Efficient bioinformatics workflow for de novo transcriptome assembly of Pelargonium zonale
Authors
Milić, DejanaPantelić, Ana
Samardžić, Jelena
Banović Đeri, Bojana
Vidović, Marija
Contributors
Morić, IvanaĐorđević, Valentina
Conference object (Published version)
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© 2023 Institute of Molecular Genetics and Genetic Engineering, University of Belgrade
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Show full item recordAbstract
Variegated Pelargonium zonale is a widely cultivated ornamental plant characterized by
green, photosynthetically active tissue (GL) and white, non-photosynthetic tissue (WL).
The aim of this study was to investigate the transcriptomic differences between these
two tissue types.
We performed RNA-seq analysis of GL and WL on Illumina HiSeq 2500 platform. The
raw reads were processed using in-house scripts to remove low-quality reads, adapter
sequences, poly-N sequences, and contaminants. High-quality clean reads were subjected
to de novo transcriptome assembly using Trinity (min_kmer_cov = 2, min_glue = 2). The
redundancy was removed and longest transcripts per cluster were selected as unigenes.
Gene expression levels were estimated using RSEM by mapping clean data back to the
assembled transcriptome (Bowtie2 with mismatch = 0). Differential expression analysis
between GL and WL (three biological replicates per each) was performed with DESeq2
R package (p values adjusted acco...rding to Benjamini and Hochberg for controlling False
Discovery Rate). Genes with abs (log2 FC) ≥ 2 and adjusted p value < 0.05 were assigned
as statistically significant differentially expressed. Functional enrichment analysis was
performed using GOseq R package and KOBAS software (corrected p < 0.05).
We annotated 85,374 unigenes (61.17%), providing a valuable resource for future
functional genomics studies. Out of 8896 gene clusters that were statistically significantly
differentially expressed between the green and white leaf tissues (p value < 0.05 and
abs(log2 fold change) ≥ 2), 5585 were upregulated in the WL, while 3311 were upregulated
in the GL. These findings shed light on the transcriptomic differences between the
two leaf tissue types in P. zonale and provide a foundation for further research on the
functional significance of these differences. Also, this study demonstrated utility of the
Trinity pipeline for de novo transcriptomic analysis of organism whose genomes are yet
not sequenced.
Keywords:
de novo transcriptomic assembly / variegated plants / Pelargonium zonale / Trinity softwareSource:
4th Belgrade Bioinformatics Conference, 2023, 4, 90-90Publisher:
- Belgrade : Institute of molecular genetics and genetic engineering
Funding / projects:
- Ministry of Science, Technological Development and Innovation of the Republic of Serbia, institutional funding - 200042 (University of Belgrade, Institute of Molecular Genetics and Genetic Engineering) (RS-MESTD-inst-2020-200042)
- Bilateral project (no. 451-03-01963/2017-09/09)
Note:
- Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 2023
Institution/Community
Institut za molekularnu genetiku i genetičko inženjerstvoTY - CONF AU - Milić, Dejana AU - Pantelić, Ana AU - Samardžić, Jelena AU - Banović Đeri, Bojana AU - Vidović, Marija PY - 2023 UR - https://belbi.bg.ac.rs/ UR - https://imagine.imgge.bg.ac.rs/handle/123456789/2035 AB - Variegated Pelargonium zonale is a widely cultivated ornamental plant characterized by green, photosynthetically active tissue (GL) and white, non-photosynthetic tissue (WL). The aim of this study was to investigate the transcriptomic differences between these two tissue types. We performed RNA-seq analysis of GL and WL on Illumina HiSeq 2500 platform. The raw reads were processed using in-house scripts to remove low-quality reads, adapter sequences, poly-N sequences, and contaminants. High-quality clean reads were subjected to de novo transcriptome assembly using Trinity (min_kmer_cov = 2, min_glue = 2). The redundancy was removed and longest transcripts per cluster were selected as unigenes. Gene expression levels were estimated using RSEM by mapping clean data back to the assembled transcriptome (Bowtie2 with mismatch = 0). Differential expression analysis between GL and WL (three biological replicates per each) was performed with DESeq2 R package (p values adjusted according to Benjamini and Hochberg for controlling False Discovery Rate). Genes with abs (log2 FC) ≥ 2 and adjusted p value < 0.05 were assigned as