First genome and transcription factor profile for Asimina triloba, a native North American fruit tree

TL;DR

This paper presents the first high-quality genome and transcription factor profile for pawpaw, a native North American fruit tree, to support future breeding and commercial development.

Contribution

The first publicly available pawpaw genome assembly and identification of transcription factors linked to agronomic traits.

Findings

The pawpaw genome is 851.7 Mbp with high contiguity and completeness scores.

47 WRKY and 43 NAC transcription factors were identified and linked to traits like disease resistance and fruit development.

The genome resource supports targeted breeding for improved pawpaw varieties.

Abstract

Pawpaw (Asimina triloba) is the only fruit‐producing tree of the soursop (custard apple) family Annonaceae that is native to temperate North America. Pawpaws are extensively cultivated in the northeast United States, but to date, there are few genetic resources and no publicly available genome assemblies. Here, we present the first high‐quality genome assembly and annotation of pawpaw (cultivar Mango), derived from high‐fidelity third‐generation sequencing. The 851.7‐Mbp assembly consists of 68 contigs with a scaffold N50 of 28.5 Mbp, guanine‐cytosine content of 37%, and a 96.1% benchmarking universal single‐copy ortholog completeness score (eudicots). We profiled agronomically relevant transcription factors in the transcription factor family with the DNA‐binding WRKY amino acid domain and no apical meristem/Arabidopsis transcription activation factor/cup‐shaped cotyledon transcription factor families, which have functions related to environmental and pathogen immunity responses and regulation of fruit traits. Our resource facilitates future genetic and breeding research for this culturally important fruiting tree, expanding its economic and commercial potential.

Third‐generation genome sequencing facilitates the generation of a high‐quality pawpaw genome assembly.The assembly was 851.7 Mbp, with 37.06% guanine‐cytosine content, 98.7% (embryophyta), and 96.1% (eudicotyledons) benchmarking universal single‐copy ortholog (BUSCO) completeness, and was highly contiguous (68 contigs, N50 = 28.6 Mbp).Forty‐seven transcription factor family with the DNA‐binding WRKY amino acid domain (WRKY) and 43 no apical meristem/Arabidopsis transcription activation factor/cup‐shaped cotyledon transcription factor family (NAC) transcriptions factors (TFs) were identified in pawpaw and compared to known TFs to predict pawpaw TFs involved in desirable agronomic traits.

Third‐generation genome sequencing facilitates the generation of a high‐quality pawpaw genome assembly.

The assembly was 851.7 Mbp, with 37.06% guanine‐cytosine content, 98.7% (embryophyta), and 96.1% (eudicotyledons) benchmarking universal single‐copy ortholog (BUSCO) completeness, and was highly contiguous (68 contigs, N50 = 28.6 Mbp).

Forty‐seven transcription factor family with the DNA‐binding WRKY amino acid domain (WRKY) and 43 no apical meristem/Arabidopsis transcription activation factor/cup‐shaped cotyledon transcription factor family (NAC) transcriptions factors (TFs) were identified in pawpaw and compared to known TFs to predict pawpaw TFs involved in desirable agronomic traits.

Pawpaw is a North American fruit tree that has significant cultural importance to Indigenous people and traditional communities in Appalachia. Most fruit are collected from the wild, but dozens of cultivated pawpaw varieties are also grown in the northeast United States. Despite this, there are no publicly available genomic resources for pawpaw. Here, we used advanced DNA sequencing techniques to assemble the first pawpaw genome. We used computational tools to identify genes that are involved in valuable agronomic traits such as stress tolerance, disease resistance, flower development, and fruiting. This research contributes to the modernization of pawpaw breeding, enabling targeted efforts to develop new varieties that could bring pawpaw closer to its market potential.

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