Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing.
Biological clock genes
Circannual
Cyprinid
Labeo rohita
Marker
Reproductive seasonality
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
22 Sep 2021
22 Sep 2021
Historique:
received:
29
11
2020
accepted:
26
05
2021
entrez:
22
9
2021
pubmed:
23
9
2021
medline:
24
9
2021
Statut:
epublish
Résumé
Carp fish, rohu (Labeo rohita Ham.) is important freshwater aquaculture species of South-East Asia having seasonal reproductive rhythm. There is no holistic study at transcriptome level revealing key candidate genes involved in such circannual rhythm regulated by biological clock genes (BCGs). Seasonality manifestation has two contrasting phases of reproduction, i.e., post-spawning resting and initiation of gonadal activity appropriate for revealing the associated candidate genes. It can be deciphered by RNA sequencing of tissues involved in BPGL (Brain-Pituitary-Gonad-Liver) axis controlling seasonality. How far such BCGs of this fish are evolutionarily conserved across different phyla is unknown. Such study can be of further use to enhance fish productivity as seasonality restricts seed production beyond monsoon season. A total of ~ 150 Gb of transcriptomic data of four tissues viz., BPGL were generated using Illumina TruSeq. De-novo assembled BPGL tissues revealed 75,554 differentially expressed transcripts, 115,534 SSRs, 65,584 SNPs, 514 pathways, 5379 transcription factors, 187 mature miRNA which regulates candidate genes represented by 1576 differentially expressed transcripts are available in the form of web-genomic resources. Findings were validated by qPCR. This is the first report in carp fish having 32 BCGs, found widely conserved in fish, amphibian, reptile, birds, prototheria, marsupials and placental mammals. This is due to universal mechanism of rhythmicity in response to environment and earth rotation having adaptive and reproductive significance. This study elucidates evolutionary conserved mechanism of photo-periodism sensing, neuroendocrine secretion, metabolism and yolk synthesis in liver, gonadal maturation, muscular growth with sensory and auditory perception in this fish. Study reveals fish as a good model for research on biological clock besides its relevance in reproductive efficiency enhancement.
Sections du résumé
BACKGROUND
BACKGROUND
Carp fish, rohu (Labeo rohita Ham.) is important freshwater aquaculture species of South-East Asia having seasonal reproductive rhythm. There is no holistic study at transcriptome level revealing key candidate genes involved in such circannual rhythm regulated by biological clock genes (BCGs). Seasonality manifestation has two contrasting phases of reproduction, i.e., post-spawning resting and initiation of gonadal activity appropriate for revealing the associated candidate genes. It can be deciphered by RNA sequencing of tissues involved in BPGL (Brain-Pituitary-Gonad-Liver) axis controlling seasonality. How far such BCGs of this fish are evolutionarily conserved across different phyla is unknown. Such study can be of further use to enhance fish productivity as seasonality restricts seed production beyond monsoon season.
RESULT
RESULTS
A total of ~ 150 Gb of transcriptomic data of four tissues viz., BPGL were generated using Illumina TruSeq. De-novo assembled BPGL tissues revealed 75,554 differentially expressed transcripts, 115,534 SSRs, 65,584 SNPs, 514 pathways, 5379 transcription factors, 187 mature miRNA which regulates candidate genes represented by 1576 differentially expressed transcripts are available in the form of web-genomic resources. Findings were validated by qPCR. This is the first report in carp fish having 32 BCGs, found widely conserved in fish, amphibian, reptile, birds, prototheria, marsupials and placental mammals. This is due to universal mechanism of rhythmicity in response to environment and earth rotation having adaptive and reproductive significance.
CONCLUSION
CONCLUSIONS
This study elucidates evolutionary conserved mechanism of photo-periodism sensing, neuroendocrine secretion, metabolism and yolk synthesis in liver, gonadal maturation, muscular growth with sensory and auditory perception in this fish. Study reveals fish as a good model for research on biological clock besides its relevance in reproductive efficiency enhancement.
Identifiants
pubmed: 34548034
doi: 10.1186/s12864-021-08001-6
pii: 10.1186/s12864-021-08001-6
pmc: PMC8456608
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
685Informations de copyright
© 2021. The Author(s).
