Illumina-based de novo transcriptome sequencing and analysis of Amanita exitialis basidiocarps

Li, Peng; Deng, Wang-Qiu; Li, Tai–Hui; Bin, Song; Shen, Ya-Heng

doi:10.1016/j.gene.2013.09.014

Cited by 49 publications

(37 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The de novo assemblies generated by both Trinity and Oases produced N50 and average contig lengths similar to many past transcriptome sequencing studies [11-13]. The N50 and average contig size of our Trinity assembly are also similar to that reported for the recently sequenced transcriptome of the common pond snail, Radix balthica [27].…”

Section: Discussionsupporting

confidence: 79%

Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of De novo assemblers

et al. 2014

View full text Add to dashboard Cite

BackgroundThe sequencing, de novo assembly and annotation of transcriptome datasets generated with next generation sequencing (NGS) has enabled biologists to answer genomic questions in non-model species with unprecedented ease. Reliable and accurate de novo assembly and annotation of transcriptomes, however, is a critically important step for transcriptome assemblies generated from short read sequences. Typical benchmarks for assembly and annotation reliability have been performed with model species. To address the reliability and accuracy of de novo transcriptome assembly in non-model species, we generated an RNAseq dataset for an intertidal gastropod mollusc species, Nerita melanotragus, and compared the assembly produced by four different de novo transcriptome assemblers; Velvet, Oases, Geneious and Trinity, for a number of quality metrics and redundancy.ResultsTranscriptome sequencing on the Ion Torrent PGM™ produced 1,883,624 raw reads with a mean length of 133 base pairs (bp). Both the Trinity and Oases de novo assemblers produced the best assemblies based on all quality metrics including fewer contigs, increased N50 and average contig length and contigs of greater length. Overall the BLAST and annotation success of our assemblies was not high with only 15-19% of contigs assigned a putative function.ConclusionsWe believe that any improvement in annotation success of gastropod species will require more gastropod genome sequences, but in particular an increase in mollusc protein sequences in public databases. Overall, this paper demonstrates that reliable and accurate de novo transcriptome assemblies can be generated from short read sequencers with the right assembly algorithms.

show abstract

Section: Discussionsupporting

confidence: 79%

Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of De novo assemblers

et al. 2014

View full text Add to dashboard Cite

show abstract

“…The MSDIN family in Ap and Ab has some overlap with the MSDIN family in A. exitialis , a mushroom implicated in multiple human poisonings in China [18]. In addition to α-amanitin, β-amanitin, and phallacidin, the transcriptome of A. exitialis contains genes encoding LFFPPDFRPP (Abis_msdin_8) and IFWFIYFP (Apha_msdin_28).…”

Section: Resultsmentioning

confidence: 99%

Expansion and diversification of the MSDIN family of cyclic peptide genes in the poisonous agarics Amanita phalloides and A. bisporigera

et al. 2016

View full text Add to dashboard Cite

BackgroundThe cyclic peptide toxins of Amanita mushrooms, such as α-amanitin and phalloidin, are encoded by the “MSDIN” gene family and ribosomally biosynthesized. Based on partial genome sequence and PCR analysis, some members of the MSDIN family were previously identified in Amanita bisporigera, and several other members are known from other species of Amanita. However, the complete complement in any one species, and hence the genetic capacity for these fungi to make cyclic peptides, remains unknown.ResultsDraft genome sequences of two cyclic peptide-producing mushrooms, the “Death Cap” A. phalloides and the “Destroying Angel” A. bisporigera, were obtained. Each species has ~30 MSDIN genes, most of which are predicted to encode unknown cyclic peptides. Some MSDIN genes were duplicated in one or the other species, but only three were common to both species. A gene encoding cycloamanide B, a previously described nontoxic cyclic heptapeptide, was also present in A. phalloides, but genes for antamanide and cycloamanides A, C, and D were not. In A. bisporigera, RNA expression was observed for 20 of the MSDIN family members. Based on their predicted sequences, novel cyclic peptides were searched for by LC/MS/MS in extracts of A. phalloides. The presence of two cyclic peptides, named cycloamanides E and F with structures cyclo(SFFFPVP) and cyclo(IVGILGLP), was thereby demonstrated. Of the MSDIN genes reported earlier from another specimen of A. bisporigera, 9 of 14 were not found in the current genome assembly. Differences between previous and current results for the complement of MSDIN genes and cyclic peptides in the two fungi probably represents natural variation among geographically dispersed isolates of A. phalloides and among the members of the poorly defined A. bisporigera species complex. Both A. phalloides and A. bisporigera contain two prolyl oligopeptidase genes, one of which (POPB) is probably dedicated to cyclic peptide biosynthesis as it is in Galerina marginata.ConclusionThe MSDIN gene family has expanded and diverged rapidly in Amanita section Phalloideae. Together, A. bisporigera and A. phalloides are predicted to have the capacity to make more than 50 cyclic hexa-, hepta-, octa-, nona- and decapeptides.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3378-7) contains supplementary material, which is available to authorized users.

show abstract

“…The genomes of A. bisporigera and other amatoxin-producing species of Amanita species contain >50 sequences homologous to the core gene, AMA1 , called the MSDIN family (Hallen et al, 2007; Li et al, 2013, 2014; Zhou et al, 2013). …”

Section: Introductionmentioning

confidence: 99%

Peptide Macrocyclization Catalyzed by a Prolyl Oligopeptidase Involved in α-Amanitin Biosynthesis

Luo

Hong

Sgambelluri

et al. 2014

Chemistry & Biology

111

164

View full text Add to dashboard Cite

SUMMARY Amatoxins are ribosomally-encoded and post-translationally modified peptides (RiPPs) that account for the majority of fatal mushroom poisonings of humans. A representative amatoxin is the bicyclic octapeptide Î±-amanitin formed via head-to-tail macrocyclization, which is ribosomally biosynthesized as a 35-amino acid propeptide in Amanita bisporigera and in the distantly related mushroom Galerina marginata. Although members of the prolyl oligopeptidase (POP) family of serine proteases were proposed to play a role in Î±- amanitin post-translational processing the exact mechanistic details are not known. Here, we show that a specific prolyl oligopeptidase (GmPOPB) is required for toxin maturation in G. marginata. Recombinant GmPOPB catalyzed two nonprocessive reactions: hydrolysis at an internal Pro to release the C-terminal 25mer from the 35mer propeptide, and transpeptidation at the second Pro to produce the cyclic octamer. On the other hand, we show that GmPOPA, the putative housekeeping POP of G. marginata, behaves like a conventional POP.

show abstract

Illumina-based de novo transcriptome sequencing and analysis of Amanita exitialis basidiocarps

Cited by 49 publications

References 38 publications

Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of De novo assemblers

Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of De novo assemblers

Expansion and diversification of the MSDIN family of cyclic peptide genes in the poisonous agarics Amanita phalloides and A. bisporigera

Peptide Macrocyclization Catalyzed by a Prolyl Oligopeptidase Involved in α-Amanitin Biosynthesis

Contact Info

Product

Resources

About