RNA-Seq-Based Transcriptome Analysis of Aflatoxigenic Aspergillus flavus in Response to Water Activity
Abstract
:1. Introduction
2. Materials and Methods
2.1. Fungal Strains and Growth Conditions
2.2. Growth Assessment and Aflatoxin Analysis
2.3. cDNA Preparation and Illumina Sequencing
2.4. Clean Reads and Sequence Assembly
2.5. Annotation and Analysis of Unigenes
2.6. Identification and Analysis of Differentially Expressed Genes
2.7. Availability of Supporting Data
3. Results and Discussion
3.1. Effect of Water Activity on Growth and Aflatoxin Production of A. flavus
3.2. Illumina Sequencing and Reads Assembling
Category | Treatments | Total number | Mean length (Nt) | N50 |
---|---|---|---|---|
Contigs | 0.93 aw | 29,420 | 663 | 1705 |
0.99 aw | 30,619 | 653 | 1623 | |
Unigenes | 0.93 aw | 25,190 | 1004 | 1740 |
0.99 aw | 24,991 | 1073 | 1829 |
3.3. Annotation and Analysis of All-Unigenes
3.4. Functional Analysis and Classification of All-Unigenes
3.5. Identification and Analysis of DEGs
3.6. Analysis of DEGs Involved in Aflatoxin Biosynthesis
3.7. Analysis of DEGs Involved in Development
Gene | ref_ID | Function | 0.99_RPKM | 0.93_RPKM | Log2 (0.99_RPKM/0.93_RPKM) | Changes (*) |
---|---|---|---|---|---|---|
aflF | XP_002379954 | Dehydrogenase | 5.2 | 0.1 | 6.3 | Up |
aflU | XP_002379953 | P450 monooxygenase | 16.3 | 1.1 | 3.9 | Up |
aflG | XP_002379937 | Cytochrome P450 monooxygenase | 50.6 | 4.2 | 3.6 | Up |
aflNa | XP_002379938 | Hypothetical protein | 121.4 | 17.5 | 2.8 | Up |
aflT | XP_002379952 | Transmembrane protein | 10.4 | 1.7 | 2.6 | Up |
aflQ | XP_002379931 | Cytochrome P450 monooxigenase | 163.3 | 28.3 | 2.5 | Up |
aflJ | XM_002379902 | Esterase | 6.1 | 1.3 | 2.2 | Up |
aflI | XP_002379934 | Cytochrome P450 monooxygenase | 1.1 | 0.3 | 1.7 | Up |
aflMa | XP_002379940 | Hypothetical protein | 11.9 | 4.1 | 1.5 | Up |
aflYb | XP_002379924 | Putative hexose transporter | 5.9 | 2.2 | 1.4 | Up |
aflYd | XP_002379922 | Sugar regulator | 2.8 | 1.1 | 1.4 | Up |
aflX | XP_002379927 | Monooxygenase oxidase | 6.4 | 2.4 | 1.4 | Up |
aflB | XP_002379947 | Fatty acid synthase beta subunit | 149.9 | 72.2 | 1.1 | Up |
aflW | XP_002379928 | Monooxygenase | 3.2 | 1.6 | 1.0 | Up |
aflY | XP_002379926 | Hypothetical protein | 4.4 | 2.2 | 1.0 | Up |
aflL | XP_002379936 | P450 monooxygenase | 4.6 | 2.4 | 0.9 | |
aflN | XP_002379939 | Monooxygenase | 3.1 | 1.7 | 0.9 | |
aflV | XP_002379929 | Cytochrome P450 monooxygenase | 2.1 | 1.2 | 0.8 | |
aflE | XP_002379942 | NOR reductase dehydrogenase | 6.5 | 4.1 | 0.7 | |