Références
Rev Reprod. 1997 Jan;2(1):55-68
pubmed: 9414466
Essays Biochem. 2011 Jun 30;49(1):119-36
pubmed: 21819388
Sci Rep. 2016 Sep 28;6:34281
pubmed: 27677591
J Biol Chem. 1983 Dec 10;258(23):14610-8
pubmed: 6358225
Fish Physiol Biochem. 2011 Sep;37(3):619-47
pubmed: 21229308
Nucleic Acids Res. 2013 Apr;41(8):4470-80
pubmed: 23470996
PLoS One. 2017 Feb 15;12(2):e0169569
pubmed: 28199332
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Mol Reprod Dev. 2016 Dec;83(12):1102-1115
pubmed: 27770608
BMC Med Genomics. 2015;8 Suppl 2:S10
pubmed: 26044212
PLoS One. 2014 Jun 12;9(6):e99172
pubmed: 24921252
PLoS One. 2015 Jul 06;10(7):e0132450
pubmed: 26148098
Hum Mol Genet. 2006 Oct 15;15 Spec No 2:R271-7
pubmed: 16987893
Fish Physiol Biochem. 2011 Jun;37(2):259-72
pubmed: 21611721
PLoS One. 2015 Dec 07;10(12):e0144158
pubmed: 26641263
BMC Genomics. 2006 Mar 09;7:46
pubmed: 16526958
PLoS One. 2014 Sep 03;9(9):e106739
pubmed: 25184355
Plant Physiol. 2007 Dec;145(4):1533-48
pubmed: 17951457
OMICS. 2014 Feb;18(2):98-110
pubmed: 24380445
Nat Commun. 2013;4:2108
pubmed: 23820554
Physiol Biochem Zool. 2010 Sep-Oct;83(5):827-35
pubmed: 20604684
BMC Genomics. 2014 Jun 30;15:541
pubmed: 24984705
Mol Ecol. 2015 Oct;24(19):4960-81
pubmed: 26339983
Physiol Genomics. 2008 Nov 12;35(3):283-95
pubmed: 18728227
Mar Biotechnol (NY). 2012 Oct;14(5):620-33
pubmed: 22298294
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
PLoS One. 2015 Jun 17;10(6):e0129299
pubmed: 26083490
Dev Growth Differ. 2017 May;59(4):219-227
pubmed: 28547762
Nature. 2000 Feb 24;403(6772):909-13
pubmed: 10706291
Int J Genomics. 2016;2016:7281585
pubmed: 27652256
Comp Biochem Physiol C Toxicol Pharmacol. 2013 Mar;157(2):227-35
pubmed: 23246600
Harvey Lect. 1960-1961;56:93-125
pubmed: 14486990
Hear Res. 2017 Apr;347:47-55
pubmed: 27665709
PLoS One. 2013 Oct 23;8(10):e76684
pubmed: 24194844
BMC Genomics. 2008 Dec 24;9:633
pubmed: 19108745
Front Endocrinol (Lausanne). 2014 Feb 26;5:19
pubmed: 24616714
PLoS Comput Biol. 2013;9(5):e1003068
pubmed: 23717196
PLoS One. 2014 Dec 08;9(12):e114176
pubmed: 25485989
J Cell Sci. 2014 Feb 1;127(Pt 3):485-95
pubmed: 24481493
J Biol Chem. 2007 Oct 19;282(42):30960-73
pubmed: 17720815
Mol Carcinog. 2006 Dec;45(12):957-67
pubmed: 16929481
Dev Dyn. 2006 Nov;235(11):3071-9
pubmed: 16929533
Gen Comp Endocrinol. 2010 Feb 1;165(3):483-515
pubmed: 19442666
J Biol Chem. 1997 Oct 10;272(41):25913-9
pubmed: 9325324
Biomed Res Int. 2014;2014:629697
pubmed: 25136606
Nucleic Acids Res. 2012 Aug;40(15):e115
pubmed: 22730293
Mol Neurodegener. 2016 Feb 24;11:21
pubmed: 26912063
Cell Mol Life Sci. 2011 Aug;68(16):2797-809
pubmed: 21104292
BMC Res Notes. 2010 Jul 29;3:215
pubmed: 20670436
Aquat Toxicol. 2013 Apr 15;130-131:58-67
pubmed: 23340333
Hum Genomics. 2011 May;5(4):283-303
pubmed: 21712190
BMC Genomics. 2016 Mar 10;17:217
pubmed: 26965070
Comp Biochem Physiol A Mol Integr Physiol. 2013 Jan;164(1):44-53
pubmed: 23051589
Protein Cell. 2011 Apr;2(4):333-46
pubmed: 21574023
Philos Trans R Soc Lond B Biol Sci. 2011 Jul 27;366(1574):2100-10
pubmed: 21690128
Genes Brain Behav. 2008 Nov;7(8):915-23
pubmed: 18700840
Genome Res. 2003 Nov;13(11):2498-504
pubmed: 14597658
Fish Shellfish Immunol. 2007 Jun;22(6):695-706
pubmed: 17116408
Adv Genet. 2016;95:1-30
pubmed: 27503352
Biol Reprod. 2013 May 23;88(5):128
pubmed: 23595902
BMC Bioinformatics. 2011 Aug 04;12:323
pubmed: 21816040
