Genes of the pig, <i>Sus scrofa</i>, reconstructed with EvidentialGene

Gilbert, Donald G

doi:10.7717/peerj.6374

Cited by 46 publications

(35 citation statements)

References 27 publications

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“…All of the de novo assembled transcripts of Pm1119 mapped onto the Pm1119 genome, thereby confirming the completeness of the gene space in the reference. The transcripts from UCR-PA7, Pm1118 and Pm449 that did not map onto the Pm1119 genome were merged using EvidentialGene ( Gilbert, 2013 ), to generate a non-redundant set of protein-CDS. We identified a total of 455 CDS encoding complete proteins that were not present in the Pm1119 reference: 11 of these were shared by two isolates, whereas 195, 98, and 151 were found only in UCR-PA7, Pm1118, and Pm449, respectively ( Supplementary Data S3 and Supplementary Data S1 : Figure S9 ).…”

Section: Resultsmentioning

confidence: 99%

“…Transcripts derived from mitochondrial genes, with internal stop codon(s), without a starting methionine or a stop codon were removed. Transcript redundancies were resolved using the tr2aacds program of EvidentialGene ( Gilbert, 2013 ), which selects from clusters of highly similar contigs the “best” representative transcript based on CDS and protein length. The set of non-redundant transcripts absent in Pm1119 was added to the reference transcriptome to compose the Pm.…”

Section: Methodsmentioning

confidence: 99%

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Whole-Genome Resequencing and Pan-Transcriptome Reconstruction Highlight the Impact of Genomic Structural Variation on Secondary Metabolite Gene Clusters in the Grapevine Esca Pathogen Phaeoacremonium minimum

et al. 2018

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The Ascomycete fungus Phaeoacremonium minimum is one of the primary causal agents of Esca, a widespread and damaging grapevine trunk disease. Variation in virulence among Pm. minimum isolates has been reported, but the underlying genetic basis of the phenotypic variability remains unknown. The goal of this study was to characterize intraspecific genetic diversity and explore its potential impact on virulence functions associated with secondary metabolism, cellular transport, and cell wall decomposition. We generated a chromosome-scale genome assembly, using single molecule real-time sequencing, and resequenced the genomes and transcriptomes of multiple isolates to identify sequence and structural polymorphisms. Numerous insertion and deletion events were found for a total of about 1 Mbp in each isolate. Structural variation in this extremely gene dense genome frequently caused presence/absence polymorphisms of multiple adjacent genes, mostly belonging to biosynthetic clusters associated with secondary metabolism. Because of the observed intraspecific diversity in gene content due to structural variation we concluded that a transcriptome reference developed from a single isolate is insufficient to represent the virulence factor repertoire of the species. We therefore compiled a pan-transcriptome reference of Pm. minimum comprising a non-redundant set of 15,245 protein-coding sequences. Using naturally infected field samples expressing Esca symptoms, we demonstrated that mapping of meta-transcriptomics data on a multi-species reference that included the Pm. minimum pan-transcriptome allows the profiling of an expanded set of virulence factors, including variable genes associated with secondary metabolism and cellular transport.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Whole-Genome Resequencing and Pan-Transcriptome Reconstruction Highlight the Impact of Genomic Structural Variation on Secondary Metabolite Gene Clusters in the Grapevine Esca Pathogen Phaeoacremonium minimum

et al. 2018

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“…It allowed us to assign the best protein hit for transcripts (contigs) and also provide taxonomic assignations based on this best hit. Then, redundant sequences were removed with the Evidentialgene pipeline [44], and only the contigs with the best diamond hit to a sequence belonging to a metazoan species were selected. This reduced data set was labeled with ani (e.g., EveBCdTP1_ani; Fig.…”

Section: Methodsmentioning

confidence: 99%

Comparison between transcriptomic responses to short-term stress exposures of a common Holarctic and endemic Lake Baikal amphipods

et al. 2019

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Background Lake Baikal is one of the oldest freshwater lakes and has constituted a stable environment for millions of years, in stark contrast to small, transient bodies of water in its immediate vicinity. A highly diverse endemic endemic amphipod fauna is found in one, but not the other habitat. We ask here whether differences in stress response can explain the immiscibility barrier between Lake Baikal and non-Baikal faunas. To this end, we conducted exposure experiments to increased temperature and the toxic heavy metal cadmium as stressors. Results Here we obtained high-quality de novo transcriptome assemblies, covering mutiple conditions, of three amphipod species, and compared their transcriptomic stress responses. Two of these species, Eulimnogammarus verrucosus and E. cyaneus, are endemic to Lake Baikal, while the Holarctic Gammarus lacustris is a potential invader. Conclusions Both Baikal species possess intact stress response systems and respond to elevated temperature with relatively similar changes in their expression profiles. G. lacustris reacts less strongly to the same stressors, possibly because its transcriptome is already perturbed by acclimation conditions.

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“…The cleaned data for each time point were assembled independently using Trinityrnaseq (v2.6.5) ( Haas et al 2013 ). Six transcriptome assemblies were merged to create the final transcripts using Evigene (v.18-01-2018) ( Gilbert 2013 ). Assembled transcripts were merged for a total of 80,804 representative genes and 108,659 alternative forms.…”

Section: Methodsmentioning

confidence: 99%

Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements

Tobias

Schwessinger

Deng

et al. 2020

G3 Genes|Genomes|Genetics

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Austropuccinia psidii, originating in South America, is a globally invasive fungal plant pathogen that causes rust disease on Myrtaceae. Several biotypes are recognized, with the most widely distributed pandemic biotype spreading throughout the Asia-Pacific and Oceania regions over the last decade. Austropuccinia psidii has a broad host range with more than 480 myrtaceous species. Since first detected in Australia in 2010, the pathogen has caused the near extinction of at least three species and negatively affected commercial production of several Myrtaceae. To enable molecular and evolutionary studies into A. psidii pathogenicity, we assembled a highly contiguous genome for the pandemic biotype. With an estimated haploid genome size of just over 1 Gb (gigabases), it is the largest assembled fungal genome to date. The genome has undergone massive expansion via distinct transposable element (TE) bursts. Over 90% of the genome is covered by TEs predominantly belonging to the Gypsy superfamily. These TE bursts have likely been followed by deamination events of methylated cytosines to silence the repetitive elements. This in turn led to the depletion of CpG sites in transposable elements and a very low overall GC content of 33.8%. Compared to other Pucciniales, the intergenic distances are increased by an order of magnitude indicating a general insertion of TEs between genes. Overall, we show how transposable elements shaped the genome evolution of A. psidii and provide a greatly needed resource for strategic approaches to combat disease spread.

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Genes of the pig, Sus scrofa, reconstructed with EvidentialGene

Cited by 46 publications

References 27 publications

Whole-Genome Resequencing and Pan-Transcriptome Reconstruction Highlight the Impact of Genomic Structural Variation on Secondary Metabolite Gene Clusters in the Grapevine Esca Pathogen Phaeoacremonium minimum

Whole-Genome Resequencing and Pan-Transcriptome Reconstruction Highlight the Impact of Genomic Structural Variation on Secondary Metabolite Gene Clusters in the Grapevine Esca Pathogen Phaeoacremonium minimum

Comparison between transcriptomic responses to short-term stress exposures of a common Holarctic and endemic Lake Baikal amphipods

Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements

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