aflM | XP_002379941 | Ketoreductase | 14.0 | 10.8 | 0.4 | |
aflYa | XP_002379925 | NADH oxidase | 2.1 | 1.6 | 0.4 | |
aflS | XP_002379945 | Pathway regulator | 0.6 | 0.5 | 0.3 | |
aflP | XP_002379932 | O-methyltransferase A | 4.7 | 4.2 | 0.2 | |
aflK | XP_002379930 | VERB synthase | 11.5 | 11.2 | 0.0 | |
aflR | XM_002379905 | Transcription activator | 0.1 | 0.1 | 0.0 | |
aflLa | XP_002379935 | Hypothetical protein | 1.4 | 1.6 | −0.1 | |
aflO | XP_002379933 | O-methyltransferase B | 6.7 | 7.7 | −0.2 | |
aflH | XP_002379944 | Short chain alcohol dehydrogenase | 4.4 | 5.5 | −0.3 | |
aflA | XP_002379948 | Fatty acid synthase alpha subunit | 4.7 | 6.0 | −0.3 | |
aflCa | XP_002379950 | Hypothetical protein | 0.4 | 0.6 | −0.4 | |
aflD | XP_002379949 | Reductase | 0.4 | 0.6 | −0.4 | |
aflYc | XP_002379923 | Glucosidase | 19.9 | 26.2 | −0.4 | |
aflC | XP_002379951 | Polyketide synthase | 4.8 | 7.7 | −0.7 |
Gene | ref_ID | Function | 0.99_RPKM | 0.93_RPKM | Log2 (0.99_RPKM/0.93_RPKM) | Changes (*) |
---|---|---|---|---|---|---|
rgsA | gi|259484767|tpe|CBF81270.1| | G protein regulator | ND | ND | ||
nsdD | gi|259485893|tpe|CBF83303.1| | DNA binding protein | ND | ND | ||
flbC | gi|259487830|tpe|CBF86815.1| | Putative zinc finger protein | 135.1 | 5.7 | 4.6 | Up |
cryA | gi|40747330|gb|EAA66486.1| | Hypothetical protein | 0.2 | 0 | 3.2 | Up |
MAT1-1 | gi|259486330|tpe|CBF84081.1| | Mating type alpha box protein | 1.1 | 0.1 | 3.2 | Up |
gprB | gi|34482020|tpg|DAA01795.1| | Pheromone receptor | 9.9 | 1.7 | 2.5 | Up |
abr1 | gi|6090821|gb|AAF03353.1| | Brown 1 | 2.8 | 0.7 | 1.9 | Up |
brnA | gi|134081843|emb|CAK42098.1| | Unnamed protein product | 2.8 | 0.7 | 1.9 | Up |
MAT1-2 | gi|259482427|tpe|CBF76901.1| | Mating type HMG-box protein | 8.6 | 2.5 | 1.8 | Up |
brlA | gi|259488735|tpe|CBF88417.1| | Regulatory protein | 7.7 | 2.3 | 1.8 | Up |
lreA | gi|259485576|tpe|CBF82714.1| | GATA-factor | 6.6 | 2.9 | 1.2 | Up |
stuA | gi|259480005|tpe|CBF70741.1| | Cell pattern formation-associated protein | 3.8 | 1.8 | 1.1 | Up |
medA | gi|259479562|tpe|CBF69898.1| | Medusa | 6.1 | 3 | 1.1 | Up |
tpsB | gi|1488038|gb|AAB05869.1| | Trehalose-6-phosphate synthase | 91.5 | 47.4 | 0.9 | |
tpsA | gi|3170246|gb|AAC18060.1| | Trehalose-6-phosphate synthase subunit 1 | 91.5 | 47.4 | 0.9 | |
steA | gi|259487683|tpe|CBF86542.1| | Transcription factor | 25 | 15 | 0.8 | |
gprA | gi|34482022|tpg|DAA01796.1| | Pheromone receptor | 4.4 | 2.8 | 0.7 | |
gprD | gi|259485627|tpe|CBF82810.1| | Integral membrane protein | 11.3 | 7 | 0.7 | |
