A haplotype resolved chromosomal level avocado genome allows analysis of novel avocado genes

Abstract

Avocado (Persea americana) is a member of the magnoliids, an early branching lineage of angiosperms that has high value globally with the fruit being highly nutritious. Here, we report a chromosome-level genome assembly for the commercial avocado cultivar Hass, which represents 80% of the world’s avocado consumption. The DNA contigs produced from Pacific Biosciences HiFi reads were further assembled using a previously published version of the genome supported by a genetic map. The total assembly was 913 Mb with a contig N50 of 84 Mb. Contigs assigned to the 12 chromosomes represented 874 Mb and covered 98.8% of benchmarked single-copy genes from embryophytes. Annotation of protein coding sequences identified 48 915 avocado genes of which 39 207 could be ascribed functions. The genome contained 62.6% repeat elements. Specific biosynthetic pathways of interest in the genome were investigated. The analysis suggested that the predominant pathway of heptose biosynthesis in avocado may be through sedoheptulose 1,7 bisphosphate rather than via alternative routes. Endoglucanase genes were high in number, consistent with avocado using cellulase for fruit ripening. The avocado genome appeared to have a limited number of translocations between homeologous chromosomes, despite having undergone multiple genome duplication events. Proteome clustering with related species permitted identification of genes unique to avocado and other members of the Lauraceae family, as well as genes unique to species diverged near or prior to the divergence of monocots and eudicots. This genome provides a tool to support future advances in the development of elite avocado varieties with higher yields and fruit quality.

Insights into the domestication of avocado and potential genetic contributors to heterodichogamy

“…Another Hass genome was published in 2021 ( Sharma et al 2021 ); this genome was 788 Mb, which was nearly 88% of the expected genome size, but it was not anchored into scaffolds. Still, more recently, a third study has further improved the assembly of the Hass genome, leading to resolved haplotypes ( Nath et al 2022 ). To date, however, Hass has remained the only avocado genome deciphered, and several important features of the evolutionary genomics of avocados still remain unexplored.…”

Structural Refinement by Direct Mapping Reveals Assembly Inconsistencies near Hi-C Junctions

“…A new technology from Nabsys for high-throughput electronic mapping, which is based on solid-state nanodetectors [ 30 ] and expected to provide higher resolution and accuracy than optical mapping, may overcome the limitations caused by low label density. Furthermore, current long-read technologies can easily generate de novo assemblies with contigs longer than 1 Mb [ 31 , 32 , 33 ].…”

Phylogenetic studies of magnoliids: Advances and perspectives

“…The reported species of magnoliids with sequenced nuclear genomes include Magnoliales, Laurales, and Piperales (17 species, 23 references in total). Examples include Laurales: Cinnamomum kanehirae ( Chaw et al., 2019 ), avocado ( Persea americana ) ( Rendón-Anaya et al., 2019 ; Nath et al., 2022 ), Litsea cubeba ( Chen Y. C. et al., 2020 ), Phoebe bournei ( Chen S. P. et al., 2020 ; Han et al., 2022 ), Cinnamomum camphora ( Jiang et al., 2022 ; Shen et al., 2022 ; Sun et al., 2022 ; Wang et al., 2022 ), C. burmannii ( Li et al., 2022 ), Litsea coreana ( Zhang et al., 2022 ) of Lauraceae, Chimonanthus praecox ( Shang et al., 2020 ; Shen et al., 2021 ) and C. salicifolius ( Lv et al., 2020 ) of Calycanthaceae; Magnoliales: L. chinense ( Chen et al., 2019 ), Magnolia biondii ( Dong et al., 2021 ), M. officinalis ( Yin et al., 2021 ); Annona muricata ( Strijk et al., 2021 ), A. glabra ( He et al., 2022 ); Pepperales: Piper nigrum ( Hu et al., 2019 ), Aristolochia fimbriata ( Qin et al., 2021 ) and A. contorta ( Cui et al., 2022 ). Twenty of the 23 references in the genome analysis magnoliids discussed the evolutionary status of magnoliids, providing new insights into the early evolution of angiosperms, but the results of the analysis are inconsistent.…”

“…221111110700), the Science and Technology Program on Developing Forestry of Henan, China (Grant No. YCHZ [2022]28), and the Fundamental Research Funds of Henan Academy of Forestry, China (Grant Nos. 2021JB01001 and 210612240).…”