De Novo Transcriptome Assembly of Cucurbita Pepo L. Leaf Tissue Infested by Aphis Gossypii
Abstract
:1. Summary
2. Data Description
2.1. Illumina Read Processing and Transcriptome Assembly
2.2. Annotation
2.3. Evaluation of Transcriptome Quality and Completeness
2.4. Value of the Data
2.5. Data Records
3. Methods
3.1. Biological Material and Experimental Design
3.2. RNA Extraction, Library Construction and Sequencing
3.3. Read Pre-Processing and De Novo Assembly
3.4. Transcriptome Annotation
3.5. Mapping Transcripts on the Reference Genome
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Sample Name | Raw Data | High Quality Data | ||
---|---|---|---|---|
# Reads | # Paired Reads | # Single Reads | ||
Control | C24_1 | 31,430,108 | 22,032,822 | 5,256,322 |
C24_2 | 28,740,043 | 21,066,607 | 4,270,278 | |
C24_3 | 33,677,909 | 25,020,509 | 4,812,235 | |
C48_1 | 36,265,357 | 28,423,670 | 4,540,249 | |
C48_3 | 35,144,118 | 27,591,869 | 4,394,338 | |
C48_4 | 37,518,763 | 28,808,248 | 5,107,225 | |
C96_2 | 33,527,557 | 25,873,268 | 4,394,873 | |
C96_3 | 31,060,525 | 24,146,031 | 4,067,956 | |
C96_4 | 35,937,098 | 28,576,994 | 4,591,206 | |
Infested | A24_1 | 35,344,346 | 23,674,612 | 7,451,885 |
A24_2 | 35,230,308 | 23,732,387 | 7,382,828 | |
A24_3 | 34,366,050 | 22,964,925 | 7,204,783 | |
A48_2 | 37,211,641 | 25,261,715 | 7,571,915 | |
A48_3 | 36,623,056 | 24,901,053 | 7,442,903 | |
A48_4 | 37,996,974 | 25,666,812 | 7,820,577 | |
A96_1 | 38,622,935 | 27,596,629 | 5,791,605 | |
A96_2 | 34,353,147 | 24,532,466 | 5,227,154 | |
A96_3 | 29,037,507 | 20,856,920 | 4,406,645 |
Total # transcripts | 71,648 |
Total # gene locus | 42,517 |
# Single sequence | 22,594 |
# Multiple variants | 19,923 |
Total sequence length (nt) | 95,354,115 |
Average transcript length (nt) | 1331 |
Maximum transcript length (nt) | 12,009 |
Minimum transcript length (nt) | 100 |
Median transcript length (nt) | 1084 |
Items | # Sequences |
---|---|
complete ORF | 23,735 |
5′ truncated 1 | 25,000 |
3′ truncated 2 | 8220 |
5′ and 3′ truncated 3 | 10,579 |
no good ORF | 4114 |
Total | 71,648 |
Sample Number | BioSample | SRA ID | Library Name |
---|---|---|---|
1 | SAMN08742104 | SRS3072843 | A24-1 |
2 | SAMN08742105 | SRS3072853 | A24-2 |
3 | SAMN08742106 | SRS3072846 | A24-3 |
4 | SAMN08742107 | SRS3072849 | A48-2 |
5 | SAMN08742108 | SRS3072852 | A48-3 |
6 | SAMN08742109 | SRS3072855 | A48-4 |
7 | SAMN08742110 | SRS3072850 | A96-1 |
8 | SAMN08742111 | SRS3072851 | A96-2 |
9 | SAMN08742112 | SRS3072848 | A96-3 |
10 | SAMN08742113 | SRS3072847 | C24-1 |
11 | SAMN08742114 | SRS3072854 | C24-2 |
12 | SAMN08742115 | SRS3072842 | C24-3 |
13 | SAMN08742116 | SRS3072845 | C48-1 |
14 | SAMN08742117 | SRS3072844 | C48-3 |
15 | SAMN08742118 | SRS3072839 | C48-4 |
16 | SAMN08742119 | SRS3072838 | C96-2 |
17 | SAMN08742120 | SRS3072841 | C96-3 |
18 | SAMN08742121 | SRS3072840 | C96-4 |
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Share and Cite
Vitiello, A.; Rao, R.; Corrado, G.; Chiaiese, P.; Digilio, M.C.; Cigliano, R.A.; D’Agostino, N. De Novo Transcriptome Assembly of Cucurbita Pepo L. Leaf Tissue Infested by Aphis Gossypii. Data 2018, 3, 36. https://doi.org/10.3390/data3030036
Vitiello A, Rao R, Corrado G, Chiaiese P, Digilio MC, Cigliano RA, D’Agostino N. De Novo Transcriptome Assembly of Cucurbita Pepo L. Leaf Tissue Infested by Aphis Gossypii. Data. 2018; 3(3):36. https://doi.org/10.3390/data3030036
Chicago/Turabian StyleVitiello, Alessia, Rosa Rao, Giandomenico Corrado, Pasquale Chiaiese, Maria Cristina Digilio, Riccardo Aiese Cigliano, and Nunzio D’Agostino. 2018. "De Novo Transcriptome Assembly of Cucurbita Pepo L. Leaf Tissue Infested by Aphis Gossypii" Data 3, no. 3: 36. https://doi.org/10.3390/data3030036