statistically significant differentially expressed. Functional enrichment analysis was performed using GOseq R package and KOBAS software (corrected p < 0.05). We annotated 85,374 unigenes (61.17%), providing a valuable resource for future functional genomics studies. Out of 8896 gene clusters that were statistically significantly differentially expressed between the green and white leaf tissues (p value < 0.05 and abs(log2 fold change) ≥ 2), 5585 were upregulated in the WL, while 3311 were upregulated in the GL. These findings shed light on the transcriptomic differences between the two leaf tissue types in P. zonale and provide a foundation for further research on the functional significance of these differences. Also, this study demonstrated utility of the Trinity pipeline for de novo transcriptomic analysis of organism whose genomes are yet not sequenced. PB - Belgrade : Institute of molecular genetics and genetic engineering C3 - 4th Belgrade Bioinformatics Conference T1 - Efficient bioinformatics workflow for de novo transcriptome assembly of Pelargonium zonale EP - 90 SP - 90 VL - 4 UR - https://hdl.handle.net/21.15107/rcub_imagine_2035 ER -
@conference{ author = "Milić, Dejana and Pantelić, Ana and Samardžić, Jelena and Banović Đeri, Bojana and Vidović, Marija", year = "2023", abstract = "Variegated Pelargonium zonale is a widely cultivated ornamental plant characterized by green, photosynthetically active tissue (GL) and white, non-photosynthetic tissue (WL). The aim of this study was to investigate the transcriptomic differences between these two tissue types. We performed RNA-seq analysis of GL and WL on Illumina HiSeq 2500 platform. The raw reads were processed using in-house scripts to remove low-quality reads, adapter sequences, poly-N sequences, and contaminants. High-quality clean reads were subjected to de novo transcriptome assembly using Trinity (min_kmer_cov = 2, min_glue = 2). The redundancy was removed and longest transcripts per cluster were selected as unigenes. Gene expression levels were estimated using RSEM by mapping clean data back to the assembled transcriptome (Bowtie2 with mismatch = 0). Differential expression analysis between GL and WL (three biological replicates per each) was performed with DESeq2 R package (p values adjusted according to Benjamini and Hochberg for controlling False Discovery Rate). Genes with abs (log2 FC) ≥ 2 and adjusted p value < 0.05 were assigned as statistically significant differentially expressed. Functional enrichment analysis was performed using GOseq R package and KOBAS software (corrected p < 0.05). We annotated 85,374 unigenes (61.17%), providing a valuable resource for future functional genomics studies. Out of 8896 gene clusters that were statistically significantly differentially expressed between the green and white leaf tissues (p value < 0.05 and abs(log2 fold change) ≥ 2), 5585 were upregulated in the WL, while 3311 were upregulated in the GL. These findings shed light on the transcriptomic differences between the two leaf tissue types in P. zonale and provide a foundation for further research on the functional significance of these differences. Also, this study demonstrated utility of the Trinity pipeline for de novo transcriptomic analysis of organism whose genomes are yet not sequenced.", publisher = "Belgrade : Institute of molecular genetics and genetic engineering", journal = "4th Belgrade Bioinformatics Conference", title = "Efficient bioinformatics workflow for de novo transcriptome assembly of Pelargonium zonale", pages = "90-90", volume = "4", url = "https://hdl.handle.net/21.15107/rcub_imagine_2035" }
Milić, D., Pantelić, A., Samardžić, J., Banović Đeri, B.,& Vidović, M.. (2023). Efficient bioinformatics workflow for de novo transcriptome assembly of Pelargonium zonale. in 4th Belgrade Bioinformatics Conference Belgrade : Institute of molecular genetics and genetic engineering., 4, 90-90. https://hdl.handle.net/21.15107/rcub_imagine_2035
Milić D, Pantelić A, Samardžić J, Banović Đeri B, Vidović M. Efficient bioinformatics workflow for de novo transcriptome assembly of Pelargonium zonale. in 4th Belgrade Bioinformatics Conference. 2023;4:90-90. https://hdl.handle.net/21.15107/rcub_imagine_2035 .
Milić, Dejana, Pantelić, Ana, Samardžić, Jelena, Banović Đeri, Bojana, Vidović, Marija, "Efficient bioinformatics workflow for de novo transcriptome assembly of Pelargonium zonale" in 4th Belgrade Bioinformatics Conference, 4 (2023):90-90, https://hdl.handle.net/21.15107/rcub_imagine_2035 .