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.

Identification of annotation artifacts concerning the chalcone synthase (CHS)

“…The Macadamia integrifolia assembly was produced with MaSuRCA v3.2.6 and ALLMAPS v.Jul-2019 [ 14 , 26 , 27 ]. The Musa balbisiana and Musa troglodytarum genome sequences were assembled with wtdbg v1.2.8 and NextDenovo v2.4.0, respectively [ 12 , 13 , 28 , 29 ]. The Nymphae colorata assembly was produced by Canu v1.3 [ 15 , 30 ].…”

“…The genome sequences and corresponding annotations of four species with apparent fusion of multiple CHS gene copies were selected for manual inspection: Musa balbisiana [ 12 ], Musa troglodytarum [ 13 ], Macadamia integrifolia [ 14 ], and Nymphaea colorata [ 15 ]. All available paired-end RNA-seq data sets of these species were retrieved from the Sequence Read Archive via fastq-dump [ 16 ] (Additional File 1 in [ 17 ]).…”

Identification of annotation artifacts concerning theCHALCONE SYNTHASE(CHS)

“…The Macadamia integrifolia assembly was produced with MaSuRCA v3.2.6 and ALLMAPS v.Jul-2019 [15, 27, 28]. The Musa balbisiana and M. troglodytarum genome sequences were assembled with wtdbg v1.2.8 and NextDenovo v2.4.0, respectively [13, 14, 29, 30]. The Nymphae colorata assembly was produced by Canu v1.3 [16, 31].…”

“…The genome sequences and corresponding annotations of four species with apparent fusion of multiple CHS gene copies were selected for manual inspection: Musa balbisiana [12], Musa troglodytarum [13], Macadamia integrifolia [14], and Nymphaea colorata [15]. All available paired-end RNA-seq data sets of these species were retrieved from the Sequence Read Archive via fastq-dump [16] (Additional File 1).…”

Genome-Wide SNP and Indel Discovery in Abaca (Musa textilis Née) and among Other Musa spp. for Abaca Genetic Resources Management

“…The quality-filtered sequence reads were used for mapping to the polished version (through the PILON v1.22 program) of the reference genome [30]. This step also included the mapping of Musa reads [33] for M. textilis (T genome, 2n = 2x = 20) as well as for other diploid relatives, namely, M. acuminata (A genome, 2n = 2x = 22), M. balbisiana (B genome, 2n = 2x = 22) and M. troglodytarum (T genome, 2n = 2x = 20) [58,59]. The BWA program was used for this step, resulting in mapping of the reads at 22-46× coverage and the calculated mean mapping qualities (MQ) having scores ranging from 35.8-38.4 across the resequenced samples (Figure 1).…”