A telomere-to-telomere gap-free reference genome assembly of avocado provides useful resources for identifying genes related to fatty acid biosynthesis and disease resistance

Abstract

Avocado (Persea americana Mill.) is an economically valuable plant because of the high fatty acid content and unique flavor of its fruits. Its fatty acid content, especially the relatively high unsaturated fatty acid content, provides significant health benefits. We herein present a telomere-to-telomere gapless genome assembly (841.6 Mb) of West Indian avocado. The genome contains 40 629 predicted protein-coding genes. Repeat sequences account for 57.9% of the genome. Notably, all telomeres, centromeres, and a nucleolar organizing region are included in this genome. Fragments from these three regions were observed via fluorescence in situ hybridization. We identified 376 potential disease resistance-related nucleotide-binding leucine-rich repeat genes. These genes, which are typically clustered on chromosomes, may be derived from gene duplication events. Five NLR genes (Pa11g0262, Pa02g4855, Pa07g3139, Pa07g0383, and Pa02g3196) were highly expressed in leaves, stems, and fruits, indicating they may be involved in avocado disease responses in multiple tissues. We also identified 128 genes associated with fatty acid biosynthesis and analyzed their expression patterns in leaves, stems, and fruits. Pa02g0113, which encodes one of 11 stearoyl-acyl carrier protein desaturases mediating C18 unsaturated fatty acid synthesis, was more highly expressed in the leaves than in the stems and fruits. These findings provide valuable insights that enhance our understanding of fatty acid biosynthesis in avocado.

Acknowledgements

We thank all the members of the laboratory for their technical and analysis assistance. We thank Liwen Bianji (Edanz) (www.liwenbianji.cn/ac) for editing the English text of a draft of this manuscript. This research was supported by Yunling Scholar Project (to Yongping Yang), the Major Science and Technology Projects (202202AE090016), Yunnan Revitalization Talents Support Plan (to Yunqiang Yang), the Digitalization, development and application of biotic resource (202002AA100007), the Postdoctoral Research Funding Projects of Yunnan Province (to Xin Yin), the National Natural Science Foundation of China (32100315, 31601999, 41771123, 31590820, and 31590823), the West Light Foundation of the Chinese Academy of Sciences (to Yunqiang Yang), and the 13th Five-year Informatization Plan of Chinese Academy of Sciences, Grant No. XXH13506. The funders had no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.

Author contributions

YQY and YPY designed the research. TYY, YFC, XYY, DNY, and XY analyzed the data. TPH, CJZ, YWD, YQY, and YPY contributed reagents/materials/analysis tools. TYY, YFC, and YQY wrote and reviewed the paper.

Data availability statement

The raw sequencing data, including ONT Ultra-long reads, PacBio HiFi reads, NGS reads, Pore-C reads, and RNA-seq reads, assembly, and annotation data are accessible in Science Data Bank (https://doi.org/10.57760/sciencedb.07602).

Conflict of interests

The authors declare no conflict of interest.

Supplementary information

Supplementary data is available at Horticulture Research online.

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