Landscape, complexity and regulation of a filamentous fungal transcriptome

Lü, Ping; Chen, Daipeng; Qi, Zhaomei; Wang, Haoming; Chen, Yitong; Wang, Qinhu; Jiang, Cong; Liu, Huiquan; Xu, Jin‐Rong

doi:10.1101/2021.11.08.467853

Cited by 2 publications

(1 citation statement)

References 98 publications

(153 reference statements)

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“…VOCs induced by herbivore feeding and oviposition are commonly referred to as herbivore-induced plant volatiles (HIPVs) [4]. HIPVs may defend plants by either directly repelling or deterring herbivores [5,6], or indirectly by attracting natural enemies of herbivores [7][8][9]. In addition to facilitating trophic and multi-trophic interactions, HIPVs are involved in information transfer between plants, which is often referred to as plant-plant communication [10].…”

Section: Introductionmentioning

confidence: 99%

Volatile-mediated between-plant communication in Scots pine and the effects of elevated ozone

Kivimäenpää

Blande

2022

Proc. R. Soc. B.

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Conifers are dominant tree species in boreal forests, but are susceptible to attack by bark beetles. Upon bark beetle attack, conifers release substantial quantities of volatile organic compounds known as herbivore-induced plant volatiles (HIPVs). Earlier studies of broadleaved plants have shown that HIPVs provide information to neighbouring plants, which may enhance their defences. However, the defence responses of HIPV-receiver plants have not been described for conifers. Here we advance knowledge of plant–plant communication in conifers by documenting a suite of receiver-plant responses to bark-feeding-induced volatiles. Scots pine seedlings exposed to HIPVs were more resistant to subsequent weevil feeding and received less damage. Receiver plants had both induced and primed volatile emissions and their resin ducts had an increased epithelial cell (EC) mean area and an increased number of cells located in the second EC layer. Importantly, HIPV exposure increased stomatal conductance and net photosynthesis rate of receiver plants. Receiver-plant responses were also examined under elevated ozone conditions and found to be significantly altered. However, the final defence outcome was not affected. These findings demonstrate that HIPVs modulate conifer metabolism through responses spanning photosynthesis and chemical defence. The responses are adjusted under ozone stress, but the defence benefits remain intact.

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Section: Introductionmentioning

confidence: 99%

Volatile-mediated between-plant communication in Scots pine and the effects of elevated ozone

Kivimäenpää

Blande

2022

Proc. R. Soc. B.

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Improved gene annotation of the fungal wheat pathogenZymoseptoria triticibased on combined Iso-Seq and RNA-Seq evidence

Lapalu

Lamothe

Petit

et al. 2023

Preprint

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Despite large omics datasets, the establishment of a reliable gene annotation is still challenging for eukaryotic genomes. Here, we used the reference genome of the major fungal wheat pathogen Zymoseptoria tritici (isolate IPO323) as a case study to develop methods to improve eukaryotic gene prediction. Four previous IPO323 annotations identified 10,933 to 13,260 gene models, but only one third of these coding sequences (CDS) have identical structures. To resolve these discrepancies and improve gene models, we generated full-length transcripts using long-read sequencing. This dataset was used together with other evidence (RNA-Seq transcripts and protein sequences) to generate novel ab initio gene models. The selection of the best structure among novel and existing gene models was performed according to transcript and protein evidence using InGenAnnot, a novel bioinformatics suite. Overall, 13,414 re-annotated gene models (RGMs) were predicted, including 671 new genes among which 53 encoded effector candidates. This process corrected many of the errors (15%) observed in previous gene models (coding sequence fusions, false introns, missing exons). While fungal genomes have poor annotations of untranslated regions (UTRs), our Iso-Seq long-read sequences outlined 5' and 3'UTRs for 73% of the RGMs. Alternative transcripts were identified for 13% of RGMs, mostly due to intron retention (75%), likely corresponding to unprocessed pre-mRNAs. A total of 353 genes displayed alternative transcripts with combinations of previously predicted or novel exons. Long non-coding transcripts (lncRNAs) and double-stranded RNAs from two fungal viruses were also identified. Most lncRNAs corresponded to antisense transcripts of genes (52%). lncRNAs that were up or down regulated during infection were enriched in antisense transcripts (70%), suggesting their involvement in the control of gene expression. Our results showed that combining different ab initio gene predictions and evidence-driven curation using InGenAnnot improved the quality of gene annotations of a compact eukaryotic genome. Our analysis also provided new insights into the transcriptional landscape of Z. tritici, helping develop an increasingly complex picture of its biology.

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Landscape, complexity and regulation of a filamentous fungal transcriptome

Cited by 2 publications

References 98 publications

Volatile-mediated between-plant communication in Scots pine and the effects of elevated ozone

Volatile-mediated between-plant communication in Scots pine and the effects of elevated ozone

Improved gene annotation of the fungal wheat pathogenZymoseptoria triticibased on combined Iso-Seq and RNA-Seq evidence

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