SMRT Sequencing Technology Was Used to Construct the Batocera horsfieldi (Hope) Transcriptome and Reveal Its Features
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Sample Collection and Preparation
2.2. Library Preparation and SMRT Sequencing
2.3. SMRT Sequencing Data Processing
2.4. Functional Annotation of Transcripts
2.5. CDS Prediction
2.6. SSR Analysis
2.7. Transcription Factor (TF) Analysis
2.8. lncRNAs Analysis
3. Results
3.1. Transcriptome Analysis Was Performed using Pacbio Sequencing
3.2. Functional Annotation of B. horsfieldi
3.3. CDS Predictions
3.4. Identification of Transcription Factors
3.5. SSR Analysis
3.6. lncRNA Forecasts
4. Discussion
5. Conclusions
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Data Type | Total Bases (bp) | Total Number | Mean Length | Min_Length | Max_Length | N50 |
---|---|---|---|---|---|---|
polymerase read | 47.83 G | 462,134 | 103,503 | - | - | 165,195 |
subread | 46.31 G | 20,356,793 | 2275 | - | - | 2465 |
CCS | - | 432,091 | 2527 | 62 | 18,215 | 2674 |
FLNC | - | 395,851 | 2407 | 86 | 14,739 | 2555 |
Sample | Library Name | Raw Reads | Clean Reads | Raw Base (G) | Clean Base (G) | Effective (%) | Error (%) | Q20 (%) | Q30 (%) | GC (%) |
---|---|---|---|---|---|---|---|---|---|---|
BHM | FRAS220000762-4r | 48699628 | 45453468 | 7.3 | 6.82 | 93.33 | 0.03 | 97.65 | 93.02 | 36.65 |
BHM1 | FRAS220000763-4r | 56680480 | 52076758 | 8.5 | 7.81 | 91.88 | 0.03 | 97.74 | 93.17 | 36.37 |
BHM2 | FRAS220000764-3r | 39332558 | 36671048 | 5.9 | 5.5 | 93.23 | 0.03 | 97.46 | 92.46 | 32.88 |
BHF | FRAS220000759-4r | 43125796 | 40408496 | 6.47 | 6.06 | 93.7 | 0.03 | 97.87 | 93.26 | 34.54 |
BHF1 | FRAS220000760-5r | 42298740 | 39126102 | 6.34 | 5.87 | 92.5 | 0.03 | 97.77 | 93.14 | 35.24 |
BHF2 | FRAS220000761-4r | 44239794 | 41348904 | 6.64 | 6.2 | 93.47 | 0.03 | 97.76 | 93.13 | 34.36 |
Transcript Length Interval | <500 bp | 500–1 kbp | 1 k–2 kbp | 2 k–3 kbp | >3 kbp | Total |
---|---|---|---|---|---|---|
Number of transcripts | 21 | 800 | 13,054 | 16,657 | 9380 | 39,912 |
Number of genes | 3 | 230 | 3930 | 6593 | 4477 | 15,233 |
Isoform number | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 |
Unigene number | 10,226 | 2059 | 887 | 523 | 313 | 223 | 159 | 137 | 86 | 620 |
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Wei, X.; Xu, D.; Liu, Z.; Liu, Q.; Zhuo, Z. SMRT Sequencing Technology Was Used to Construct the Batocera horsfieldi (Hope) Transcriptome and Reveal Its Features. Insects 2023, 14, 625. https://doi.org/10.3390/insects14070625
Wei X, Xu D, Liu Z, Liu Q, Zhuo Z. SMRT Sequencing Technology Was Used to Construct the Batocera horsfieldi (Hope) Transcriptome and Reveal Its Features. Insects. 2023; 14(7):625. https://doi.org/10.3390/insects14070625
Chicago/Turabian StyleWei, Xinju, Danping Xu, Zhiqian Liu, Quanwei Liu, and Zhihang Zhuo. 2023. "SMRT Sequencing Technology Was Used to Construct the Batocera horsfieldi (Hope) Transcriptome and Reveal Its Features" Insects 14, no. 7: 625. https://doi.org/10.3390/insects14070625