Chromosome‐level reference genome assembly provides insights into aroma biosynthesis in passion fruit (Passiflora edulis)

Abstract

Passion fruit, native to tropical America, is an agriculturally, economically and ornamentally important fruit plant that is well known for its acid pulp, rich aroma and distinctive flavour. Here, we present a chromosome‐level genome assembly of passion fruit by incorporating PacBio long HiFi reads and Hi‐C technology. The assembled reference genome is 1.28 Gb size with a scaffold N50 of 126.4 Mb and 99.22% sequences anchored onto nine pseudochromosomes. This genome is highly repetitive, accounting for 86.61% of the assembled genome. A total of 39,309 protein‐coding genes were predicted with 93.48% of those being functionally annotated in the public databases. Genome evolution analysis revealed a core eudicot‐common γ whole‐genome triplication event and a more recent whole‐genome duplication event, possibly contributing to the expansion of certain gene families. The 33 rapidly expanded gene families were significantly enriched in the pathways of isoflavone biosynthesis, galactose metabolism, diterpene biosynthesis and fatty acid metabolism, which might be responsible for the formation of featured flavours in the passion fruit. Transcriptome analysis revealed that genes related to ester and ethylene biosynthesis were significantly upregulated in the mature fruit and the expression levels of those genes were consistent with the accumulation of volatile lipid compounds. The passion fruit genome analysis improves our understanding of the genome evolution of this species and sheds new lights into the molecular mechanism of aroma biosynthesis in passion fruit.

Genome-Wide Identification and Expression Profiling of KCS Gene Family in Passion Fruit (Passiflora edulis) Under Fusarium kyushuense and Drought Stress Conditions

“…To identify and characterize the KCS genes in the passion fruit ( Passiflora edulis ) genome, passion fruit proteins, CDS, gff3, genome files were downloaded from the passion fruit genome 1 ( Ma et al, 2021 ). We performed two methods, which are Basic Local Alignment Search Tool for proteinsT (BLASTp) and Hidden Markov Models (HMMER) search tool, to identify the KCS genes in the passion fruit genome.…”

“…Furthermore, the multiple collinearity analysis of KCS genes in P. edulis , A. thaliana , M. domestica , and A. hypogaea whole genomes were also performed by Multiple synteny Plot packages in TBTools software. The Ka), Ks nucleotide substitution rates, and the Ka/Ks ratios of duplicated PeKCS genes were annotated using TBTools and divergence time (T, MYA; million years ago) was calculated by the following formula; T = Ks/2x ( x = 6.38 × 10 –9 ) ( Ma et al, 2021 ).…”

“…The leave samples were from yellow Huangjinguo (HJG) cold-sensitive and purple Tainong-1 cold-tolerant cultivars under normal temperature (NT) and chilling stress (CS) conditions. The RNA-Seq raw reads were quality controlled and filtered by fastp package ( Chen S. et al, 2018 ) and mapped to the passion fruit reference genome ( Ma et al, 2021 ) with HISAT2 package ( Kim and Langmead, 2015 ) in Ubuntu wsl v 20.04.3 23 . The sequence alignment map (SAM) files were transformed to binary alignment map (BAM) and sorted with Samtools packages ( Li et al, 2009 ).…”

“…Passion fruit is an economically important fruit plant that is demanded its fresh juice, rich in aroma and distinctive nutritional values ( Rizwan et al, 2021 ). Recently, the passion fruit genome has been sequenced and published ( Ma et al, 2021 ), a comprehensive genome-wide study for the first time to determine the KCS gene family in passion fruit was conducted. Moreover, their in silico prediction of TFs, subcellular localization, evolutionary relationship via phylogenic and syntenic analysis, conserved motifs, gene structures, cis -regulatory-elements, prediction of putative miRNA, GO and KEGG annotation have been characterized.…”

Chromosome-level Genome Assembly for Takin (Budorcas taxicolor) Provides Insights into Its Taxonomic Status and Genetic Diversity

“…Recently, highly accurate long high-fidelity (HiFi) reads was generated by PacBio single-molecule real-time (SMRT) sequencing with circular consensus sequencing (CCS) (Wenger et al 2019). HiFi reads combined with Hi-C technology have been used to construct chromosome-level reference genome of various animals (Wu et al 2021) and plants (Chen et al 2021, Ma et al 2021, Sharma et al 2021. In this study, we performed the PacBio long HiFi reads and Hi-C technology to construct a high-quality chromosome-level reference genome of takin.…”