Gene Expression Differences among Three Neurospora Species Reveal Genes Required for Sexual Reproduction in Neurospora crassa

Abstract

Many fungi form complex three-dimensional fruiting bodies, within which the meiotic machinery for sexual spore production has been considered to be largely conserved over evolutionary time. Indeed, much of what we know about meiosis in plant and animal taxa has been deeply informed by studies of meiosis in Saccharomyces and Neurospora. Nevertheless, the genetic basis of fruiting body development and its regulation in relation to meiosis in fungi is barely known, even within the best studied multicellular fungal model Neurospora crassa. We characterized morphological development and genome-wide transcriptomics in the closely related species Neurospora crassa, Neurospora tetrasperma, and Neurospora discreta, across eight stages of sexual development. Despite diverse life histories within the genus, all three species produce vase-shaped perithecia. Transcriptome sequencing provided gene expression levels of orthologous genes among all three species. Expression of key meiosis genes and sporulation genes corresponded to known phenotypic and developmental differences among these Neurospora species during sexual development. We assembled a list of genes putatively relevant to the recent evolution of fruiting body development by sorting genes whose relative expression across developmental stages increased more in N. crassa relative to the other species. Then, in N. crassa, we characterized the phenotypes of fruiting bodies arising from crosses of homozygous knockout strains of the top genes. Eight N. crassa genes were found to be critical for the successful formation of perithecia. The absence of these genes in these crosses resulted in either no perithecium formation or in arrested development at an early stage. Our results provide insight into the genetic basis of Neurospora sexual reproduction, which is also of great importance with regard to other multicellular ascomycetes, including perithecium-forming pathogens, such as Claviceps purpurea, Ophiostoma ulmi, and Glomerella graminicola.

A WD40 Protein Encoding Gene Fvcpc2 Positively Regulates Mushroom Development and Yield in Flammulina velutipes

“…Although orthologs of CPC-2 have been predicted in the genomes of several mushrooms, including model mushroom species (C. cinerea and S. commune) and cultivated mushrooms (Flammulina velutipes, Volvariella volvacea, Pleurotus ostreatus, Ganoderma lucidum, and Lentinus edodes) (Ohm et al, 2010;Stajich et al, 2010;Grigoriev et al, 2012;Bao et al, 2013;Park et al, 2014;Riley et al, 2014;Sakamoto et al, 2017), none of them has been functionally characterized. Similarly as that cpc-2 is up-regulated after crossing in N. crassa (Lehr et al, 2014), CPC-2 orthologs have an increased expression during fruiting body development in many mushroom species (Ohm et al, 2010;Yu et al, 2012;Cheng et al, 2013;Liu et al, 2015;Zhang et al, 2015;Sakamoto et al, 2017), suggesting that CPC-2 orthologs are likely involved in fruiting body development in these mushroom species. If it is true, CPC-2 ortholog encoding genes have potential to be a new group of reference genes for mushroom breeding.…”

Altering Neurospora crassa MOB2A exposes its functions in development and affects its interaction with the NDR kinase COT1

“…First, a slight decrease in the secretion of melanin to the medium was evident. This may indicate improper melanin biosynthesis, which is part of successful fruiting body development (Lehr et al ., ). Moreover, the mob‐2a(Y117F,Y119F);Δmob‐2b double mutant was affected in female fertility.…”

“…In a previous report, deletion of mob‐2a or mob‐2b was shown to not affect female fertility or ascospore abundance and shape (Maerz et al ., ). Although the functional link between MOB2A/B and sexual development has not been established, Lehr et al ., () found changes in mob‐2a and mob‐2b expression levels during perithecia formation. In this study, while using double mutants, in which mob‐2a was altered in a Δ mob‐2b background, we were able to expose a role for MOB2A/B during sexual development of the fungus.…”

“…In the future, we envision expanding these techniques to include both spatial as well as temporal views of developmental events of structures that have cell walls (Kaminskyj and Dahms, ; Sarkar et al ., ; Kumar and Elbaum, ). This could well include further analysis of perithecial development, using model systems like Neurospora and Podospora (Harris et al ., ; Raju and Leslie, ; Lehr et al ., ; Teichert et al ., ) as well as other fungi.…”

A-to-I RNA editing independent of ADARs in filamentous fungi

“…Stage-specific RNA editing also occurs during sexual reproduction in F. verticillioides. 13 Analysis with published RNA-seq data 16,17 showed that genome-wide A-to-I RNA editing also occurs in the model filamentous fungus Neurospora crassa 13 and its closely related species N. tetrasperma. However, because these published RNA-seq data of F. verticillioides and Neurospora species were un-stranded and generated from early sequencing platforms with short single end reads, they had high error rate and were not suitable for systematic identification of A-to-I editing sites.…”