lreB | gi|259481867|tpe|CBF75789.1| | GATA-factor | 76.3 | 51.6 | 0.6 | |
rosA | gi|259484624|tpe|CBF81007.1| | Repressor of sexual development | 47.1 | 30.7 | 0.6 | |
nosA | gi|259487198|tpe|CBF85681.1| | NosA protein | 47.1 | 30.7 | 0.6 | |
wetA | gi|259487296|tpe|CBF85858.1| | Regulatory protein | 5.3 | 3.6 | 0.6 | |
phnA | gi|259489726|tpe|CBF90234.1| | Phosducin-like protein | 33.1 | 21.7 | 0.6 | |
arp2 | gi|6090729|gb|AAF03314.1| | Tetrahydroxynaphthalene reductase | 14 | 10.8 | 0.4 | |
kapA | gi|259487521|tpe|CBF86262.1| | Karyopherin alpha | 281.4 | 221.4 | 0.4 | |
arp1 | gi|2555060|gb|AAC49843.1| | Scytalone dehydratase | 63 | 52.6 | 0.3 | |
nsdC | gi|259481122|tpe|CBF74364.1| | NSDC | 8 | 6.5 | 0.3 | |
schA | gi|259481151|tpe|CBF74417.1| | CAMP-dependent protein kinase-like | 2.9 | 2.4 | 0.3 | |
abaA | gi|167998|gb|AAA33286.1| | AbaA protein | 6 | 5.7 | 0.1 | |
pkaA | gi|259479481|tpe|CBF69742.1| | CAMP-dependent protein kinase | 23.3 | 21.1 | 0.1 | |
mpkB | gi|259481736|tpe|CBF75537.1| | Mitogen-activated protein kinase | 26.4 | 25.2 | 0.1 | |
flbB | gi|259483861|tpe|CBF79600.1| | bZIP-type transcription factor | 48 | 43.4 | 0.1 | |
fphA | gi|259486541|tpe|CBF84471.1| | Phytochrome | 10.1 | 9 | 0.1 | |
steC | gi|259487662|tpe|CBF86503.1| | MAPKK kinase | 17.3 | 16.3 | 0.1 | |
veA | gi|259488644|tpe|CBF88249.1| | Mutant VeA1 protein | 32.2 | 30.7 | 0.1 | |
laeA | gi|259488911|tpe|CBF88745.1| | Methyltransferase | 19.3 | 17.5 | 0.1 | |
flbE | gi|259489004|tpe|CBF88918.1| | Putative uncharacterized protein | 54.4 | 51.4 | 0.1 | |
flbA | gi|259479939|tpe|CBF70620.1| | Developmental regulator | 18.4 | 18.4 | 0.0 | |
gpgA | gi|259486344|tpe|CBF84107.1| | G protein gamma subunit | 248.6 | 247 | 0.0 | |
sfaD | gi|259489728|tpe|CBF90238.1| | G-protein beta subunit | 78 | 77.2 | 0.0 | |
abr2 | gi|6090815|gb|AAF03349.1| | Brown 2 | 6.8 | 7.5 | −0.2 | |
gpaA | gi|27524346|emb|CAC81704.1| | GMP binding protein alpha subunit | 43.8 | 47.3 | −0.2 | |
gpaB | gi|27524350|emb|CAC81805.1| | GMP binding protein alpha subunit | 1.6 | 1.9 | −0.2 | |
pkaB | gi|67537094|ref|XP_662321.1| | Hypothetical protein | 0.6 | 0.7 | −0.2 | |
gaoC | gi|83773752|dbj|BAE63877.1| | Unnamed protein product | 43.8 | 47.3 | −0.2 | |
yA | gi|259480215|tpe|CBF71142.1| | Laccase-1 Precursor | 6.8 | 7.5 | −0.2 | |
ganB | gi|259488687|tpe|CBF88328.1| | G protein alpha subunit | 1.6 | 1.9 | −0.2 | |
fadA | gi|259489081|tpe|CBF89057.1| | GMP binding protein subunit alpha | 43.8 | 47.3 | −0.2 | |
velB | gi|259489398|tpe|CBF89638.1| | VelB | 15.1 | 16.6 | −0.2 | |
