Mapping of known effector genes on five Meloidogyne genomes (doi:10.15454/P5YIGX)

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Document Description

Citation

Title:

Mapping of known effector genes on five Meloidogyne genomes

Identification Number:

doi:10.15454/P5YIGX

Distributor:

Portail Data INRAE

Date of Distribution:

2021-04-26

Version:

1

Bibliographic Citation:

Danchin, Etienne; Grynberg, Priscila, 2021, "Mapping of known effector genes on five Meloidogyne genomes", https://doi.org/10.15454/P5YIGX, Portail Data INRAE, V1

Study Description

Citation

Title:

Mapping of known effector genes on five Meloidogyne genomes

Identification Number:

doi:10.15454/P5YIGX

Authoring Entity:

Danchin, Etienne (INRA - Institut National de la Recherche Agronomique)

Grynberg, Priscila (Embrapa)

Distributor:

Portail Data INRAE

Access Authority:

Danchin, Etienne

Depositor:

Danchin, Etienne

Date of Deposit:

2020-11-25

Study Scope

Keywords:

Plant Health and Pathology

Abstract:

Based on the literature, we established a manually curated list of M. incognita genes specifically expressed in sub-ventral or dorsal secretory gland cells. We started from the list published in (Truong, Nguyen, Abad, Quentin, & Favery, 2015) and manually checked the figures associated with the cited references to only keep genes with evidence for specific expression via in-situ hybridization. We completed this list with the Mi-PNF3 gene published more recently (Leelarasamee, Zhang, & Gleason, 2018) and eliminated redundancy between the sequences at the protein level.<p> We retrieved the corresponding CDS sequences and aligned them to the M. incognita, M. arenaria, M. javanica, M. enterolobii and M. hapla genome sequences (Blanc-Mathieu et al., 2017; Koutsovoulos et al., 2020, Opperman et al. 2008) using the splice aware aligner SPALN (Iwata & Gotoh, 2012) with the following parameters.<p> 'spaln -Q7 -O4 -M -d Mi.mfa CDS > input.gff<p> -M = report multiple hits and only the best<p> -Q4= DP mode, 5-7 = maximum number of reported hsp<p> -O4= megablast-like format<p> We performed this operation for the subventral (SvG) and (DG) subsets, separtely and provide a summary of the results in MS Word and PDF Format.

Kind of Data:

Dataset

Kind of Data:

Text

Kind of Data:

Other

Methodology and Processing

Sources Statement

Data Access

Notes:

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Other Study Description Materials

Other Study-Related Materials

Label:

DG-Mel-Genus.docx

Text:

Mapping of genes known to be specifically expressed in DG on the genomes of five Meloidogyne species. Spaln spliced alignments of 34 non-redundant M. incognita effector genes known to be specifically expressed in dorsal gland (DG) cells. Percent identities <90% and query length coverage <66% are indicated in parentheses. Columns are as follows: 1) arbitrary effector gene number; 2) effector gene name and synonym; 3) NCBI protein accession number; 4) M. incognita genome scaffold number; 5) M. incognita gene model accession number; 6) strand; 7-8) alignment start and end coordinates on the scaffold; 9) Query length; 10) percent identity; 11) percent coverage of query length; 12) start codon covered by the alignment; 13) reference.

Notes:

application/vnd.openxmlformats-officedocument.wordprocessingml.document

Other Study-Related Materials

Label:

DG-Minc-Table.docx

Text:

Mapping of genes known to be specifically expressed in DG on the M. incognita genome and identification of corresponding predicted genes. Spaln spliced alignments of 34 non-redundant effector genes known to be specifically expressed in dorsal gland (DG) cells. One candidate effector (28B04) did not map on the genome. Columns are as follows: 1) arbitrary effector gene number; 2) effector gene name and synonym; 3) NCBI protein accession number; 4) M. incognita genome scaffold number; 5) M. incognita gene model accession number; 6) strand; 7-8) alignment start and end coordinates on the scaffold; 9) Query length; 10) percent identity; 11) percent coverage of query length; 12) start codon covered by the alignment; 13) reference. NA: not applicable.

Notes:

application/vnd.openxmlformats-officedocument.wordprocessingml.document

Other Study-Related Materials

Label:

DG-Minc-Table.pdf

Text:

Mapping of genes known to be specifically expressed in DG on the M. incognita genome and identification of corresponding predicted genes. Spaln spliced alignments of 34 non-redundant effector genes known to be specifically expressed in dorsal gland (DG) cells. One candidate effector (28B04) did not map on the genome. Columns are as follows: 1) arbitrary effector gene number; 2) effector gene name and synonym; 3) NCBI protein accession number; 4) M. incognita genome scaffold number; 5) M. incognita gene model accession number; 6) strand; 7-8) alignment start and end coordinates on the scaffold; 9) Query length; 10) percent identity; 11) percent coverage of query length; 12) start codon covered by the alignment; 13) reference. NA: not applicable.

Notes:

application/pdf

Other Study-Related Materials

Label:

SvG-Mel-Genus.docx

Text:

Mapping of genes known to be specifically expressed in SvG on the genomes of five Meloidogyne species. Spaln spliced alignments of 48 non-redundant M. incognita effector genes known to be specifically expressed in sub-ventral gland (SvG) cells. Percent identities <90% are indicated in parenthesis. Columns are as follows: 1) arbitrary effector gene number; 2) effector gene name and synonym; 3) NCBI protein accession number; 4-8) number of matches on the genomes of M. incognita, M. arenaria, M. javanica, M. enterolobii and M. hapla, respectively.

Notes:

application/vnd.openxmlformats-officedocument.wordprocessingml.document

Other Study-Related Materials

Label:

SvG-Minc-Table.docx

Text:

Mapping of genes known to be specifically expressed in SvG on the M. incognita genome and identification of corresponding predicted genes. Spaln spliced alignments of 48 non-redundant effector genes known to be specifically expressed in sub-ventral gland (SvG) cells. Columns as follows: 1) arbitrary effector gene number; 2) effector gene name and synonym; 3) NCBI protein accession number; 4) M. incognita genome scaffold number; 5) M. incognita gene model accession number; 6) strand; 7-8) alignment start and end coordinates on the scaffold; 9) Query length; 10) percent identity; 11) percent coverage of query length; 12) start codon covered by the alignment; 13) reference.

Notes:

application/vnd.openxmlformats-officedocument.wordprocessingml.document

Other Study-Related Materials

Label:

SvG-Minc-Table.pdf

Text:

Mapping of genes known to be specifically expressed in SvG on the M. incognita genome and identification of corresponding predicted genes. Spaln spliced alignments of 48 non-redundant effector genes known to be specifically expressed in sub-ventral gland (SvG) cells. Columns as follows: 1) arbitrary effector gene number; 2) effector gene name and synonym; 3) NCBI protein accession number; 4) M. incognita genome scaffold number; 5) M. incognita gene model accession number; 6) strand; 7-8) alignment start and end coordinates on the scaffold; 9) Query length; 10) percent identity; 11) percent coverage of query length; 12) start codon covered by the alignment; 13) reference.

Notes:

application/pdf