Informacja

Drogi użytkowniku, aplikacja do prawidłowego działania wymaga obsługi JavaScript. Proszę włącz obsługę JavaScript w Twojej przeglądarce.

Tytuł pozycji:

A chromosome-level genome assembly of Hong Kong catfish (Clarias fuscus) uncovers a sex-determining region.

Tytuł:
A chromosome-level genome assembly of Hong Kong catfish (Clarias fuscus) uncovers a sex-determining region.
Autorzy:
Tian CX; Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China. .; Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang, 524088, China. .; Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524088, China. .
Lin XH; Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China.; Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang, 524088, China.
Zhou DY; Guangxi Introduction and Breeding Center of Aquaculture, Nanning, 530001, China.
Chen Y; Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China.; Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang, 524088, China.
Shen YJ; Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China.; Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang, 524088, China.
Ye MH; Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China.; Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang, 524088, China.
Duan CY; Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China.; Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang, 524088, China.
Zhang YL; Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China.; Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang, 524088, China.
Yang BL; Guangxi Introduction and Breeding Center of Aquaculture, Nanning, 530001, China.
Deng SP; Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China.; Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang, 524088, China.; Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524088, China.
Zhu CH; Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China.; Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang, 524088, China.; Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524088, China.
Li GL; Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China. .; Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang, 524088, China. .; Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524088, China. .
Źródło:
BMC genomics [BMC Genomics] 2023 May 30; Vol. 24 (1), pp. 291. Date of Electronic Publication: 2023 May 30.
Typ publikacji:
Journal Article
Język:
English
Imprint Name(s):
Original Publication: London : BioMed Central, [2000-
MeSH Terms:
Chromosomes*
Catfishes*/genetics
Animals ; Phylogeny ; Hong Kong ; Genome ; Y Chromosome
References:
Gigascience. 2016 Aug 22;5(1):39. (PMID: 27549802)
Endocrinology. 2011 Jan;152(1):272-80. (PMID: 21084449)
Cytogenet Genome Res. 2005;110(1-4):462-7. (PMID: 16093699)
Mol Biol Evol. 2007 Aug;24(8):1586-91. (PMID: 17483113)
Proc Biol Sci. 2022 Mar 30;289(1971):20212645. (PMID: 35291838)
Front Cell Dev Biol. 2021 Mar 25;9:647103. (PMID: 33842473)
Nat Commun. 2016 Jun 02;7:11757. (PMID: 27249958)
Cell Mol Life Sci. 2019 Jun;76(11):2217-2229. (PMID: 30980108)
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W435-9. (PMID: 16845043)
Genet Med. 2019 Jan;21(1):62-70. (PMID: 29895858)
Cell. 2014 Dec 18;159(7):1665-80. (PMID: 25497547)
Science. 2017 Apr 7;356(6333):92-95. (PMID: 28336562)
Dev Biol. 2019 Nov 15;455(2):382-392. (PMID: 31315026)
Endocrinology. 2007 Oct;148(10):4560-7. (PMID: 17584971)
Bioinformatics. 2014 May 1;30(9):1312-3. (PMID: 24451623)
Nucleic Acids Res. 1997 Mar 1;25(5):955-64. (PMID: 9023104)
Genomics. 2021 Sep;113(5):3349-3356. (PMID: 34343676)
Nucleic Acids Res. 1999 Jan 15;27(2):573-80. (PMID: 9862982)
BMC Genomics. 2018 Dec 20;19(1):952. (PMID: 30572844)
Proc Natl Acad Sci U S A. 2013 Mar 19;110(12):4616-21. (PMID: 23487765)
Mar Biotechnol (NY). 2007 Mar-Apr;9(2):273-80. (PMID: 17308998)
Mol Ecol Resour. 2022 Aug;22(6):2411-2428. (PMID: 35429227)
Bioinformatics. 2015 Oct 1;31(19):3210-2. (PMID: 26059717)
Mol Biol Rep. 2011 Aug;38(6):3945-52. (PMID: 21108043)
Gigascience. 2018 Nov 1;7(11):. (PMID: 30256939)
BMC Bioinformatics. 2013 Jan 31;14:33. (PMID: 23363224)
PLoS One. 2019 Apr 1;14(4):e0214687. (PMID: 30933994)
BMC Biol. 2019 Jan 25;17(1):6. (PMID: 30683095)
Nat Methods. 2017 Nov;14(11):1072-1074. (PMID: 28945707)
Cell Syst. 2016 Jul;3(1):99-101. (PMID: 27467250)
BMC Bioinformatics. 2016 May 04;17(1):199. (PMID: 27142976)
Gene. 2021 Feb 15;769:145194. (PMID: 33007376)
Genome Res. 2003 Sep;13(9):2178-89. (PMID: 12952885)
