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Genome-Wide Identification from Ascomycota Fungal Genomes and Classification of GATA Transcription Factors

Authors:
  • InfoBoss, south Korea, Seoul

Abstract

GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17-20CX2C) followed by a basic region. With 349 Ascomycota fungal genomes belonging to 159 genera, we successfully identified 2,437 GATA genes (2,486 GATA TFs) to understand phylogenomic position of Ascomycota fungal GATA TFs. Number of GATA genes in 349 fungal genomes ranges from 2 to 22 and proportion against whole genes is from 0.017% to 0.224%. In only 8 genomes, some GATA genes contain alternative splicing forms, presenting uncommon alternative splicing events in Ascomycota. Based on previous research of fungal GATA TFs, we found some different number of GATA TFs of fungal species, such as Aspergillus oryzae, Fusarium graminearum, and Neurospora crassa. Until now, at least 35 research papers have been revealed biological function of GATA genes, so that combined regulatory networks of GATA genes based on these references were reconstructed. In genus level, 30 genera belonging to 7 classes were selected for further analyses, presenting classification based on fungal characteristics. Bioinformatic pipeline to maintain fungal GATA TFs efficiently has been constructed with the aid of Fungal Genome Database (http://fungalgenome.info/). The results of this study and the pipeline can be a guide for classifying fungal GATA TFs, which can be utilized for understanding its biological roles as well as for inspiring evolutionary history of GATA TFs in fungal kingdom.
Genome-Wide Identification from Ascomycota Fungal Genomes and
Classification of GATA Transcription Factors
Mangi Kim, Hong Xi, and Jongsun Park*
1InfoBoss Research Center, 301 room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea, 06088
2InfoBoss, Co., Ltd., 301 room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea, 06088
GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-
binding domain is a class IV zinc finger motif (CX2CX17-20CX2C) followed by a
basic region. With 349 Ascomycota fungal genomes belonging to 159 genera, we
successfully identified 2,437 GATA genes (2,486 GATA TFs) to understand
phylogenomic position of Ascomycota fungal GATA TFs. Number of GATA genes in
349 fungal genomes ranges from 2 to 22 and proportion against whole genes is
from 0.017% to 0.224%. In only 8 genomes, some GATA genes contain alternative
splicing forms, presenting uncommon alternative splicing events in Ascomycota.
Based on previous research of fungal GATA TFs, we found some different number
of GATA TFs of fungal species, such as Aspergillus oryzae, Fusarium graminearum,
and Neurospora crassa. Until now, at least 35 research papers have been revealed
biological function of GATA genes, so that combined regulatory networks of GATA
genes based on these references were reconstructed. In genus level, 30 genera
belonging to 7 classes were selected for further analyses, presenting classification
based on fungal characteristics. Bioinformatic pipeline to maintain fungal GATA TFs
efficiently has been constructed with the aid of Fungal Genome Database
(http://fungalgenome.info/). The results of this study and the pipeline can be a
guide for classifying fungal GATA TFs, which can be utilized for understanding its
biological roles as well as for inspiring evolutionary history of GATA TFs in fungal
kingdom.
Abstract
GATA Transcription Factors
The Sequence (left) and ribbon
representation (right) of the DNA-binding
domain of the fungal GATA factor AreA.
(Claudio Scazzocchio, 2000, Current Opinion
in Microbiology 3:126-131)
- GATA transcription factors are a class of
transcriptional regulators present in
fungi, metazoans and plants.
- The DNA-binding domains of
eukaryotic GATA factors comprise a four-
cysteine Zn finger and an adjacent basic
region.
- Plant GATA factors plant various roles
including regulation of light and
circadian clock responsive[1], control of
nitrite reductase genes[1], control genes related to low nitrogen stress[2], light-
responsive development[3], and chlorophyll-level regulation[3].
1. Reyes, J.C., Muro-Pastor, M.I. and Florencio, F.J., 2004. The GATA family of transcription factors in
Arabidopsis and rice. Plant physiology,134(4), pp.1718-1732.
2. Chen, H., Shao, H., Li, K., Zhang, D., Fan, S., Li, Y., Han, M., Genome-wide identification, evolution, and
expression analysis of GATA transcription factors in apple (Malus × domestica Borkh.). Gene, 627, pp.460-
472.
3. Zhang, C., Hou, Y., Hao, Q., Chen, H., Chen, L., Yuan, S, Shan, Z., Zhang, X., Yang, Z., Qiu, D., Zhou, X., Huang,
W., Genome-Wide Survey of the Soybean GATA Transcription Factor Gene Family and Expression Analysis
