The First Highly Contiguous Genome Assembly of Pikeperch (Sander lucioperca), an Emerging Aquaculture Species in Europe
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection, Library Preparation
2.2. Whole Genome Sequencing, Quality Control
2.3. K-mer Based Genome Characteristics Estimation
2.4. Genome Assembly with Long PacBio Reads
2.5. Quality Assessment of the Assembly
2.6. Repeats Annotation
2.7. Gene Structure Prediction
2.8. Preliminary Functional Annotation of Protein-Coding Genes
2.9. Gene Orthologs Analysis
3. Results
4. Discussion and Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Ethical Statements
Abbreviations
References
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Categories | Actinopterygii | Vertebrata | ||
---|---|---|---|---|
#Genes | Percentage | #Genes | Percentage | |
Complete single-copy | 4413 | 96.27 | 2523 | 97.56 |
Complete duplicated | 112 | 2.45 | 26 | 1.01 |
Fragmented | 89 | 1.94 | 40 | 1.54 |
Missing | 82 | 1.79 | 23 | 0.89 |
A-ASSEMBLY | |
Total size (nt) | 900,477,756 |
No. of contigs | 1966 |
Contigs N50 (nt) | 2,995,800 |
Longest contig (nt) | 17,774,792 |
No. of scaffolds | 1313 |
Scaffold N50 (nt) | 4,929,547 |
Longest scaffold (nt) | 19,065,786 |
Average scaffold (nt) | 685,817 |
GC-content (%) | 40.91 |
B-PROTEIN-CODING GENES | |
Number of coding genes | 21,249 |
mean gene length (nt) | 10,961 |
Mean coding sequence (CDS) length (nt) | 1313 |
Mean intron length (nt) | 1696 |
Mean exon length (nt) | 196 |
Average no. of exons per CDS | 6.7 |
% of genome covered by genes | 25.9 |
% of genome covered by CDS | 3.1 |
C-FUNCTIONAL DATABASES | |
Non-redundant (NR) hits | 18,536 (87.2%) |
Swissprot hits | 13,783 (64.8%) |
trEMBL hits | 18,171 (85.5%) |
Interpro hits | 18,486 (87.0 %) |
D-NON-CODING RNA PREDICTION | |
tRNA | 2313 |
rRNA | 180 |
miRNA | 166 |
Estimated Repeat Content (%) | Total Assembly Length (Mb) | Ungapped Length (Mb)/(%) | Number of Contigs | Contigs N50 (Mb) | #Coding Genes | |
---|---|---|---|---|---|---|
Yellow perch | 41 | 877.4 | 877.0 (99.9%) | 1097 | 4.2 | 23,749 |
Pikeperch | 39 | 900.5 | 899.8 (99.9%) | 1966 | 3.0 | 21,249 |
Eurasian perch | 33 | 958.2 | 851.6 (88.9%) | 100,821 | 0.0182 | 23,397 |
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Nguinkal, J.A.; Brunner, R.M.; Verleih, M.; Rebl, A.; Ríos-Pérez, L.d.l.; Schäfer, N.; Hadlich, F.; Stüeken, M.; Wittenburg, D.; Goldammer, T. The First Highly Contiguous Genome Assembly of Pikeperch (Sander lucioperca), an Emerging Aquaculture Species in Europe. Genes 2019, 10, 708. https://doi.org/10.3390/genes10090708
Nguinkal JA, Brunner RM, Verleih M, Rebl A, Ríos-Pérez Ldl, Schäfer N, Hadlich F, Stüeken M, Wittenburg D, Goldammer T. The First Highly Contiguous Genome Assembly of Pikeperch (Sander lucioperca), an Emerging Aquaculture Species in Europe. Genes. 2019; 10(9):708. https://doi.org/10.3390/genes10090708
Chicago/Turabian StyleNguinkal, Julien Alban, Ronald Marco Brunner, Marieke Verleih, Alexander Rebl, Lidia de los Ríos-Pérez, Nadine Schäfer, Frieder Hadlich, Marcus Stüeken, Dörte Wittenburg, and Tom Goldammer. 2019. "The First Highly Contiguous Genome Assembly of Pikeperch (Sander lucioperca), an Emerging Aquaculture Species in Europe" Genes 10, no. 9: 708. https://doi.org/10.3390/genes10090708
APA StyleNguinkal, J. A., Brunner, R. M., Verleih, M., Rebl, A., Ríos-Pérez, L. d. l., Schäfer, N., Hadlich, F., Stüeken, M., Wittenburg, D., & Goldammer, T. (2019). The First Highly Contiguous Genome Assembly of Pikeperch (Sander lucioperca), an Emerging Aquaculture Species in Europe. Genes, 10(9), 708. https://doi.org/10.3390/genes10090708