Unraveling the telomere-to-telomere haplotype-resolved reference genome of cavendish bananas: A breakthrough in understanding disease resistance and cultivar evolution

Bananas, originating from Southeast Asia and west Oceania region over 7000 years ago, have evolved into a diverse array of cultivars, primarily through hybridization within Musa species. Cavendish bananas, with a monospecific Musa acuminata  origin(AAA), dominate global production and are critical for food security in less-developed countries. Despite advances in sequencing technologies enabling high-quality genome assemblies for various Musa species, the complex genomes of banana cultivars, especially Cavendish-types, remain largely undeciphered. This gap in genomic knowledge hinders breeding efforts for disease resistance and improved traits, as Cavendish bananas, making up half of the world's production, suffer from a narrow genetic basis and vulnerability to diseases like fusarium wilt. Addressing this challenge, the research seeks to produce a high-quality, haplotype-resolved reference genome for these cultivars, which is vital for future genetic improvements and sustainable banana production.

In August 2023, Horticulture Research published a research entitled by “Telomere-to-telomere haplotype-resolved reference genome reveals subgenome divergence and disease resistance in triploid Cavendish banana”.

In this study, researchers utilized an integrated assembly scheme, combining PacBio high-fidelity (HiFi) reads, Oxford Nanopore Technology (ONT) ultra-long reads, and Hi-C reads, to develop a telomere-to-telomere (T2T) reference genome of the 'Baxijiao' banana cultivar (AAA, Cavendish). This approach achieved a high-quality, phased triploid reference genome. The 'Baxijiao' genome was assembled using 102.06 Gb of PacBio HiFi reads, 48.00 Gb of ONT reads, and 156.14 Gb of Hi-C data, achieving extensive coverage of the genome. The haploid genome size was approximately 457.31 Mb, with a heterozygous rate of 2.855%. This genome assembly, named BXJ, comprises three haploid assemblies (BXJ1, BXJ2, BXJ3) with a total length of 1.42 Gb. The assembly revealed substantial differences among the three haploid genomes, with low sequence collinearity, indicating the complex hybrid origin of Cavendish bananas. The gene density, transposable element (TE) density, and GC contents were analyzed across the genome, uncovering significant genomic features. The genome annotation identified repetitive regions and predicted high-confidence protein-coding genes, slightly more than those in the M. acuminata double-haploid genome.

The study also explored T2T chromosome construction, centromere identification, and genome quality assessment. The high-quality, accuracy, and reliability of the BXJ assembly were confirmed through various evaluations, including genome size, read mapping, LTR Assembly Index, and BUSCO completeness scores. The syntenic analysis revealed low levels of nucleotide sequence collinearity, consistent with the complex hybridization history of Cavendish bananas. Structural variations, including large reciprocal translocations, were identified, emphasizing the genomic complexity. Furthermore, the study conducted gene family evolution analysis, highlighting expansions and contractions of gene families in 'Baxijiao'. Gene families related to fruit quality and aroma, as well as parthenocarpy and sterility, were significantly expanded. Resistance genes were found to be fewer in 'Baxijiao' compared to M. acuminata, shedding light on the cultivar's susceptibility to fusarium wilt. Homoeolog expression patterns were analyzed, revealing non-balanced expression patterns in about 40% of homoeolog triads, suggesting diverse contributions of subgenomes to gene expression.

In conclusion, this study provides a detailed, high-quality reference genome for 'Baxijiao', a key Cavendish banana cultivar. The T2T haplotype-resolved reference genome offers insights into the domestication process, genomic diversity, and biological traits of the cultivar, and has significant implications for future research and breeding programs focused on banana varieties.

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References

Authors

Hui-Run Huang^1,2,†, Xin Liu^1,2,3,†, Rida Arshad^4,†, Xu Wang⁴, Wei-Ming Li⁵, Yongfeng Zhou^4,6,* and Xue-Jun Ge^1,2,*

†These authors contributed equally to the work.

Affiliations

¹Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China

²South China National Botanical Garden, Guangzhou 510650, China

³University of Chinese Academy of Sciences, Beijing 100049, China

⁴State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China

⁵School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning 530008, China

⁶State Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China

About Xue-Jun Ge

He is currently a scientist at the South China Botanical Garden of the Chinese Academy of Sciences. His research interests include plant phylogeny and evolution, biogeography, the genetic basis of adaptation, and DNA barcoding.