Detection of Abrin-Like and Prepropulchellin-Like Toxin Genes and Transcripts Using Whole Genome Sequencing and Full-Length Transcript Sequencing of Abrus precatorius

Hovde, Blake T.; Daligault, Hajnalka E.; Hanschen, Erik R.; Kunde, Yuliya A.; Johnson, Matthew; Starkenburg, Shawn R.; Johnson, Shannon L.

doi:10.3390/toxins11120691

Cited by 8 publications

(7 citation statements)

References 23 publications

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“…Thus, it can meet the requirements of genetic studies and analyses of nonmodel plants. In recent years, full-length transcriptome sequencing studies of some plants, such as Dendrobium officinale 32 , Abrus precatorius 33 , and Pogostemon cablin 34 , have been reported. In addition, the published studies have shown that the obtained transcriptome sequences contain large numbers of EST-SSRs 14,35 .…”

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confidence: 99%

Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis

Zang

Xie³

et al. 2020

Sci Rep

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Populus wulianensis is an endangered species endemic to Shandong Province, China. Despite the economic and ornamental value of this species, few genomics and genetic studies have been performed. In this study, we performed a relevant analysis of the full-length transcriptome sequencing data of P. wulianensis and obtained expressed sequence tag (EST)-simple sequence repeat (SSR) markers with polymorphisms that can be used for further genetic research. In total, 8.18 Gb (3,521,665) clean reads with an average GC content of 42.12% were obtained. From the corrected 64,737 high-quality isoforms, 42,323 transcript sequences were obtained after redundancy analysis with CD-HIT. Among these transcript sequences, 41,876 sequences were annotated successfully. A total of 23,539 potential EST-SSRs were identified from 16,057 sequences. Excluding mononucleotides, the most abundant motifs were trinucleotide SSRs (47.80%), followed by di- (46.80%), tetra- (2.98%), hexa- (1.58%) and pentanucleotide SSRs (0.84%). Among the 100 designed EST-SSRs, 18 were polymorphic with high PIC values (0.721 and 0.683) and could be used for analyses of the genetic diversity and population structure of P. wulianensis. These full-length transcriptome sequencing data will facilitate gene discovery and functional genomics research in P. wulianensis, and the novel EST-SSRs developed in our study will promote molecular-assisted breeding, genetic diversity and conservation biology research in this species.

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confidence: 99%

Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis

Zang

Xie³

et al. 2020

Sci Rep

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“…To identify all abrin‐like, prepropulchellin‐like, and agglutinin‐like genes in A. cantoniensis , BLAST searches against the assembled Abrus genome were performed using published abrin and pulchellin sequences (Hovde et al., 2019). Software iqtree was used in phylogeny and cluster analysis of homologous toxin gene.…”

Section: Methodsmentioning

confidence: 99%

“…Abrin poisoning symptoms usually appear only after the incubation period of a few hours to several days with multiple symptoms such as burning in the mouth, difficulty swallowing, nausea, vomiting, among others (Silva et al., 2005). Genomic studies of the Abrus genus firstly focus on Abrus precatorius L. Compared with almost nonposionous (except seeds and pods) A. cantoniensis , A. precatorius is a highly poisonous plant (Hovde et al., 2019). However, the reason for the toxicity differences between these two Abrus species remains elusive.…”

Section: Introductionmentioning

confidence: 99%

Complete genome sequence and phylogenetic analysis of medicinal plant Abrus cantoniensis for evolutionary research and germplasm utilization

et al. 2022

The Plant Genome

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Abrus cantoniensis Hance, a native medicinal plant in southern China, is officially recorded in the Chinese Pharmacopoeia. Here, we presented the first high‐quality genome in Abrus genus, A. cantoniensis genome, as well as the detailed genomic information. The assembled genome size was 381.27 Mb with a scaffold N50 of 18.95 Mb, and 98.97% of the assembled sequences were anchored on 11 pseudochromosomes. The A. cantoniensis genome comprised 25,058 protein‐coding genes and 45.12% of the assemblies were repetitive sequences. Comparative genome analysis suggested that chromosome translocation and inversion played an important role in the differentiation of Abrus. In addition, 24 toxin‐related genes were identified, which formed two tandem gene clusters on chromosomes 2 and 3. The chromosome‐level genome of A. cantoniensis obtained in this work provides a valuable resource for understanding the evolution, active ingredient biosynthesis, and genetic improvement for A. cantoniensis and Abrus species.

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“…It is probably due to the difference in stereo structure and heterogeneous glycosylation of the same abrin isoform. In addition, according to previous reports [ 25 ], it would be helpful to elaborate on the content distribution of the four abrin isoforms from the perspective of transcription and genome levels.…”

Section: Resultsmentioning

confidence: 99%

Rapid Differential Detection of Abrin Isoforms by an Acetonitrile- and Ultrasound-Assisted On-Bead Trypsin Digestion Coupled with LC-MS/MS Analysis

Liang¹,

Yang²,

Geng³

et al. 2021

Toxins

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The high toxic abrin from the plant Abrus precatorius is a type II ribosome-inactivating protein toxin with a human lethal dose of 0.1–1.0 µg/kg body weight. Due to its high toxicity and the potential misuse as a biothreat agent, it is of great importance to developing fast and reliable methods for the identification and quantification of abrin in complex matrices. Here, we report rapid and efficient acetonitrile (ACN)- and ultrasound-assisted on-bead trypsin digestion method combined with HPLC-MS/MS for the quantification of abrin isoforms in complex matrices. Specific peptides of abrin isoforms were generated by direct ACN-assisted trypsin digestion and analyzed by HPLC-HRMS. Combined with in silico digestion and BLASTp database search, fifteen marker peptides were selected for differential detection of abrin isoforms. The abrin in milk and plasma was enriched by immunomagnetic beads prepared by biotinylated anti-abrin polyclonal antibodies conjugated to streptavidin magnetic beads. The ultrasound-assisted on-bead trypsin digestion method was carried out under the condition of 10% ACN as denaturant solvent, the entire digestion time was further shortened from 90 min to 30 min. The four peptides of T3Aa,b,c,d, T12Aa, T15Ab, and T9Ac,d were chosen as quantification for total abrin, abrin-a, abrin-b, and abrin-c/d, respectively. The absolute quantification of abrin and its isoforms was accomplished by isotope dilution with labeled AQUA peptides and analyzed by HPLC-MS/MS (MRM). The developed method was fully validated in milk and plasma matrices with quantification limits in the range of 1.0-9.4 ng/mL for the isoforms of abrin. Furthermore, the developed approach was applied for the characterization of abrin isoforms from various fractions from gel filtration separation of the seeds, and measurement of abrin in the samples of biotoxin exercises organized by the Organization for the Prohibition of Chemical Weapons (OPCW). This study provided a recommended method for the differential identification of abrin isoforms, which are easily applied in international laboratories to improve the capabilities for the analysis of biotoxin samples.

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Detection of Abrin-Like and Prepropulchellin-Like Toxin Genes and Transcripts Using Whole Genome Sequencing and Full-Length Transcript Sequencing of Abrus precatorius

Cited by 8 publications

References 23 publications

Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis

Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis

Complete genome sequence and phylogenetic analysis of medicinal plant Abrus cantoniensis for evolutionary research and germplasm utilization

Rapid Differential Detection of Abrin Isoforms by an Acetonitrile- and Ultrasound-Assisted On-Bead Trypsin Digestion Coupled with LC-MS/MS Analysis

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