The Genome of Blue-Capped Cordon-Bleu Uncovers Hidden Diversity of LTR Retrotransposons in Zebra Finch
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sequencing, Genome Assembly and Karyotyping
2.2. Computational and Manual Curation of Transposable Elements
2.3. Data Analysis
2.4. Data Deposition
3. Results
3.1. Genome Assembly and Karyotype of Blue-Capped Cordon-Bleu
3.2. The Transposable Element Landscape of Blue-Capped Cordon-Bleu
3.3. Comparative Genomics Revealed Extensive Shared Diversity of LTRs among Estrildid Finches
3.4. Analysis of a Recently Active TE
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Statistic | Quantity |
---|---|
Assembly size | 1099.6 Mb |
“N” nucleotides | 105.6 Mb |
Weighted mean molecule length | 42.4 kb |
Number of reads | 254.2 million |
Scaffolds | 26,389 |
Scaffold N50 | 10.9 Mb |
Contigs | 51,469 |
Contig N50 | 66.3 kb |
BUSCO (complete) | 90.1% |
BUSCO (fragmented) | 5.9% |
BUSCO (missing) | 4% |
Repeat Type | Copies | Total bp | % of Genome |
---|---|---|---|
SINE | 7163 | 852,236 | 0.08 |
LINE | 132,734 | 37,876,706 | 3.44 |
LTR | 61,457 | 29,437,443 | 2.68 |
DNA | 14,100 | 2,195,734 | 0.20 |
Unclassified | 2367 | 416,198 | 0.04 |
Total interspersed repeats | 217,821 | 70,778,317 | 6.44 |
Small RNA | 1479 | 199,270 | 0.02 |
Satellites | 1960 | 581,825 | 0.05 |
Simple repeats | 211,440 | 9,408,016 | 0.86 |
Low complexity | 43,325 | 2,238,772 | 0.20 |
Total tandem repeats | 258,204 | 12,427,883 | 1.17 |
Total repeats | 746,059 | 83,206,200 | 7.61 |
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Boman, J.; Frankl-Vilches, C.; da Silva dos Santos, M.; de Oliveira, E.H.C.; Gahr, M.; Suh, A. The Genome of Blue-Capped Cordon-Bleu Uncovers Hidden Diversity of LTR Retrotransposons in Zebra Finch. Genes 2019, 10, 301. https://doi.org/10.3390/genes10040301
Boman J, Frankl-Vilches C, da Silva dos Santos M, de Oliveira EHC, Gahr M, Suh A. The Genome of Blue-Capped Cordon-Bleu Uncovers Hidden Diversity of LTR Retrotransposons in Zebra Finch. Genes. 2019; 10(4):301. https://doi.org/10.3390/genes10040301
Chicago/Turabian StyleBoman, Jesper, Carolina Frankl-Vilches, Michelly da Silva dos Santos, Edivaldo H. C. de Oliveira, Manfred Gahr, and Alexander Suh. 2019. "The Genome of Blue-Capped Cordon-Bleu Uncovers Hidden Diversity of LTR Retrotransposons in Zebra Finch" Genes 10, no. 4: 301. https://doi.org/10.3390/genes10040301
APA StyleBoman, J., Frankl-Vilches, C., da Silva dos Santos, M., de Oliveira, E. H. C., Gahr, M., & Suh, A. (2019). The Genome of Blue-Capped Cordon-Bleu Uncovers Hidden Diversity of LTR Retrotransposons in Zebra Finch. Genes, 10(4), 301. https://doi.org/10.3390/genes10040301