Single‐molecule real‐time sequencing of the full‐length transcriptome of purple garlic (Allium sativumL. cv. Leduzipi) and identification of serine O‐acetyltransferase family proteins involved in cysteine biosynthesis

Abstract

BACKGROUND Garlic (Allium sativum L.), whose bioactive components are mainly organosulfur compounds (OSCs), is a herbaceous perennial widely consumed as a green vegetable and a condiment. Yet, the metabolic enzymes involved in the biosynthesis of OSCs are not identified in garlic. RESULTS Here, a full‐length transcriptome of purple garlic was generated via PacBio and Illumina sequencing, to characterize the garlic transcriptome and identify key proteins mediating the biosynthesis of OSCs. Overall, 22.56 Gb of clean data were generated, resulting in 454 698 circular consensus sequence (CCS) reads, of which 83.4% (379 206) were identified as being full‐length non‐chimeric reads – their further transcript clustering facilitated identification of 36 571 high‐quality consensus reads. Once corrected, their genome‐wide mapping revealed that 6140 reads were novel isoforms of known genes, and 2186 reads were novel isoforms from novel genes. We detected 1677 alternative splicing events, finding 2902 genes possessing either two or more poly(A) sites. Given the importance of serine O‐acetyltransferase (SERAT) in cysteine biosynthesis, we investigated the five SERAT homologs in garlic. Phylogenetic analysis revealed a three‐tier classification of SERAT proteins, each featuring a serine acetyltransferase domain (N‐terminal) and one or two hexapeptide transferase motifs. Template‐based modeling showed that garlic SERATs shared a common homo‐trimeric structure with homologs from bacteria and other plants. The residues responsible for substrate recognition and catalysis were highly conserved, implying a similar reaction mechanism. In profiling the five SERAT genes’ transcript levels, their expression pattern varied significantly among different tissues. CONCLUSION This study's findings deepen our knowledge of SERAT proteins, and provide timely genetic resources that could advance future exploration into garlic's genetic improvement and breeding. © 2021 Society of Chemical Industry.

Turning Garlic into a Modern Crop: State of the Art and Perspectives

“…Analysis of the synteny between garlic and A. officinalis uncovered 3 WGD events in the evolutionary history of garlic, which occurred 120–130, 89.8 (prior to the divergence of garlic and Asparagus ) and 17.9 mya. Two transcriptome assemblies have recently been performed using third-generation sequencing technologies [ 83 , 86 ], which promise to lead to a better annotation of the garlic genome.…”

Genome-wide analysis of the Thaumatin-like gene family in Qingke (Hordeum vulgare L. var. nudum) uncovers candidates involved in plant defense against biotic and abiotic stresses

“…Sequence information of TLPs in the Arabidopsis thaliana, Cucumis melo, Hordeum vulgare, Oryza sativa, and Brachypodium distachyon genomes were obtained from previous reports (Iqbal et al, 2020;Liu et al, 2020;Zhang et al, 2021;Sharma et al, 2022). The phylogenic relationships among TLPs of the six species was inferred from a tree built in MEGA 11 9 using the maximum likelihood (ML) method (Tamura et al, 2021).…”

“…As the staple food of Tibetanese, Qingke is tightly linked to food security and feed production in high-elevation areas. Recent developments in sequencing technology have propelled gene analysis forward, making it now feasible to comprehensively analyze a gene family using its transcriptomic or genomic sequencing data ( Wang et al, 2021 ). In the present study, we carried out a comprehensive analysis of the TLP family genes in Qingke, by considering their pleiotropic role.…”