Chromosome-level genome assemblies of Musa ornata and Musa velutina provide insights into pericarp dehiscence and anthocyanin biosynthesis in banana

Abstract

Musa ornata and Musa velutina are members of the Musaceae family and are indigenous to the South and Southeast Asia. They are very popular in the horticultural market, but the lack of genomic sequencing data and genetic studies has hampered efforts to improve their ornamental value. In this study, we generated the first chromosome-level genome assemblies for both species by utilizing Oxford Nanopore long reads and Hi-C reads. The genomes of M. ornata and M. velutina were assembled into 11 pseudochromosomes with genome sizes of 427.85 Mb and 478.10 Mb, respectively. Repetitive sequences comprised 46.70% and 50.91% of the total genomes for M. ornata and M. velutina, respectively. Differentially expressed gene (DEG) and Gene Ontology (GO) enrichment analyses indicated that upregulated genes in the mature pericarps of M. velutina were mainly associated with the saccharide metabolic processes, particularly at the cell wall and extracellular region. Furthermore, we identified polygalacturonase (PG) genes that exhibited higher expression level in mature pericarps of M. velutina compared to other tissues, potentially being accountable for pericarp dehiscence. This study also identified genes associated with anthocyanin biosynthesis pathway. Taken together, the chromosomal-level genome assemblies of M. ornata and M. velutina provide valuable insights into the mechanism of pericarp dehiscence and anthocyanin biosynthesis in banana, which will significantly contribute to future genetic and molecular breeding efforts.

Acknowledgements

This work was financially supported by the National Natural Science Foundation of China (No. 32070237, 31261140366). We thank Yu-Ying Zhou of South China Botany Garden CAS for her help in material freezing and Xiao-Xia Zhang from the Institute of Botany CAS for her suggestions on gene family analysis.

Author contributions

X.-J.G. and H.-R.H conceived the project. X.-J.G. and T.-W.X. collected the materials. T.-W.X., X.L., N.F., T.-J.L., and Z.-F.W. performed the analyses. T.-W.X. wrote the manuscript. X.-J.G., H.-R.H., and Z.-F.W. revised the manuscript. All authors approved the final manuscript.

Data availability

All the raw sequence data were deposited in the Genome Sequence Archive in the National Genomics Data Center (NGDC), China National Center for Bioinformation (CNCB) with the accession number of CRA013014 under BioProject PRJCA020485 (https://ngdc.cncb.ac.cn/). The genome assemblies reported in this study were deposited in the Genome Warehouse in NGDC, CNCB under the accession number GWHDVGC00000000 (M. ornata) and GWHDVGD00000000 (M. velutina). In addition, the genome assemblies, protein-coding sequences, as well as genome annotations were deposited in the Science Data Bank [115] and figshare [116].

Conflict of interest statement

The authors declare that they have no competing interests.

Supplementary data

Supplementary data is available at Horticulture Research online.

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