The Musa troglodytarum L. genome provides insights into the mechanism of non-climacteric behaviour and enrichment of carotenoids

Abstract

Background: Karat (Musa troglodytarum L.) is an autotriploid Fe'i banana of the Australimusa section. Karat was domesticated independently in the Pacific region, and karat fruit are characterized by a pink sap, a deep yellow-orange flesh colour, and an abundance of β-carotene. Karat fruit showed non-climacteric behaviour, with an approximately 215-day bunch filling time. These features make karat a valuable genetic resource for studying the mechanisms underlying fruit development and ripening and carotenoid biosynthesis.

Results: Here, we report the genome of M. troglodytarum, which has a total length of 603 Mb and contains 37,577 predicted protein-coding genes. After divergence from the most recent common ancestors, M. troglodytarum (T genome) has experienced fusion of ancestral chromosomes 8 and 9 and multiple translocations and inversions, unlike the high synteny with few rearrangements found among M. schizocarpa (S genome), M. acuminata (A genome) and M. balbisiana (B genome). Genome microsynteny analysis showed that the triplication of MtSSUIIs due to chromosome rearrangement may lead to the accumulation of carotenoids and ABA in the fruit. The expression of duplicated MtCCD4s is repressed during ripening, leading to the accumulation of α-carotene, β-carotene and phytoene. Due to a long terminal repeat (LTR)-like fragment insertion upstream of MtERF11, karat cannot produce large amounts of ethylene but can produce ABA during ripening. These lead to non-climacteric behaviour and prolonged shelf-life, which contributes to an enrichment of carotenoids and riboflavin.

Conclusions: The high-quality genome of M. troglodytarum revealed the genomic basis of non-climacteric behaviour and enrichment of carotenoids, riboflavin, flavonoids and free galactose and provides valuable resources for further research on banana domestication and breeding and the improvement of nutritional and bioactive qualities.

Keywords: Banana; Carotenoids; Chromosome-level genome; Non-climacteric behaviour.

Fig. 1

Overview of the T genome. a Chromosome overview of the T genome. A, GC content; B, repeat content; C LTR Copia content; D, LTR gypsy content; and E, gene content. b Erect fruit bunch of 25 DAF karat, which is pictured at Danzhou, Hainan, China. c Ancestor genome analysis and chromosome rearrangements. The bars representing the chromosomes of the A, B, S and T genomes are divided into 11 groups. Each colour presents one of the ancestral chromosomes. Phylogenetic analysis (d) and distribution of the 4 dTv distances between gene pairs (e) of the A, B, S and T genomes

Fig. 2

Targeted metabolomics and widely targeted metabolomics analysis of karat pulp at different developmental stages. a Transverse section of karat fruit at different developmental stages. Quantitation of carotenoids (b and c, μg/g) and relative quantification of flavonoids (c) and vitamin B (c). F1, (E/Z)-phytoene; F2, Lutein; F3, α-Carotene; F4, β-Carotene; B2, riboflavin; B5, D-pantothenic acid; B6, pyridoxine; F1, 4′-hydroxy-5,7-dimethoxyflavanone; F2, epicatechin; F3, myricetin-3-O-rutinoside; and F4, delphinidin-3-O-rutinoside. d Pink sap of pesudostem and fruits at 25 DAF. e Quantitation of flavonoids in pink sap. f Heatmap of metabolites in fruit pulp

Fig. 3

Schematic representation of the carotenoid biosynthesis pathway and duplication of key enzymes in karat. Geranylgeranyl pyrophosphate synthase small subunit (SSU-II) and carotenoid cleavage dioxygenase 4 (CCD4) are duplicated in the T genome compared to the A, B, and S genomes. Phytoene, α-carotene and β-carotene contents were highly enriched in karat pulp. a Schematic representation of the vitamin E and carotenoid biosynthesis pathways in karat. Interactions are represented by red dotted lines. IPP, isopentenyl diphosphate; DMAPP, dimethylallyl diphosphate; GGPP, geranylgeranyl pyrophosphate; GGPPS, geranylgeranyl pyrophosphate synthase; PSY, phytoene synthase; PDS, phytoene desaturase; ZDS, ζ-carotene desaturase; LCYB, lycopene β-cyclase; LCYE, lycopene ε-cyclase; β-OH, carotene β-hydroxylase; ε-OH, ε-hydroxylase; ZEP, zeaxanthin epoxidase; and NCED, 9-cis-epoxycarotenoid dioxygenase. b Distribution of SSUll and CCD4 genes and the distribution and synteny between the T genome and A genome. c Heatmap of carotenoid biosynthesis pathway genes in different tissues

Fig. 4

Schematic representation of the flavonoid biosynthesis pathway and duplication of key enzymes in karat. a Schematic representation of the flavonoid biosynthesis pathway. PAL, phenylalanine ammonia-lyase; C4H, cinnamate-4-hydroxylase; 4CL, 4-coumarate-CoA ligase; CHS, chalcone synthase; CHI, chalcone isomerase; F3H, flavanone 3-hydroxylase; F3′H, flavonoid 3′-hydroxylase; F3′5′H, flavonoid 3′,5′-hydroxylase; DFR, dihydroflavonol 4-reductase; ANS, leucoanthocyanidin dioxygenase; ANR, anthocyanidin reductase; LAR, leucoanthocyanidin reductase; FNS, flavone synthase; FLS, flavonol synthase; UFGT, anthocyanidin 3-O-glucosyltransferase; RT, UDP-rhamnose; and MT, anthocyanin O-methyltransferase. b Distribution of duplicated F3′5′Hs in the T and A genomes. c Heatmap of flavonoid biosynthesis pathway genes in different tissues. d Characteristic of the 5′ UTR upstream of F3′H

Fig. 5

Modulation of fruit ripening by ABA and ethylene. a Characteristics of the ERF11, ACO1 and RIBA1 gene sequences. b Relative quantitation of plant hormones involved in fruit ripening. c Expression patterns of NCED6, ERF11 and ACS1. d Coexpression network of genes involved in the modulation of fruit ripening. DAF, days after flowering; DPH, days post-harvest

Fig. 6

Accumulation of sugars in karat. a Schematic representation of D-galactose biosynthesis in karat. GATK, galactokinase; BGAL, β-galactosidase. b Alternative splicing and characteristics of GATK gene sequences. c Three ORFs in the mRNA of GATKs. d Quantification of sugars in the pulp of ripe fruit. f Expression patterns AMY3 and BGAL3. DAF, days after flowering; DPH, days post-harvest