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 technology-related limitations.

In a study published in Horticulture Research, researchers from Xishuangbanna Tropical Botanical Garden (XTBG) and Kunming Institute of Botany (KIB) used a combination of sequencing technologies to perform whole genome sequencing on West Indian avocado varieties. They successfully assembled the first telomere-to-telomere gapless 841.6Mb avocado genome sequence.

Using iterative identification and clustering methods, they found that the West Indian variety of avocado contained 40,629 protein-coding genes and 4,879 non-coding RNAs. They predicted12 chromosome-specific centromere sequences (CSCR) which had complex structures containing multiple types of transposable elements(TEs) with low coverage depth of HiFi and ONT reads, especially 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 (NOR) in the avocado genome sequence. They identified 376 nucleotide-binding leucine-rich repeat receptor (NLR) 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 (TAG) formation stage. 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.

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

Contact

YANG Yunqiang Ph.D

Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, Yunnan, China
E-mail: yangyunqiang@xtbg.ac.cn
First published: 22 April 2024