Analysis of MADS-box genes revealed modified flowering gene network and diurnal expression in pineapple.
Ananas
/ genetics
Arabidopsis
/ genetics
Conserved Sequence
/ genetics
Evolution, Molecular
Flowers
/ genetics
Gene Expression Regulation, Plant
/ genetics
Gene Regulatory Networks
/ genetics
Genome, Plant
/ genetics
MADS Domain Proteins
/ genetics
Multigene Family
/ genetics
Photosynthesis
/ genetics
Phylogeny
Plant Development
/ genetics
CAM photosynthesis
Diurnal clock
MADS-box genes
Pineapple
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
02 Jan 2020
02 Jan 2020
Historique:
received:
04
06
2019
accepted:
22
12
2019
entrez:
4
1
2020
pubmed:
4
1
2020
medline:
4
6
2020
Statut:
epublish
Résumé
Pineapple is the most important crop with CAM photosynthesis, but its molecular biology is underexplored. MADS-box genes are crucial transcription factors involving in plant development and several biological processes. However, there is no systematic analysis of MADS-box family genes in pineapple (Ananas comosus). Forty-eight MADS-box genes were identified in the pineapple genome. Based on the phylogenetic studies, pineapple MADS-box genes can be divided into type I and type II MADS-box genes. Thirty-four pineapple genes were classified as type II MADS-box genes including 32 MIKC-type and 2 Mδ-type, while 14 type I MADS-box genes were further divided into Mα, Mβ and Mγ subgroups. A majority of pineapple MADS-box genes were randomly distributed across 19 chromosomes. RNA-seq expression patterns of MADS-box genes in four different tissues revealed that more genes were highly expressed in flowers, which was confirmed by our quantitative RT-PCR results. There is no FLC and CO orthologs in pineapple. The loss of FLC and CO orthologs in pineapple indicated that modified flowering genes network in this tropical plant compared with Arabidopsis. The expression patterns of MADS-box genes in photosynthetic and non-photosynthetic leaf tissues indicated the potential roles of some MADS-box genes in pineapple CAM photosynthesis. The 23% of pineapple MADS-box genes showed diurnal rhythm, indicating that these MADS-box genes are regulated by circadian clock. MADS-box genes identified in pineapple are closely related to flowering development. Some MADS-box genes are involved in CAM photosynthesis and regulated by the circadian clock. These findings will facilitate research on the development of unusual spiral inflorescences on pineapple fruit and CAM photosynthesis.
Sections du résumé
BACKGROUND
BACKGROUND
Pineapple is the most important crop with CAM photosynthesis, but its molecular biology is underexplored. MADS-box genes are crucial transcription factors involving in plant development and several biological processes. However, there is no systematic analysis of MADS-box family genes in pineapple (Ananas comosus).
RESULTS
RESULTS
Forty-eight MADS-box genes were identified in the pineapple genome. Based on the phylogenetic studies, pineapple MADS-box genes can be divided into type I and type II MADS-box genes. Thirty-four pineapple genes were classified as type II MADS-box genes including 32 MIKC-type and 2 Mδ-type, while 14 type I MADS-box genes were further divided into Mα, Mβ and Mγ subgroups. A majority of pineapple MADS-box genes were randomly distributed across 19 chromosomes. RNA-seq expression patterns of MADS-box genes in four different tissues revealed that more genes were highly expressed in flowers, which was confirmed by our quantitative RT-PCR results. There is no FLC and CO orthologs in pineapple. The loss of FLC and CO orthologs in pineapple indicated that modified flowering genes network in this tropical plant compared with Arabidopsis. The expression patterns of MADS-box genes in photosynthetic and non-photosynthetic leaf tissues indicated the potential roles of some MADS-box genes in pineapple CAM photosynthesis. The 23% of pineapple MADS-box genes showed diurnal rhythm, indicating that these MADS-box genes are regulated by circadian clock.
CONCLUSIONS
CONCLUSIONS
MADS-box genes identified in pineapple are closely related to flowering development. Some MADS-box genes are involved in CAM photosynthesis and regulated by the circadian clock. These findings will facilitate research on the development of unusual spiral inflorescences on pineapple fruit and CAM photosynthesis.
