Genome Survey Sequencing of Betula platyphylla
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials and Sequencing
2.2. Data Cleaning
2.3. Genome Size Estimation by k-mer Analysis
2.4. Preliminary Genome Assembly and GC Content Analysis
2.5. Identification and Filtration of Genomic Pollutants
2.6. Scaffold Construction, Gap Closing, and Sequence Polishing
2.7. SSR Identification and Analysis
2.8. Acquisition and Culture of Tissue Culture Seedlings of B. platyphylla
2.9. Sequencing and GC Content Analysis of Tissue Culture Plantlets
3. Results
3.1. Sequencing and Data Cleaning
3.2. Genome Size Estimation by k-mer Analysis
3.3. Preliminary Genome Assembly and GC Content Analysis
3.4. Identification and Filtration of Genomic Pollutants
3.5. Scaffold Construction, Gap Closure, and Sequence Polishing
3.6. SSR Identification and Analysis
3.7. Sequencing and GC Content Analysis of Tissue Culture Plantlets
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Medium | Basic Medium | Plant Hormone (mg/L) | Sucrose (g/L) | Agar (g/L) | pH | Others (g/L) |
---|---|---|---|---|---|---|
Dedifferentiation medium | WPM | NAA 0.02 6-BA 1.0 | 30 | 6.0 | 5.8~6.0 | -- |
Redifferentiation medium | WPM | NAA 0.02 | 30 | 6.0 | 5.8~6.0 | -- |
6-BA 1.0 GA3 0.5 | ||||||
Rooting medium | 1/2 MS | IBA 0.4 | 20 | 6.5 | 5.8~6.0 | Activated carbon 2.0 |
NAA 0.02 |
Library | 200 bp | 500 bp | 800 bp | 300 bp * |
---|---|---|---|---|
Raw reads length (bp) | 100 | 100 | 100 | 150 |
Raw data (Gb) | 14.5 | 12.0 | 5.0 | 23.5 |
Raw Q20 (%) | 96.9 | 94.4 | 86.5 | 94.8 |
Clean reads length | 90 | 90 | 90 | 135 |
Clean data (Gb) | 12.3 | 9.6 | 3.2 | 18.4 |
Clean Q20 (%) | 99.1 | 98.6 | 97.4 | 97.7 |
Species Name | Hit Number | Species Name | Hit Number |
---|---|---|---|
Mycobacterium chimaera | 229 | Cutibacterium avidum | 1 |
Mycobacterium intracellulare | 187 | Mycobacterium gilvum | 1 |
Mycobacterium marseillense | 186 | Mycobacterium vanbaalenii | 1 |
Mycobacterium yongonense | 106 | Malus x | 1 |
Mycobacterium indicus | 76 | Mycobacterium dioxanotrophicus | 1 |
Mycobacterium avium | 26 | Kocuria palustris | 1 |
Mycobacterium colombiense | 12 | Acidiphilium multivorum | 1 |
Mycobacterium abscessus | 4 | Gluconobacter oxydans | 1 |
Juglans regia | 4 | Mycobacterium ulcerans | 1 |
Mycobacterium marinum | 4 | Mycobacterium sinense | 1 |
Roseomonas gilardii | 2 | Theobroma cacao | 1 |
Mycobacterium thermoresistibile | 2 | Mycobacterium lepraemurium | 1 |
Xanthobacter autotrophicus | 1 | Prunus avium | 1 |
Cajanus cajan | 1 | Paracoccus yeei | 1 |
Mycobacterium liflandii | 1 | Glycine max | 1 |
Mycobacterium rhodesiae | 1 | Prunus persica | 1 |
Acidiphilium cryptum | 1 | Herrania umbratica | 1 |
Rhodococcus jostii | 1 | Vitis vinifera | 1 |
Item | Scaffold | Contig |
---|---|---|
No. of sequences | 79,580 | 97,097 |
Total length (bp) | 250,090,936 | 249,878,124 |
N50 length (bp) | 4312 | 3081 |
N90 length (bp) | 1336 | 1244 |
Max length (bp) | 85,240 | 85,240 |
GC content (%) | 34.8 | 34.8 |
Species Name | Hit Number | Align Length (bp) | Species Name | Hit Number | Align Length (bp) |
---|---|---|---|---|---|
Juglans regia | 8726 | 5,851,287 | Ziziphus jujuba | 89 | 51,320 |
Vitis vinifera | 638 | 658,331 | Prunus persica | 89 | 70,721 |
Theobroma cacao | 332 | 194,640 | Betula nana | 84 | 57,369 |
Betula pendula | 263 | 667,040 | Malus x | 66 | 27,903 |
Corylus avellana | 217 | 211,681 | Hevea brasiliensis | 65 | 36,133 |
Betula platyphylla | 197 | 64,844 | Fragaria vesca | 55 | 26,960 |
Betula luminifera | 191 | 98,488 | Prunus mume | 55 | 33,181 |
Quercus robur | 162 | 110,642 | Pyrus x | 54 | 23,152 |
Prunus avium | 141 | 77,758 | Glycine max | 54 | 29,659 |
Populus trichocarpa | 135 | 83,113 | Citrus clementina | 43 | 29,869 |
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Wang, S.; Chen, S.; Liu, C.; Liu, Y.; Zhao, X.; Yang, C.; Qu, G.-Z. Genome Survey Sequencing of Betula platyphylla. Forests 2019, 10, 826. https://doi.org/10.3390/f10100826
Wang S, Chen S, Liu C, Liu Y, Zhao X, Yang C, Qu G-Z. Genome Survey Sequencing of Betula platyphylla. Forests. 2019; 10(10):826. https://doi.org/10.3390/f10100826
Chicago/Turabian StyleWang, Sui, Su Chen, Caixia Liu, Yi Liu, Xiyang Zhao, Chuanping Yang, and Guan-Zheng Qu. 2019. "Genome Survey Sequencing of Betula platyphylla" Forests 10, no. 10: 826. https://doi.org/10.3390/f10100826