flbD | gi|259489501|tpe|CBF89824.1| | Putative uncharacterized protein | 9.9 | 11.4 | −0.2 | |
alb1 | gi|3136092|gb|AAC39471.1| | Polyketide synthase | 13.9 | 17.4 | −0.3 | |
chsC | gi|4519181|dbj|BAA75501.1| | Chitin synthase | 8.8 | 11 | −0.3 | |
fwnA | gi|134078436|emb|CAL00851.1| | Unnamed protein product | 13.9 | 17.4 | −0.3 | |
sfgA | gi|259480894|tpe|CBF73944.1| | SfgA | 0.8 | 0.9 | −0.3 | |
treB | gi|2827392|gb|AAB99831.1| | Neutral trehalase | 43.2 | 62.1 | −0.5 | |
pptA | gi|134080185|emb|CAK46165.1| | Unnamed protein product | 38.3 | 54.6 | −0.5 | |
cyaA | gi|259481514|tpe|CBF75105.1| | Adenylate cyclase | 1.6 | 2.4 | −0.5 | |
vosA | gi|259487318|tpe|CBF85898.1| | VosA | 4.3 | 6.2 | −0.5 | |
ppoB | gi|259479464|tpe|CBF69709.1| | Fatty acid oxygenase | 15.4 | 27.7 | −0.7 | |
ppoC | gi|259482096|tpe|CBF76249.1| | Fatty acid oxygenase | 15.4 | 27.7 | −0.7 | |
ppoA | gi|259487326|tpe|CBF85912.1| | Fatty acid oxygenase | 15.4 | 27.7 | −0.7 | |
rasA | gi|259489610|tpe|CBF90024.1| | Ras-like protein | 1.1 | 1.8 | −0.7 | |
chsA | gi|465390|dbj|BAA04806.1| | Chitin synthase | 8.7 | 19.6 | −1.3 | Down |
fluG | gi|259482332|tpe|CBF76713.1| | FluG | 11.8 | 34.5 | −1.7 | Down |
chiB | gi|259485098|tpe|CBF81882.1| | Class V chitinase | 0.1 | 0.1 | −1.7 | Down |
rolA | gi|28875529|dbj|BAC65230.1| | Hydrophobin putative | 1.5 | 6.9 | −2.3 | Down |
rodB | gi|70996676|ref|XP_753093.1| | Conidial hydrophobin | 1.5 | 6.9 | −2.3 | Down |
rodA | gi|259482991|tpe|CBF77990.1| | Rodlet protein | 1.5 | 6.9 | −2.3 | Down |
ganA | gi|259485962|tpe|CBF83426.1| | G protein alpha subunit homolog | ND | ND |
4. Conclusions
Supplementary Materials
Supplementary Files
Supplementary File 1Acknowledgments
Author Contributions
Conflicts of Interest
References
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Zhang, F.; Guo, Z.; Zhong, H.; Wang, S.; Yang, W.; Liu, Y.; Wang, S. RNA-Seq-Based Transcriptome Analysis of Aflatoxigenic Aspergillus flavus in Response to Water Activity. Toxins 2014, 6, 3187-3207. https://doi.org/10.3390/toxins6113187
Zhang F, Guo Z, Zhong H, Wang S, Yang W, Liu Y, Wang S. RNA-Seq-Based Transcriptome Analysis of Aflatoxigenic Aspergillus flavus in Response to Water Activity. Toxins. 2014; 6(11):3187-3207. https://doi.org/10.3390/toxins6113187
Chicago/Turabian StyleZhang, Feng, Zhenni Guo, Hong Zhong, Sen Wang, Weiqiang Yang, Yongfeng Liu, and Shihua Wang. 2014. "RNA-Seq-Based Transcriptome Analysis of Aflatoxigenic Aspergillus flavus in Response to Water Activity" Toxins 6, no. 11: 3187-3207. https://doi.org/10.3390/toxins6113187