De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp ( Penaeus monodon ) transcriptome
De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp ( Penaeus monodon ) transcriptome
Abstract The black tiger shrimp (Penaeus monodon) remains the second most widely cultured shrimp species globally. However, issues with disease and domestication have seen production levels stagnate over the past two decades. To help identify innovative solutions needed to resolve bottlenecks hampering the culture of this species, it is important to generate genetic and genomic resources. Towards this aim, we have produced the most complete publicly available P. monodon transcriptome database to date. The assembly was carried out in multiple assemblers using 2×125 bp HiSeq data from PolyA selected, ribo-depleted RNA extracted from nine adult tissues and eight early life-history stages. In total, approximately 700 million high-quality sequence reads were obtained and assembled into 236,388 clusters. These were then further segregated into 99,203 adult tissue specific clusters, and 58,678 early life-history stage specific clusters. The final transcriptome had a high TransRate score of 0.37, with 88% of all reads successfully mapping back to the transcriptome. BUSCO statistics showed the assembly to be highly complete with low fragmentation, few genes missing, but higher redundancy or transcript duplication (Complete: 98.2% (Duplicated: 51.3%), Fragmented: 0.8%, Missing: 1.0%), and to greatly exceed the completeness of existing P. monodon transcriptomes. While annotation rates were low (approximately 30%), as is typical for a non-model organisms, annotated transcript clusters were successfully mapped to several hundred functional KEGG pathways. To help address the lack of annotation, transcripts were clustered into groups within tissues and early life-history stages, providing initial evidence for their roles in specific tissue functions, or developmental transitions. Additionally, transcripts of shrimp viruses previously not known to occur in Australia were also discovered. We expect the transcriptome to provide an essential resource to investigate the molecular basis of commercially relevant-significant traits in P. monodon and other shrimp species.
Huerlimann Roger、Montenegro Juan D、Tinning Matthew、Siemering Kirby、Condon Kelly、Coman Greg J、Raadsma Herman W、Maes Gregory、McWilliam Sean、Khatkar Mehar S、Goodall Jake、Gordon Lavinia、Sellars Melony J、Cowley Jeff A、Donovan Dallas、Giardina Erika、Zenger Kyall R、Jerry Dean R、Wade Nicholas M
ARC Research Hub for Advanced Prawn Breeding||Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook UniversityAustralian Genome Research Facility Ltd, The Walter and Eliza Hall InstituteARC Research Hub for Advanced Prawn Breeding||Australian Genome Research Facility Ltd, The Walter and Eliza Hall InstituteARC Research Hub for Advanced Prawn Breeding||Australian Genome Research Facility Ltd, The Walter and Eliza Hall InstituteARC Research Hub for Advanced Prawn Breeding||Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook UniversityARC Research Hub for Advanced Prawn Breeding||CSIRO Agriculture and Food, Integrated Sustainable Aquaculture ProgramARC Research Hub for Advanced Prawn Breeding||Sydney School of Veterinary Science, Faculty of Science, The University of SydneyLaboratory of Biodiversity and Evolutionary Genomics, KU Leuven||Center for Human Genetics, UZ Leuven-Genomics Core, KU LeuvenCSIRO Agriculture and Food, Integrated Sustainable Aquaculture ProgramARC Research Hub for Advanced Prawn Breeding||Sydney School of Veterinary Science, Faculty of Science, The University of SydneyARC Research Hub for Advanced Prawn Breeding||CSIRO Agriculture and Food, Integrated Sustainable Aquaculture ProgramARC Research Hub for Advanced Prawn Breeding||Australian Genome Research Facility Ltd, The Walter and Eliza Hall InstituteARC Research Hub for Advanced Prawn Breeding||CSIRO Agriculture and Food, Integrated Sustainable Aquaculture ProgramARC Research Hub for Advanced Prawn Breeding||CSIRO Agriculture and Food, Integrated Sustainable Aquaculture ProgramARC Research Hub for Advanced Prawn Breeding||Seafarms Group LtdARC Research Hub for Advanced Prawn Breeding||Seafarms Group LtdARC Research Hub for Advanced Prawn Breeding||Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook UniversityARC Research Hub for Advanced Prawn Breeding||Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook UniversityARC Research Hub for Advanced Prawn Breeding||CSIRO Agriculture and Food, Integrated Sustainable Aquaculture Program
分子生物学遗传学动物学
Huerlimann Roger,Montenegro Juan D,Tinning Matthew,Siemering Kirby,Condon Kelly,Coman Greg J,Raadsma Herman W,Maes Gregory,McWilliam Sean,Khatkar Mehar S,Goodall Jake,Gordon Lavinia,Sellars Melony J,Cowley Jeff A,Donovan Dallas,Giardina Erika,Zenger Kyall R,Jerry Dean R,Wade Nicholas M.De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp ( Penaeus monodon ) transcriptome[EB/OL].(2025-03-28)[2025-06-06].https://www.biorxiv.org/content/10.1101/280420.点此复制
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