Genome-wide analysis of flavonoid biosynthetic genes in Musaceae (Ensete, Musella, and Musa species) reveals amplification of flavonoid 3’,5’-hydroxylase
biorxiv(2024)
摘要
Flavonoids in Musaceae are involved in pigmentation and stress responses, including pathogen defense and UV protection, and are a component of the healthy human diet. Identification and analysis of the sequence and copy number of flavonoid biosynthetic genes are valuable for understanding the nature and diversity of flavonoid evolution in Musaceae species. In this study, we identified 71 to 80 flavonoid biosynthetic genes in chromosome-scale genome sequence assemblies of Musaceae, including those of Ensete glaucum , Musella lasiocarpa , Musa beccarii , M. acuminata , M. balbisiana , and M. schizocarpa, checking annotations with BLAST and determining the presence of conserved domains. The number of genes increased through segmental duplication and tandem duplication. Orthologues of both structural and regulatory genes in the flavonoid biosynthetic pathway are highly conserved across Musaceae. The flavonoid 3’,5’-hydroxylase gene F3’5’Hs was amplified in Musaceae and ginger compared with grasses (rice, Brachypodium, Avena longiglumis, and sorghum). One group of genes from this gene family amplified near the centromere of chromosome 2 in the x = 11 Musaceae species. Flavonoid biosynthetic genes displayed few consistent responses in the yellow and red bracts of Musella lasiocarpa when subjected to low temperatures. The expression levels of MlDFR2/3 increased while MlLAR was reduced by half. These results establish the range of diversity in both sequence and copy number of flavonoid biosynthetic genes during evolution of Musaceae. The combination of allelic variants of genes, changes in their copy numbers, and variation in transcription factors with the modulation of expression under cold treatments and between bract-colours suggests the variation may be exploited in plant breeding programmes, particularly for improvement of stress-resistance in the banana crop.
### Competing Interest Statement
The authors have declared no competing interest.
* 4CL
: 4 coumarate
CoA
: ligase
ANR
: anthocyanidin reductase
ANS/LDOX
: anthocyanidin synthase/leucoanthocyanidin dioxygenase
C4H
: cinnamic acid 4-hydroxylase
CHI
: chalcone isomerase
CHS
: chalcone synthase
DFR
: dihydroflavonol reductase
EBG
: early biosynthetic gene
F3’5’H
: flavanone 3’5’-hydroxylase
F3’H
: flavanone 3’-hydroxylase
F3H
: flavanone 3-hydroxylase
FBG
: flavonoid biosynthetic gene
FLS
: flavonol synthase
FNS
: flavone synthase
GPP
: general phenylpropanoid pathway
IFS
: isoflavone synthase
Ka
: non-synonymous
Ks
: synonymous
LAR
: leucoanthocyanidin reductase
LBG
: late biosynthetic gene
NJ
: neighbor joining
PAL
: phenylalanine ammonia lyase
SMART
: simple modular architecture research tool
TF
: transcription factor
TMM
: trimmed mean of M-values
TPM
: transcripts per million
UGP/UFGT
: UDP-flavonoid glucosyl transferase
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