic classification with reference to available sequence data.

Inhibiting Protein Aggregation Using Cellulose Nanocrystal in MALDI-TOF MS Analysis: Improving the Sensitivity and Repeatability of Intact Protein in Pueraria

Protein aggregation can induce low sensitivity and poor repeatability of matrix-assisted laser desorption/ionization time-of-fight mass spectrometry (MALDI-TOF MS) analysis for intact protein. Herein, we introduced a strategy to decrease protein aggregation in the sample solution by using cellulose nanocrystal (CNC). The results indicated that protein granule size was effectively reduced by adding CNC to the sample solution. Through MALDI-TOF MS analysis, the signal-to-noise ratio of [M + H]+ peak increased 2-fold, and the detection of limit was <10 μg/mL for intact protein. The CNC also contributed to excellent point-to-point repeatability for MALDI-TOF MS analysis with the coefficient of variation (CV) of 10.0% with CNC vs 48.9% without CNC in Hb solution. Also, the repeatability of Pueraria protein ion signals was improved by using CNC, and the CV with and without CNC was 16.1% and 39.6%, respectively. Moreover, protein ion intensity exhibited great linear relationship (y = 53.04x - 3.474, R2 = 0.9936) with the concentrations (ranging from 0.1 to 10 mg/mL) when using CNC. Further investigation revealed that m/z 19,000 and m/z 21,000 peaks of Pueraria could be used for the adulteration analysis and post-translational modification research, demonstrating our method has the potential for broad applications.

Chromosome-Level Genome Assembly and Multi-Omics Dataset Provide Insights into Isoflavone and Puerarin Biosynthesis in Pueraria lobata (Wild.) Ohwi

Pueraria lobata (wild.) Ohwi is a leguminous plant and one of the traditional Chinese herbal medicines. Its puerarin extract is widely used in the pharmaceutical industry. This study reported a chromosome-level genome assembly for P. lobata and its characteristics. The genome size was ~939.2 Mb, with a contig N50 of 29.51 Mbp. Approximately 97.82% of the assembled sequences were represented by 11 pseudochromosomes. We identified that the repetitive sequences accounted for 63.50% of the P. lobata genome. A total of 33,171 coding genes were predicted, of which 97.34% could predict the function. Compared with other species, P. lobata had 757 species-specific gene families, including 1874 genes. The genome evolution analysis revealed that P. lobata was most closely related to Glycine max and underwent two whole-genome duplication (WGD) events. One was in a gamma event shared by the core dicotyledons at around 65 million years ago, and another was in the common ancestor shared by legume species at around 25 million years ago. The collinearity analysis showed that 61.45% of the genes (54,579 gene pairs) in G. max and P. lobata had collinearity. In this study, six unique PlUGT43 homologous genes were retrieved from the genome of P. lobata, and no 2-hydroxyisoflavanone 8-C-glucoside was found in the metabolites. This also revealed that the puerarin synthesis was mainly from the glycation of daidzein. The combined transcriptome and metabolome analysis suggested that two bHLHs, six MYBs and four WRKYs were involved in the expression regulation of puerarin synthesis structural genes. The genetic information obtained in this study provided novel insights into the biological evolution of P. lobata and leguminous species, and it laid the foundation for further exploring the regulatory mechanism of puerarin synthesis.

Evaluation of pathways to the C-glycosyl isoflavone puerarin in roots of kudzu (Pueraria montana lobata)