Gigascience. 2018 Jan 1;7(1):1-6. (PMID: 29220494)
Curr Protoc Bioinformatics. 2014 Dec 12;48:4.11.1-4.11.39. (PMID: 25501943)
Gen Comp Endocrinol. 2019 Oct 1;282:113218. (PMID: 31301284)
Curr Protoc Bioinformatics. 2009 Mar;Chapter 4:4.10.1-4.10.14. (PMID: 19274634)
Biomed Res Int. 2020 Oct 13;2020:9060356. (PMID: 33150185)
Mol Ecol Resour. 2021 Jul;21(5):1575-1592. (PMID: 33503304)
Biol Reprod. 2021 Nov 15;105(5):1205-1220. (PMID: 34333627)
Mob DNA. 2019 Dec 12;10:48. (PMID: 31857828)
Front Genet. 2021 Jan 05;11:562856. (PMID: 33584785)
Mol Cell Probes. 2009 Oct;23(5):235-9. (PMID: 19401231)
Curr Protoc Bioinformatics. 2003 Feb;Chapter 10:Unit 10.3. (PMID: 18428693)
Sci Bull (Beijing). 2018 Nov 15;63(21):1420-1430. (PMID: 36658982)
Am J Transl Res. 2020 Dec 15;12(12):8185-8191. (PMID: 33437391)
Int J Biol Sci. 2013 Nov 05;9(10):1043-9. (PMID: 24250249)
PLoS One. 2014 Nov 19;9(11):e112963. (PMID: 25409509)
Bioinformatics. 2006 May 15;22(10):1269-71. (PMID: 16543274)
PeerJ. 2019 Apr 24;7:e6827. (PMID: 31086747)
DNA Res. 2021 Jan 19;28(1):. (PMID: 33416875)
BMC Biol. 2006 Dec 07;4:41. (PMID: 17156431)
Sci China Life Sci. 2015 Feb;58(2):124-36. (PMID: 25563981)
Hum Mol Genet. 2019 Mar 15;28(6):1052. (PMID: 30517620)
Bioinformatics. 2013 Nov 15;29(22):2933-5. (PMID: 24008419)
J Mol Biol. 1990 Oct 5;215(3):403-10. (PMID: 2231712)
Gene Expr Patterns. 2007 Aug;7(7):777-83. (PMID: 17604233)
Bioinformatics. 2009 May 15;25(10):1329-30. (PMID: 19349283)
Hum Mol Genet. 2009 Sep 15;18(18):3484-95. (PMID: 19561169)
PLoS Biol. 2014 Jul 01;12(7):e1001899. (PMID: 24983465)
Grant Information:
2019A1515110619 Guangdong Basic and Applied Basic Research Foundation; K22221 Modern Seed Industry Park for Whiteleg Shrimp of Guangdong Province; 202210566003 National College Students Innovation and Entrepreneurship Training Program; pdjh2022b0239 Special Funds for the Cultivation of Guangdong College Students' Scientific and Technological Innovation; Z2019123 Self-financing Project of Guangxi Agricultural Science and Technology
Contributed Indexing:
Keywords: Clarias fuscus; Gene; Genome; Phylogenetic analysis; Sex chromosome
Entry Date(s):
Date Created: 20230530 Date Completed: 20230601 Latest Revision: 20230602
Update Code:
20240105
PubMed Central ID:
PMC10230808
DOI:
10.1186/s12864-023-09394-2
PMID:
37254055
Czasopismo naukowe
Background: Hong Kong catfish (Clarias fuscus) is an ecologically and economically important species that is widely distributed in freshwater regions of southern China. Hong Kong catfish has significant sexual growth dimorphism. The genome assembly of the Hong Kong catfish would facilitate study of the sex determination and evolution mechanism of the species.
Results: The first high-quality chromosome-level genome of the Hong Kong catfish was constructed. The total genome was 933.4 Mb, with 416 contigs and a contig N50 length of 8.52 Mb. Using high-throughput chromosome conformation capture (Hi-C) data, the genome assembly was divided into 28 chromosomes with a scaffold N50 length of 36.68 Mb. A total of 23,345 protein-coding genes were predicted in the genome, and 94.28% of the genes were functionally annotated in public databases. Phylogenetic analysis indicated that C. fuscus and Clarias magur diverged approximately 63.7 million years ago. The comparative genome results showed that a total of 60 unique, 353 expanded and 851 contracted gene families were identified in Hong Kong catfish. A sex-linked quantitative trait locus identified in a previous study was located in a sex-determining region of 30.26 Mb (0.02 to 30.28 Mb) on chromosome 13 (Chr13), the predicted Y chromosome. This QTL region contained 785 genes, of which 18 were identified as sex-related genes.
Conclusions: This study is the first to report the chromosome-level genome assembly of Hong Kong catfish. The study provides an excellent genetic resource that will facilitate future studies of sex determination mechanisms and evolution in fish.
(© 2023. The Author(s).)
Zaloguj się, aby uzyskać dostęp do pełnego tekstu.

Ta witryna wykorzystuje pliki cookies do przechowywania informacji na Twoim komputerze. Pliki cookies stosujemy w celu świadczenia usług na najwyższym poziomie, w tym w sposób dostosowany do indywidualnych potrzeb. Korzystanie z witryny bez zmiany ustawień dotyczących cookies oznacza, że będą one zamieszczane w Twoim komputerze. W każdym momencie możesz dokonać zmiany ustawień dotyczących cookies