Item request has been placed!
×
Item request cannot be made.
×
![loading](/sites/all/modules/hf_eds/images/loading.gif)
Processing Request
RNA-seq analysis to identify genes related to resting egg production of panarctic Daphnia pulex.
Item request has been placed!
×
Item request cannot be made.
×
![loading](/sites/all/modules/hf_eds/images/loading.gif)
Processing Request
- معلومة اضافية
- المصدر:
Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE
- بيانات النشر:
Original Publication: London : BioMed Central, [2000-
- الموضوع:
- نبذة مختصرة :
Background: The genus Daphnia switches its reproductive mode from subitaneous egg production to resting egg production in response to environmental stimuli. Although this life history trait is essential for surviving unsuitable environments, the molecular mechanism of resting egg production is little understood. In this study, we examined genes related to induction of resting egg production using two genotypes of panarctic Daphnia pulex, the JPN1 and JPN2 lineages, which differ genetically in the frequency of resting egg production. We reared these genotypes under high and low food levels. At the high food level, individuals of both genotypes continually produced subitaneous eggs, whereas at the low food level, only the JPN2 genotype produced resting eggs. Then, we performed RNA-seq analysis on specimens of three instars, including before and after egg production.
Results: These results showed that expressed genes differed significantly between individuals grown under high and low food levels and among individuals of different instars and genotypes. Among these differentially expressed genes (DEGs), we found 16 that changed expression level before resting egg production. Some of these genes showed high-level expression only before resting egg production and one gene was an ortholog of bubblegum (bgm), which is reportedly up-regulated before diapause in bumblebees. According to gene ontology (GO) enrichment analysis, one GO term annotated as long-chain fatty acid biosynthetic process was enriched among these 16 genes. In addition, GO terms related to glycometabolism were enriched among down-regulated genes of individuals holding resting eggs, compared to those before resting egg production.
Conclusions: We found candidate genes highly expressed only before resting egg production. Although functions of candidate genes found in this study have not been reported previously in Daphnia, catabolism of long-chain fatty acids and metabolism of glycerates are related to diapause in other organisms. Thus, it is highly probable that candidate genes identified in this study are related to the molecular mechanism regulating resting egg production in Daphnia.
(© 2023. The Author(s).)
- References:
Adv Lipid Res. 1993;25:65-90. (PMID: 8368154)
J Biochem. 2002 Aug;132(2):229-36. (PMID: 12153720)
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D258-61. (PMID: 14681407)
G3 (Bethesda). 2017 May 5;7(5):1405-1416. (PMID: 28235826)
Zoolog Sci. 2022 Oct;39(5):407-412. (PMID: 36205361)
Nat Rev Mol Cell Biol. 2008 Feb;9(2):139-50. (PMID: 18216770)
Nat Biotechnol. 2015 Mar;33(3):290-5. (PMID: 25690850)
Zoolog Sci. 2016 Feb;33(1):106-15. (PMID: 26853876)
Biochim Biophys Acta. 2008 Sep;1781(9):424-34. (PMID: 18619555)
Comp Biochem Physiol B Biochem Mol Biol. 2018 Apr;218:23-29. (PMID: 29427614)
Nature. 2001 Dec 20-27;414(6866):899-901. (PMID: 11780060)
J Insect Physiol. 2009 Jun;55(6):593-8. (PMID: 19418600)
Sleep. 2015 May 01;38(5):801-14. (PMID: 25409104)
J Morphol. 2014 Jul;275(7):760-7. (PMID: 24500908)
Evolution. 2005 Apr;59(4):800-13. (PMID: 15926690)
Nature. 2012 Feb 19;483(7389):350-4. (PMID: 22343897)
Oecologia. 1991 Apr;86(2):243-250. (PMID: 28313207)
Evodevo. 2022 Aug 8;13(1):16. (PMID: 35941607)
Science. 2011 Feb 4;331(6017):555-61. (PMID: 21292972)
BMC Bioinformatics. 2013 Jul 09;14:219. (PMID: 23837715)
Nat Biotechnol. 2019 Aug;37(8):907-915. (PMID: 31375807)
Bioinformatics. 2018 Sep 1;34(17):i884-i890. (PMID: 30423086)
Nat Genet. 2000 May;25(1):25-9. (PMID: 10802651)
Science. 2007 Jun 29;316(5833):1895-8. (PMID: 17600215)
Sci Rep. 2016 Sep 27;6:34241. (PMID: 27671106)
Gen Comp Endocrinol. 2007 Mar;151(1):66-71. (PMID: 17222840)
Genome Biol. 2010;11(3):R25. (PMID: 20196867)
PLoS Med. 2004 Dec;1(3):e62. (PMID: 15602591)
Bioinformatics. 2010 Jan 1;26(1):139-40. (PMID: 19910308)
Sci Rep. 2018 Jul 18;8(1):10872. (PMID: 30022098)
Mol Biol Evol. 2016 Dec;33(12):3194-3204. (PMID: 27660296)
Front Cell Neurosci. 2014 Feb 20;8:25. (PMID: 24600344)
Mol Ecol. 2018 Aug 13;:. (PMID: 30105798)
Mol Ecol. 2016 Oct;25(19):4805-17. (PMID: 27542169)
Mol Ecol. 2015 Nov;24(22):5596-615. (PMID: 26453894)
Bioinformatics. 2009 Aug 15;25(16):2078-9. (PMID: 19505943)
Oecologia. 1999 May;119(2):159-165. (PMID: 28307964)
Science. 1999 Jun 18;284(5422):1985-8. (PMID: 10373116)
Sci Rep. 2020 Nov 16;10(1):19928. (PMID: 33199823)
Dis Model Mech. 2018 Jun 15;11(6):. (PMID: 29739804)
- Grant Information:
19J21014 Japan Society for the Promotion of Science; 16H02522 Japan Society for the Promotion of Science
- Contributed Indexing:
Keywords: Daphnia; Diapause; Obligate parthenogenesis; RNA-seq; Resting egg
- الموضوع:
Date Created: 20230517 Date Completed: 20230519 Latest Revision: 20231213
- الموضوع:
20231215
- الرقم المعرف:
PMC10190107
- الرقم المعرف:
10.1186/s12864-023-09369-3
- الرقم المعرف:
37198540
No Comments.