Kudzu (Pueraria montana lobata) is used as a traditional medicine in China and Southeast Asia but is a noxious weed in the Southeastern United States. It produces both O- and C-glycosylated isoflavones, with puerarin (C-glucosyl daidzein) as an important bioactive compound. Currently, the stage of the isoflavone pathway at which the C-glycosyl unit is added remains unclear, with a recent report of direct C-glycosylation of daidzein contradicting earlier labeling studies supporting C-glycosylation at the level of chalcone. We have employed comparative mRNA sequencing of the roots from two Pueraria species, one of which produces puerarin (field collected P. montana lobata) and one of which does not (commercial Pueraria phaseoloides), to identify candidate uridine diphosphate glycosyltransferase (UGT) enzymes involved in puerarin biosynthesis. Expression of recombinant UGTs in Escherichia coli and candidate C-glycosyltransferases in Medicago truncatula were used to explore substrate specificities, and gene silencing of UGT and key isoflavone biosynthetic genes in kudzu hairy roots employed to test hypotheses concerning the substrate(s) for C-glycosylation. Our results confirm UGT71T5 as a C-glycosyltransferase of isoflavone biosynthesis in kudzu. Enzymatic, isotope labeling, and genetic analyses suggest that puerarin arises both from the direct action of UGT71T5 on daidzein and via a second route in which the C-glycosidic linkage is introduced to the chalcone isoliquiritigenin.

Chromosome-level and graphic genomes provide insights into metabolism of bioactive metabolites and cold-adaption of Pueraria lobata var. montana

Pueraria lobata var. montana (P. montana) belongs to the genus Pueraria and originated in Asia. Compared with its sister P. thomsonii, P. montana has stronger growth vigour and cold-adaption but contains less bioactive metabolites such as puerarin. To promote the investigation of metabolic regulation and genetic improvement of Pueraria, the present study reports a chromosome-level genome of P. montana with length of 978.59 Mb and scaffold N50 of 80.18 Mb. Comparative genomics analysis showed that P. montana possesses smaller genome size than that of P. thomsonii owing to less repeat sequences and duplicated genes. A total of 6,548 and 4,675 variety-specific gene families were identified in P. montana and P. thomsonii, respectively. The identified variety-specific and expanded/contracted gene families related to biosynthesis of bioactive metabolites and microtubules are likely the causes for the different characteristics of metabolism and cold-adaption of P. montana and P. thomsonii. Moreover, a graphic genome was constructed based on 11 P. montana accessions. Total 92 structural variants were identified and most of which are related to stimulus-response. In conclusion, the chromosome-level and graphic genomes of P. montana will not only facilitate the studies of evolution and metabolic regulation, but also promote the breeding of Pueraria.

Endorsement and phylogenetic analysis of some Fabaceae plants based on DNA barcoding

Background

DNA barcoding have been considered as a tool to facilitate species identification based on its simplicity and high-level accuracy in compression to the complexity and subjective biases linked to morphological identification of taxa. MaturaseK gene (MatK gene) of the chloroplast is very vital in the plant system which is involved in the group II intron splicing. The main objective of this study is to determine the relative utility of the “MatK” chloroplast gene for barcoding in 15 legume as a tool to facilitate species identification based on their simplicity and high-level accuracy linked to morphological identification of taxa.

Methods and Results

MatK gene sequences were submitted to GenBank and the accession numbers were obtained with sequence length ranging from 730 to 1545 nucleotides. These DNA sequences were aligned with database sequence using PROMALS server, Clustal Omega server and Bioedit program. Maximum likelihood and neighbor-joining algorithms were employed for constructing phylogeny. Overall, these results indicated that the phylogenetic tree analysis and the evolutionary distances of an individual dataset of each species were agreed with a phylogenetic tree of all each other consisting of two clades, the first clade comprising (Enterolobium contortisiliquum, Albizia lebbek), Acacia saligna, Leucaena leucocephala, Dichrostachys Cinerea, (Delonix regia, Parkinsonia aculeata), (Senna surattensis, Cassia fistula, Cassia javanica) and Schotia brachypetala were more closely to each other, respectively. The remaining four species of Erythrina humeana, (Sophora secundiflora, Dalbergia Sissoo, Tipuana Tipu) constituted the second clade.

Conclusion

Moreover, their sequences could be successfully utilized in single nucleotide polymorphism or as part of the sequence as DNA fragment analysis utilizing polymerase chain reaction in plant systematic. Therefore, MatK gene is considered promising a candidate for DNA barcoding in the plant family Fabaceae and provides a clear relationship between the families.