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First Gapless Avocado Genome Assembly Generated

May 15, 2024

Avocado (Persea americana ) is an economically valuable tropical plant species, because its fruits are a rich source of nutrients and have a unique flavor. The generation of a high-quality genome assembly is necessary for avocado research. However, no complete genome assemblies were available from previous studies, due to technological limitations.
In a study published in Horticulture Research, researchers from the Xishuangbanna Tropical Botanical Garden (XTBG) and the Kunming Institute of Botany of the Chinese Academy of Sciences used a combination of sequencing technologies to perform whole-genome sequencing of West Indian avocado varieties. They assembled the first telomere-to-telomere gapless 841.6 Mb avocado genome sequence.

Using iterative identification and clustering methods, the researchers found that the West Indian variety of avocado contained 40,629 protein-coding genes and 4,879 non-coding RNAs. They predicted 12 chromosome-specific centromere sequences that had complex structures containing multiple types of transposable elements with low coverage depth of HiFi and ONT reads, particularly the long centromeric regions of chromosomes Pa03 and Pa07. 

Using fluorescence in situ hybridization (FISH), they further verified the accuracy of all predicted centromeres, telomeres, and nucleolus organizer regions in the avocado genome sequence.

They identified 376 nucleotide-binding leucine-rich repeat receptor genes related to disease resistance and 128 genes related to fatty acid biosynthesis, among which Pa07g1095, Pa07g1091, and Pa12g0002 (FAD2 gene) were specifically expressed in fruit during the triacylglycerol formation stage.

Pa02g0113, which encodes one of 11 stearoyl-acyl carrier protein desaturases that mediate C18 unsaturated fatty acid synthesis, was more highly expressed in the leaves than in the stems and fruit.  

"Our telomere-to-telomere genome assembly can provide the basis for future research on disease resistance and fatty acid biosynthesis in avocado," said YANG Yunqiang of XTBG. 

Contact

YANG Yunqiang

Xishuangbanna Tropical Botanical Garden

E-mail:

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

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