Banana is one of the most important crops of the world. Cavendish-type bananas, which have a monospecific Musa acuminata origin, account for around half of the global banana production, thereby are of great significance for human societies. However, the high-quality haplotype-resolved reference genome was previously undecoded for banana cultivars. Researchers from the South China Botanical Garden and the Agricultural Genomics Institute at Shenzhen have now released the first telomere-to-telomere and haplotype-resolved reference genome of the banana cultivar ‘Baxijiao’ (Cavendish).
Developing fruits of a banana. Image credit: Josch13.
Banana originated in Southeast Asia and the west Oceania region, where it was domesticated at least 7,000 years ago.
Most banana cultivars are unseeded clones, mainly diploids or triploids, derived from wild fertile diploid Musa species.
The genetic diversity of banana cultivars mostly resulted from hybridization events within Musa acuminata, and between this species and Musa balbisiana; meanwhile, to a minor extent, Musa schizocarpa and the species of Australimusa section also contributed to the genetic contents of edible banana cultivars.
Banana cultivars are among the most consumed fruits worldwide: over 100 million tons of banana are produced yearly.
Besides, banana cultivars are also the fifth most produced food crop in the least-developed countries; as a result, they play an important role in maintaining food security in these regions.
The demand for cultivated bananas continues to grow; however, their production is greatly affected by a complex of biotic and abiotic stresses.
“In banana, the most efficient ploidy level for agronomic performance is triploid, which has given rise to more vigorous plants, higher sterility, and larger fruits without seeds,” said co-senior author Dr. Xue-Jun Ge from the South China Botanical Garden and colleagues.
“Cavendish-type bananas, which have a monospecific M. acuminata origin, account for around half of the global banana production.”
“Nearly all of the global banana export trade relies on the clones derived from a unique triploid cultivar of Cavendish banana, leading to a narrow genetic basis in this type of banana.”
In the new study, the authors developed a telomere-to-telomere reference genome of a banana cultivar ‘Baxijiao’ consisting of three haploid assemblies.
“This reference genome consists of three haploid assemblies, the sizes of which were estimated to be 477.16 Mb, 477.18 Mb, and 469.57 Mb, respectively,” they said.
“Genome quality assessments confirmed the contiguity (LAI: 19.84, 20.65 and 20.22) and completeness (BUSCOs: 97.40%, 97.80% and 93.80%) of the genome.”
“Within the three haploid assemblies, 19, 17 and 17 telomeres were identified, respectively.”
“In terms of repetitive regions, 256.48 Mb (53.76%), 258.29 Mb (54.14%), and 258.84 Mb (55.13%) were identified.”
“In addition, a total of 37,185, 37,241, and 37,178 high-confidence protein-coding genes were predicted from each assembly.”
“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.”
The researchers detected an expansion of gene families that might affect fruit quality and aroma, such as those belonging to sucrose/disaccharide/oligosaccharide catabolic processes, sucrose metabolic process, starch metabolic process, and aromatic compound biosynthetic process.
They also observed an expansion of gene families related to anther and pollen development, which could be associated with parthenocarpy and sterility of the Cavendish cultivar.
Finally, much fewer resistance genes were identified in ‘Baxijiao’ than in Musa 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 telomere-to-telomere and haplotype-resolved reference genome will thus be a valuable genetic resource for biological studies, molecular breeding and genetic improvement of banana,” the scientists concluded.
The results were published in the journal Horticulture Research.
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Hui-Run Huang et al. Telomere-to-telomere haplotype-resolved reference genome reveals subgenome divergence and disease resistance in triploid Cavendish banana. Horticulture Research, published online August 1, 2023; doi: 10.1093/hr/uhad153