under Low Nitrogen Stress, PLoS One, 10(4), e0125174.
References Acknowledgements
- This research was fully supported by InfoBoss Grant (IBI-0001).
- It is also supported by
endless sacrifice of high-
end servers stayed in
InfoBoss DataCenter
Identification of Alternative Splicing
Forms of GATA gene in Ascomycota fungi
Statistics of GATA TFs from 349 Ascomycota fungi
Comparison between fungal GATA gene datasets in 18 genomes
Regulatory network of Ascomycota GATA TFs
Analysis of Alternative Splicing Forms of FVEG_00478
0
5
10
15
20
25
30
35
40
#of number
: GATA genes
: GATA TFs
0 2 4 6 8 10 12 14 16 18
Aspergillus oryzae
Fusarium graminearum
Fusarium solani
Fusarium verticillioides
Neurospora crassa
Sclerotinia sclerotiorum
Stagonospora nodorum
Schizosaccharomyces pombe
Candida albicans
Candida dubliniensis
Candida guilliermondii
Candida lusitaniae
Candida tropicalis
Debaryomyces hansenii
Kluyveromyces lactis
Lodderomyces elongisporus
Pichia stipitis
Yarrowia lipolytica
# of GATA TFs
: 2019
: 2006
0
20
40
60
80
100
120
0 5 10 15 20 25
Numbers of genome
Numbers of
GATA gene
0.0000
0.0005
0.0010
0.0015
0.0020
0.0025
050 100 150 200 250 300 350 400
Proportion of GATA genes
against whole genes
349 Ascomycota
fungal genomes
Numbers of genomes against number of GATA gene Proportion of GATA genes against whole genes
Histoplasma
Aurobasidium
Cenococcum
Alternaria
Phialophora
Talaromyces
Aspergillus
Penicillium
Blastomyces
Paracoccidioides
Trichophyton
Coccidioides
Erysiphe
Botrytis
Arthrobotrys
Candida
Saccharomyces
Cryphonectria
Colletotrichum
Beauveria
Hirstella
Metarhizium
Verticillium
Fusarium
Trichoderma
Gaeumannomyces
Ophiostoma
Chaetomium
Neurospora
Eutypa
Genus
Ajellomycetaceae
Aureobasidiaceae
Gloniaceae
Pleosporaceae
Herpotrichiellaceae
Trichocomaceae
Ajellomycetaceae
Arthrodermataceae
Onygenaceae
Erysiphaceae
Sclerotiniaceae
Orbiliaceae
Saccharomycetaceae
Cryphonectriaceae
Glomerellaceae
Cordycipitaceae
Ophiocordycipitaceae
Clavicipitaceae
Plectosphaerellaceae
Nectriaceae
Hypocreaceae
Magnaporhaceae
Ophiostomataceae
Chaetomiaceae
Sordariaceae
Diatrypaceae
Family
Onygenales
Dothideales
Mytilinidiales
Pleosporales
Chaetothyriales
Eurotiales
Onygenales
Erysiphales
Helotiales
Orbiliales
Saccharomycetales
Diaporthales
Glomerellales
Hypocreales
Magnaporthales
Ophiosomatales
Sordariales
Xylariales
Order
Ascomycetes
Dothideomycetes
Eurotiomycetes
Leotiomycetes
Orbiliomycetes
Saccharomycetes
Sordariomycetes
ClassPhylum
Ascomycota
510 15 20
Number of Genome
Pipeline for Identifying Fungal GATA Transcription
Factors
343 fungal
genomes
from Fungal
Genome Database
supported by
Identification of GATA
Transcription factor
based on InterPro Term
Filtering
false positive
results
Fungal GATA
TF Database
Further in-depth analyses
for comparative analyses
Identification of Fungal GATA Transcription factors along with taxonomy
- More than 100 fungal genomes presents 6 GATA TFs in their genomes.
- Maximum number of GATA TFs in fungal genome is 22.
- Based on proportion of number of GATA TFs (# of GATA TFs/# of total proteins in
genome), three groups were found: one is around 0.05%, the other is 0.125%, and
another is 0.175%.
-In total, 14 networks were reconstructed.
-37 references dealt with functional
analysis of fungal GATA TFs were reviewed
in detail to construct their regulatory
network.
- Most of regulatory networks are from
yeast species, which have been studied
intensively for long time.
- Based on this network, other fungal GATA
TFs can be mapped for inferring their
biological functions with considering each
species characteristics.
- For example, WC1 and WC2 are involved
in circadian clock in fungi, most of
homologous genes may have similar
function because of light sensing domains
which only exists in WC1 and WC2in GATA
TFs.
- Some of fungal genomes have alternative splicing gene model, which is
good resource to understand alternative splicing forms of GATA TFs.
- For example, FVEG_00478 gene from Fusarium verticilioides has 17
alternative forms named as FVEG_00478T0 to FVEG_00478T16.
- Among them, 2 transcripts missed GATA domains, which may not function
as GATA TF.
- The remaining 15 alternative forms were displayed, showing that intros in
both GAT domains and outside of domain exists.
- Once more gene models considering with alternative splicing forms are
available, it will be useful to understand nature of alternative splicing
events in fungal GATA TFs by comparing with plant GATA TFs.
- Gene model of fungal genome has been
improvised as time goes one based on
accumulated experimental data, such as
transcriptome data.
-By comparing with previous study of
fungal GATA TFs, many of fungal species
presents increment of number of fungal
GATA TFs.
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