Telomere-to-telomere haplotype-resolved reference genome reveals subgenome divergence and disease resistance in triploid Cavendish banana

Abstract

Banana is one of the most important crops of the world. Cavendish-type bananas, which have a monospecific Musa acuminata origin (AAA), account for around half of the global banana production, thereby are of great significance for human societies. However, until now, the high-quality haplotype-resolved reference genome was still undecoded for banana cultivars. Here, we reported the telomere-to-telomere (T2T) and haplotype-resolved reference genome of ‘Baxijiao’ (Cavendish) consisting of three haploid assemblies. The sizes of the three haploid assemblies were estimated to be 477.16 Mb, 477.18 Mb, and 469.57 Mb, respectively. Although with monospecific origins, the three haploid assemblies showed great differences with low levels of sequence collinearity. Several large reciprocal translocations were identified among chromosomes 1, 4 and 7. An expansion of gene families that might affect fruit quality and aroma was detected, such as those belonging to sucrose/disaccharide/oligosaccharide catabolic processes, sucrose metabolic process, starch metabolic process, and aromatic compound biosynthetic process. Besides, an expansion of gene families related to anther and pollen development was observed, which could be associated with parthenocarpy and sterility of the Cavendish cultivar. Finally, much fewer resistance genes were identified in ‘Baxijiao’ than in M. acuminata, particularly in the gene clusters in chromosomes 3 and 10, providing potential targets to explore for molecular analysis of disease resistance in banana. This T2T haplotype-resolved reference genome will thus be a valuable genetic resource for biological studies, molecular breeding and genetic improvement of banana.

Super Pangenome of Grapevines Empowers Improvement of the Oldest Domesticated Fruit

“…For in silico centromere identification, tandem repeat annotation was carried out using TRASH 80 , with the parameter configuration as ‘2 7 7 80 10 50 500 -f -d -m’. The relative positions within the centromere were aligned with blast-2.13.0+ concurrently by utilizing the tandem repeat sequence units of the centromeres identified by Huang et al 81 . The colorful identity heatmaps of genomic sequence were generated using StainGlass 82 .…”

Special Issue “Bioinformatics of Unusual DNA and RNA Structures”

“…Contemporary, specific antibodies against cruciforms [62,63], lefthanded nucleic acids [64], G-quadruplexes [65], and i-motifs [66] have also been developed, allowing effective analyses of UNas both in vitro and in situ. Even if UNas are often difficult to sequence, current methods and their modifications [67] allow accurate sequencing and determination in genomes, leading to the finalization of telomere-to-telomere gapless assemblies [68][69][70][71]. Although there are currently many tools for the prediction and experimental validation of UNas, their structural bioinformatical characterization or modeling is somewhat lagging.…”

A chromosome-level, haplotype-resolved genome assembly and annotation for the Eurasian minnow (Leuciscidae: Phoxinus phoxinus) provide evidence of haplotype diversity

“…Resultantly, the number of studies acknowledging genetic variation between haplomes, is rapidly increasing including e.g. Cavendish banana (Huang et al, 2023), African cassava (Mansfeld et al, 2021), Australian lime…”

“…Resultantly, the number of studies acknowledging genetic variation between haplomes is rapidly increasing, e.g. in Cavendish banana (Huang et al, 2023), ginger (S.-P. Cheng et al, 2021), carnation (L. Jiang et al, 2022), African cassava (Mansfeld et al, 2021), Australian lime (Nakandala et al, 2023), carnation (H. Jiang et al, 2023), cattle (Low et al, 2020), pearl oyster (Takeuchi et al, 2022), turkey (Barros et al, 2023), and ocellated puffer fish (Zeng et al, 2023).…”