Dis Model Mech. 2013 Mar;6(2):414-23
pubmed: 23038063
Comp Biochem Physiol Part D Genomics Proteomics. 2011 Sep;6(3):244-55
pubmed: 21612991
PLoS One. 2015 Sep 14;10(9):e0137726
pubmed: 26367311
Bioinformatics. 2010 Jan 1;26(1):139-40
pubmed: 19910308
Dev Dyn. 2010 Jun;239(6):1632-44
pubmed: 20503360
Bioinformatics. 2011 Nov 1;27(21):2987-93
pubmed: 21903627
Fish Physiol Biochem. 1989 Jun;7(1-6):109-18
pubmed: 24221761
Endocr Pathol. 2005 Fall;16(3):163-72
pubmed: 16299399
PLoS One. 2010 Oct 14;5(10):e13342
pubmed: 20976280
Ann N Y Acad Sci. 2010 Jul;1200:67-74
pubmed: 20633134
BMC Genomics. 2016 Jan 15;17:60
pubmed: 26768650
Acta Anat (Basel). 1967;68(3):379-99
pubmed: 5591908
Blood. 1997 May 15;89(10):3615-23
pubmed: 9160666
Gen Comp Endocrinol. 2002 Sep;128(2):123-34
pubmed: 12392685
Bioinformatics. 2005 Sep 15;21(18):3674-6
pubmed: 16081474
Zoological Lett. 2017 Feb 28;3:2
pubmed: 28265462
Nucleic Acids Res. 2001 May 1;29(9):e45
pubmed: 11328886
Curr Top Membr. 2013;72:1-37
pubmed: 24210426
Dev Comp Immunol. 2015 Mar;49(1):103-12
pubmed: 25463511
Animal. 2007 Mar;1(3):419-32
pubmed: 22444340
Genes Dev. 2002 Oct 1;16(19):2509-17
pubmed: 12368262
Comp Hepatol. 2003 Mar 6;2(1):4
pubmed: 12685931
Proc Natl Acad Sci U S A. 2006 Feb 21;103(8):2959-64
pubmed: 16477031
Front Neurosci. 2015 Jun 05;9:195
pubmed: 26097446
PLoS One. 2013 May 08;8(5):e62355
pubmed: 23667470
Prostaglandins. 1975 Apr;9(4):597-607
pubmed: 1153811
Neuroscience. 1999 Jan;88(2):425-35
pubmed: 10197764
Genome Biol Evol. 2017 Jun 1;9(6):1471-1486
pubmed: 28541439
Gen Comp Endocrinol. 2017 Jan 1;240:35-45
pubmed: 27641683
J Endocrinol. 2003 Oct;179(1):1-13
pubmed: 14529560
Meta Gene. 2015 Nov 11;7:28-33
pubmed: 26702399
Biol Open. 2017 Jun 15;6(6):818-824
pubmed: 28619994
Gen Comp Endocrinol. 2015 Sep 15;221:9-15
pubmed: 25660470
Dev Biol. 2012 Jan 1;361(1):79-89
pubmed: 22020047
Tissue Barriers. 2013 Jul 1;1(3):e25391
pubmed: 24665402
BMC Genomics. 2015 Mar 17;16:201
pubmed: 25885637
J Endocrinol. 2017 Mar;232(3):R141-R159
pubmed: 27999088
Comp Biochem Physiol C Pharmacol Toxicol Endocrinol. 1998 Jun;119(3):325-38
pubmed: 9827005
Theor Appl Genet. 2003 Feb;106(3):411-22
pubmed: 12589540
Am J Physiol Regul Integr Comp Physiol. 2009 Nov;297(5):R1421-9
pubmed: 19710390
Nat Protoc. 2013 Aug;8(8):1494-512
pubmed: 23845962
FEBS Lett. 2011 May 20;585(10):1485-94
pubmed: 21486566
BMC Genomics. 2012 Jul 17;13:319
pubmed: 22805612
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D140-4
pubmed: 16381832
Nucleic Acids Res. 2015 Jan;43(Database issue):D76-81
pubmed: 25262351
BMC Genomics. 2014 Oct 08;15:874
pubmed: 25294025
Gene. 2013 Jul 15;524(1):1-14
pubmed: 23583682
Horm Behav. 2016 Jun;82:87-100
pubmed: 27156808
BMC Dev Biol. 2008 Apr 15;8:41
pubmed: 18412968
J Endocrinol. 2016 Jun;229(3):R117-27
pubmed: 27068698
G3 (Bethesda). 2012 Nov;2(11):1325-39
pubmed: 23173084
Nat Rev Mol Cell Biol. 2008 Oct;9(10):770-80
pubmed: 18797474
Genome Biol. 2003;5(1):R1
pubmed: 14709173
Aging Cell. 2014 Dec;13(6):965-74
pubmed: 25059688
PLoS Genet. 2007 Apr 6;3(4):e54
pubmed: 17411344
Int J Pediatr Otorhinolaryngol. 2016 May;84:174-9
pubmed: 27063776
PLoS One. 2013 Aug 06;8(8):e70670
pubmed: 23936463
PLoS One. 2015 Nov 11;10(11):e0142814
pubmed: 26560106
BMC Genomics. 2011 Mar 31;12:171
pubmed: 21453527
PLoS Comput Biol. 2015 Sep 22;11(9):e1004504
pubmed: 26393364
Sci Rep. 2017 Mar 06;7:43850
pubmed: 28262836