De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome.

Autor: Huerlimann R; ARC Research Hub for Advanced Prawn Breeding, Townsville, QLD, 4811, Australia. roger.huerlimann@jcu.edu.au.; Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia. roger.huerlimann@jcu.edu.au., Wade NM; ARC Research Hub for Advanced Prawn Breeding, Townsville, QLD, 4811, Australia.; Aquaculture, CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia., Gordon L; ARC Research Hub for Advanced Prawn Breeding, Townsville, QLD, 4811, Australia.; Australian Genome Research Facility Ltd, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, VIC, 3050, Australia., Montenegro JD; Australian Genome Research Facility Ltd, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, VIC, 3050, Australia., Goodall J; ARC Research Hub for Advanced Prawn Breeding, Townsville, QLD, 4811, Australia.; Aquaculture, CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia., McWilliam S; Aquaculture, CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia., Tinning M; ARC Research Hub for Advanced Prawn Breeding, Townsville, QLD, 4811, Australia.; Australian Genome Research Facility Ltd, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, VIC, 3050, Australia., Siemering K; ARC Research Hub for Advanced Prawn Breeding, Townsville, QLD, 4811, Australia.; Australian Genome Research Facility Ltd, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, VIC, 3050, Australia., Giardina E; ARC Research Hub for Advanced Prawn Breeding, Townsville, QLD, 4811, Australia.; Seafarms Group Ltd, Level 11 225 St Georges Terrace, Perth, WA, 6000, Australia., Donovan D; ARC Research Hub for Advanced Prawn Breeding, Townsville, QLD, 4811, Australia.; Seafarms Group Ltd, Level 11 225 St Georges Terrace, Perth, WA, 6000, Australia., Sellars MJ; ARC Research Hub for Advanced Prawn Breeding, Townsville, QLD, 4811, Australia.; Aquaculture, CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia., Cowley JA; ARC Research Hub for Advanced Prawn Breeding, Townsville, QLD, 4811, Australia.; Aquaculture, CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia., Condon K; ARC Research Hub for Advanced Prawn Breeding, Townsville, QLD, 4811, Australia.; Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia., Coman GJ; ARC Research Hub for Advanced Prawn Breeding, Townsville, QLD, 4811, Australia.; Aquaculture, CSIRO Agriculture and Food, 144 North Street, Woorim, QLD, 4507, Australia., Khatkar MS; ARC Research Hub for Advanced Prawn Breeding, Townsville, QLD, 4811, Australia.; Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW, Australia., Raadsma HW; ARC Research Hub for Advanced Prawn Breeding, Townsville, QLD, 4811, Australia.; Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW, Australia., Maes GE; Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia.; Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, 3000, Belgium.; Center for Human Genetics, UZ Leuven- Genomics Core, KU Leuven, Leuven, 3000, Belgium., Zenger KR; ARC Research Hub for Advanced Prawn Breeding, Townsville, QLD, 4811, Australia.; Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia., Jerry DR; ARC Research Hub for Advanced Prawn Breeding, Townsville, QLD, 4811, Australia.; Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia.
Jazyk: angličtina
Zdroj: Scientific reports [Sci Rep] 2018 Sep 10; Vol. 8 (1), pp. 13553. Date of Electronic Publication: 2018 Sep 10.
DOI: 10.1038/s41598-018-31148-4
Abstrakt: 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 based on nine adult tissues and eight early life-history stages (BUSCO - Complete: 98.2% [Duplicated: 51.3%], Fragmented: 0.8%, Missing: 1.0%). The assembly resulted in 236,388 contigs, which were then further segregated into 99,203 adult tissue specific and 58,678 early life-history stage specific clusters. 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. 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. 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.
Databáze: MEDLINE
Externí odkaz:
Nepřihlášeným uživatelům se plný text nezobrazuje