The interspecific fungal hybrid Verticillium longisporum displays sub-genome-specific gene expression

Article activity feed

1. 

   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/341636: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   Subsequently, adapter sequences were identified and removed using Porechop (version 0.2.3; default settings); adapters at the end of the reads were trimmed and reads with internal adapters were discarded.	Porechop suggested: (Porechop, RRID:SCR_016967)
   The V. longisporum PD589 genome was de novo assembled using Canu (version 1.8; genomeSize=70m, corOutCoverage=100, batOptions=’-dg 3 -db 3 -dr 1 -ca 500 -cp 50’) (71).	Canu suggested: (Canu, RRID:SCR_015880)
   Juicer (v1.6) was then used to map Hi-C sequencing reads to the previously obtained assemblies (74).	Juicer suggested: (Juicer, RRID:SCR_017226)
   Coverage …

   SciScore for 10.1101/341636: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   Subsequently, adapter sequences were identified and removed using Porechop (version 0.2.3; default settings); adapters at the end of the reads were trimmed and reads with internal adapters were discarded.	Porechop suggested: (Porechop, RRID:SCR_016967)
   The V. longisporum PD589 genome was de novo assembled using Canu (version 1.8; genomeSize=70m, corOutCoverage=100, batOptions=’-dg 3 -db 3 -dr 1 -ca 500 -cp 50’) (71).	Canu suggested: (Canu, RRID:SCR_015880)
   Juicer (v1.6) was then used to map Hi-C sequencing reads to the previously obtained assemblies (74).	Juicer suggested: (Juicer, RRID:SCR_017226)
   Coverage of the ONT for the V. longisporum PD589 assembly was determined for 20 kb windows with samtools depth (v1.9) (77) and reads were mapped with minimap2 (v2.17-r941) (78).	samtools suggested: (SAMTOOLS, RRID:SCR_002105)
   A single copy of the mitochondrial genome was excised using BEDTools getfasta (v2.23.0) (Quinlan and Hall 2010)	BEDTools suggested: (BEDTools, RRID:SCR_006646)
   Filtered V. longisporum sub-reads were mapped to these single-copy mitochondrial assemblies using circlator (v1.5.5) (Hunt et al. 2015).	circlator suggested: (Circlator, RRID:SCR_016058)
   Gene prediction and functional characterization: The V. longisporum assemblies of strains VLB2, VL20 and PD589 and the previously published assemblies of V. dahliae strains JR2 and CQ2 (46, 61) were annotated using the BRAKER v2.1.4 pipeline with RNA-Seq data with the options “--softmasking” and “-- fungus” enabled (47).	BRAKER suggested: (BRAKER, RRID:SCR_018964)
   RNA-seq reads from Verticillium grown in axenic culture (all replicates) were mapped to the assemblies using TopHat v2.1.1 (79).	TopHat suggested: (TopHat, RRID:SCR_013035)
   Pfam and Gene Ontology (GO) function domains were predicted using InterProScan (v5.42-78.0) (81).	InterProScan suggested: (InterProScan, RRID:SCR_005829)
   A protein was considered a CAZyme if at least two of the three tools (HMMER,DIAMOND and Hotpep) predicted a CAZyme function.	HMMER suggested: (Hmmer, RRID:SCR_005305) DIAMOND suggested: (DIAMOND, RRID:SCR_009457)
   The features to indicate the biparental origin of the V. longisporum genomes were visualized using the R package circlize (v.0.4.10) (88).	circlize suggested: (circlize, RRID:SCR_002141)
   Genome analysis: The quality of genome assemblies was assessed by screening the presences of Benchmarking Universal Single-Copy Orthologs (BUSCOs) using the BUSCO software version 4.0.6 with the database “ascomycota_odb10” (89).	Benchmarking Universal Single-Copy Orthologs suggested: (BUSCO, RRID:SCR_015008) BUSCO suggested: (BUSCO, RRID:SCR_015008)
   Repeats were de novo identified using RepeatModeler (v1.0.11) and combined with the repeat library from RepBase (release 20170127) (90).	RepeatModeler suggested: (RepeatModeler, RRID:SCR_015027)
   The genomic location of repeats was identified with RepeatMasker (v4.0.6).	RepeatMasker suggested: (RepeatMasker, RRID:SCR_012954)
   Nucleotide sequences were separately aligned using MAFFT (v7.464) (91).	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   Phylogenetic trees were inferred using RAxML with the GTRGAMMA substitution model (v8.2.11) (92).	RAxML suggested: (RAxML, RRID:SCR_006086)
   Homologs in Verticillium were determined using nucleotide BLAST (v2.2.31+).	BLAST suggested: (BLASTX, RRID:SCR_001653)
   Global nucleotide alignments using the Needle-Wunsch algorithm of the EMBOSS package were used to determine homologous gene pairs in VLB2 and VL20 (v6.6.0.0) (87)	EMBOSS suggested: (EMBOSS, RRID:SCR_008493)
   The alignments were used to calculate Ka/Ks for every branch of the species phylogeny using codeml module of PAML (v4.9) with the following parameters: F3X4 codon frequency model, wag.	PAML suggested: (PAML, RRID:SCR_014932)
   Gene expression analysis: The RNA sequencing reads were filtered using the Trinity software (v2.9.1) option trimmomatic under the standard settings (97).	Trinity suggested: (Trinity, RRID:SCR_013048) trimmomatic suggested: (Trimmomatic, RRID:SCR_011848)
   Reads were counted to the predicted gene coding regions using the R package Rsubread (v1.34.7) Significant differential expression of a locus was calculated using the R package edgeR (v3.26.8) (99).	Rsubread suggested: (Rsubread, RRID:SCR_016945) edgeR suggested: (edgeR, RRID:SCR_012802)
   : Raw RNAseq reads and genome assemblies are deposited at NCBI under the BioProject PRJNA473305.	BioProject suggested: (NCBI BioProject, RRID:SCR_004801)

   ---

   Results from OddPub: Thank you for sharing your data.

   ---

   Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

   ---

   Results from TrialIdentifier: No clinical trial numbers were referenced.

   ---

   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

   ---

   Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on page 15. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

   ---

   Results from rtransparent:

   • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
   • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
   • No protocol registration statement was detected.

   ---

   Read the original source
2. 

   Version published to 10.1101/341636v2 on bioRxiv

   Feb 22, 2021
3. 

   Version published to 10.1101/341636v1 on bioRxiv

   Jun 7, 2018