Chromosome-Level Genome Assembly Provides New Insights into Genome Evolution and Tuberous Root Formation of Potentilla anserina
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials and High-Throughput Sequencing
2.2. Estimation of Genome Size and Genome Assembly
2.3. Non-Coding RNA and Repeat Identification
2.4. Gene Prediction and Functional Annotation
2.5. Comparative Genomics and Phylogenetic Analysis
2.6. Whole Genome Duplication (WGD) Analysis
2.7. Sub-Genome Analysis and Expression Bias of Homeologs
2.8. Identification of Resistance Genes and Starch Biosynthesis Related Genes
3. Results
3.1. Genome Sequencing and Assembly
3.2. Assessment of Genome Quality
3.3. Genome Annotation
3.4. Comparative Genomics and Evolutionary Analysis
3.5. Sub-Genome Structure and Expression Bias Analysis
3.6. Resistance Gene Number Variation
3.7. Genes Involved in Starch Biosynthesis
4. Discussion
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Type | Number | Total Length (bp) | Proportion in the Genome (%) | |
---|---|---|---|---|
miRNA | 479 | 58,847 | 0.013 | |
tRNA | 1116 | 83,079 | 0.018 | |
Non-coding RNA | rRNA | 148 | 98,151 | 0.022 |
snRNA | 655 | 77,523 | 0.017 | |
Total | 2398 | 317,600 | 0.07 | |
Retroelements | 166,482 | 118,458,221 | 26.08 | |
LINEs | 39,955 | 12,791,517 | 2.82 | |
SINEs | 2373 | 269,946 | 0.06 | |
LTR elements | 124,154 | 105,396,758 | 23.20 | |
TE | Gypsy | 56,850 | 53,227,095 | 11.72 |
Copia | 31,449 | 38,942,113 | 8.57 | |
DNA transposons | 167,514 | 4,317,7431 | 9.50 | |
Others | 27,886 | 6,454,876 | 1.42 | |
Total | 368,838 | 169,737,457 | 37.26 |
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Gan, X.; Li, S.; Zong, Y.; Cao, D.; Li, Y.; Liu, R.; Cheng, S.; Liu, B.; Zhang, H. Chromosome-Level Genome Assembly Provides New Insights into Genome Evolution and Tuberous Root Formation of Potentilla anserina. Genes 2021, 12, 1993. https://doi.org/10.3390/genes12121993
Gan X, Li S, Zong Y, Cao D, Li Y, Liu R, Cheng S, Liu B, Zhang H. Chromosome-Level Genome Assembly Provides New Insights into Genome Evolution and Tuberous Root Formation of Potentilla anserina. Genes. 2021; 12(12):1993. https://doi.org/10.3390/genes12121993
Chicago/Turabian StyleGan, Xiaolong, Shiming Li, Yuan Zong, Dong Cao, Yun Li, Ruijuan Liu, Shu Cheng, Baolong Liu, and Huaigang Zhang. 2021. "Chromosome-Level Genome Assembly Provides New Insights into Genome Evolution and Tuberous Root Formation of Potentilla anserina" Genes 12, no. 12: 1993. https://doi.org/10.3390/genes12121993