Identifiants
pubmed: 31896347
doi: 10.1186/s12864-019-6421-7
pii: 10.1186/s12864-019-6421-7
pmc: PMC6941321
doi:
Substances chimiques
MADS Domain Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
8Subventions
Organisme : Fujian Provincial Department of Science and Technology
ID : 2016NZ0001-1
Références
Genome Biol Evol. 2017 Sep 1;9(9):2170-2190
pubmed: 28922793
Yi Chuan. 2007 Aug;29(8):1023-6
pubmed: 17681935
Sci Rep. 2017 Apr 21;7(1):1025
pubmed: 28432294
BMC Genomics. 2007 Jul 18;8:242
pubmed: 17640358
J Mol Biol. 1988 Dec 5;204(3):593-606
pubmed: 3066908
Science. 2000 Jun 2;288(5471):1613-6
pubmed: 10834834
PLoS One. 2014 Jan 13;9(1):e84781
pubmed: 24454749
Nat Rev Genet. 2001 Mar;2(3):186-95
pubmed: 11256070
EMBO J. 1990 Mar;9(3):605-13
pubmed: 1968830
Curr Biol. 2009 Jul 14;19(13):1128-32
pubmed: 19559614
Ann Bot. 2004 Jun;93(6):629-52
pubmed: 15150072
J Exp Bot. 2010 May;61(9):2247-54
pubmed: 20413527
Bioinformatics. 2014 May 1;30(9):1312-3
pubmed: 24451623
PLoS One. 2017 Jul 25;12(7):e0181443
pubmed: 28742823
Trends Genet. 2010 Apr;26(4):149-53
pubmed: 20219261
Cold Spring Harb Symp Quant Biol. 2007;72:353-63
pubmed: 18419293
Semin Cell Dev Biol. 2010 Feb;21(1):73-9
pubmed: 19883777
Plant Mol Biol. 2001 Jul;46(5):515-20
pubmed: 11516144
Plant Cell. 2014 Jul;26(7):2792-802
pubmed: 25082857
Sci Rep. 2017 Jun 14;7(1):3467
pubmed: 28615681
Biol Chem. 1997 Oct;378(10):1079-101
pubmed: 9372178
Nucleic Acids Res. 2015 Jul 1;43(W1):W30-8
pubmed: 25943547
Planta. 2002 Jan;214(3):334-44
pubmed: 11855638
J Exp Bot. 2010 Jun;61(6):1795-806
pubmed: 20335407
Cell. 1988 Dec 23;55(6):989-1003
pubmed: 3203386
Nat Genet. 2010 Oct;42(10):833-9
pubmed: 20802477
Genes Dev. 2003 Jun 15;17(12):1540-53
pubmed: 12815071
Plant Cell. 2008 Aug;20(8):2088-101
pubmed: 18713950
BMC Genomics. 2016 Jan 27;17:80
pubmed: 26818751
Mol Genet Genomics. 2014 Oct;289(5):903-20
pubmed: 24859011
J Genet Genomics. 2012 Apr 20;39(4):157-65
pubmed: 22546537
Nucleic Acids Res. 2016 Jan 4;44(D1):D279-85
pubmed: 26673716
Plant Cell. 2004;16 Suppl:S18-31
pubmed: 15037730
Nature. 1991 Sep 5;353(6339):31-7
pubmed: 1715520
Eur J Biochem. 1995 Apr 1;229(1):1-13
pubmed: 7744019
BMC Plant Biol. 2016 Apr 16;16:87
pubmed: 27083416
Plant Cell. 2003 Jul;15(7):1538-51
pubmed: 12837945
Gene. 2006 Aug 15;378:84-94
pubmed: 16831523
PLoS One. 2017 Jan 17;12(1):e0169838
pubmed: 28095462
Development. 2012 Sep;139(17):3081-98
pubmed: 22872082
Nature. 1990 Jul 5;346(6279):35-9
pubmed: 1973265
Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9903-8
pubmed: 15161969
PLoS Biol. 2005 Feb;3(2):e38
pubmed: 15685292
Nat Genet. 2015 Dec;47(12):1435-42
pubmed: 26523774