De novo assembly and characterization of the Welsh onion (Allium fistulosum L.) transcriptome using Illumina technology

Abstract

Welsh onion (Allium fistulosum L.) has long been cultivated as a vegetable and spice for its flavor and aroma. However, transcriptomic and genomic data for A. fistulosum remain scarce. The goal of this study was to generate transcript sequences for functional genomic analyses, and identify genes potentially involved in sulfur, selenium, and vitamin metabolism. In total, 53,378,674 high-quality reads were generated, and de novo assembly resulted in 103,286 contigs and 53,837 unigenes. The average unigene length was 619 bp with an N50 of 832 bp. Similarity searches revealed that 36,155 sequences were similar to those of known proteins in public databases. Of these, 35,250 unigenes sequences were significantly similar to sequences in the NCBI non-redundant protein database and 22,804 were annotated in the Swiss-Prot database. Additionally, 13,125 and 26,660 unigenes were annotated in the Cluster of Orthologous Group and Gene Ontology databases, respectively. A total of 20,680 unigenes were classified into 128 pathways via functional annotation against the Kyoto Encyclopedia of Genes and Genomes pathway database. Key enzymes involved in sulfur and selenium metabolism were also identified. Additionally, our transcriptome revealed a number of unigenes encoding important enzymes involved in vitamin metabolism. We also identified 2014 simple sequence repeats in 1892 unigenes. This transcriptome analysis provides valuable information to further our understanding of the molecular mechanisms regulating the biosynthesis of organic sulfur compounds. The detected simple sequence repeats may facilitate marker-assisted selection in Welsh onion breeding experiments.

New insight into foregut functions of xenobiotic detoxification in the cockroach Periplaneta americana

“…Although general incomplete and with some admissible errors, transcriptome has been used to analyze many specific tissues or organisms (Pauchet et al ., ; Yang et al ., ). In this study, 53 853 unigenes assembled from approximately 54 193 166 clean reads, with an average length of 366 bp and an N50 length of 424 bp, were obtained through Illumina sequencing, indicating our sequencing data were efficiently assembled compared to a previous study (Sun et al ., ). Furthermore, after cycloxaprid treatment, 7336 up‐regulated unigenes were gained and the expression of xenobiotic detoxification unigenes was significantly enhanced, implying that these unigenes might be involved in the adaptation of cycloxaprid application.…”

Comparative transcriptomics provide insight into the morphogenesis and evolution of fistular leaves in Allium

“…garlic, onion, welsh onion, and Chinese chive) have been analyzed [15–19]. Therefore, in the present study, the transcriptomes of nine Allium species were sequenced and assembled de novo , and large numbers of genes were identified in each species.…”

“…In Allium , the transcriptome of four species, i.e. garlic [15, 16], onion [17], Chinese chive [18], and welsh onion [19], have been sequenced and de novo assembled. Among these, onion and Welsh onion are fistular-leaved species, whereas the other two produce solid leaves.…”

Selenium and Sulfur to Produce Allium Functional Crops

“…Once in the leaf cells, both selenate and sulfate are assimilated in a similar way [ 13 , 49 ] ( Figure 2 ). Both compounds are initially activated by reacting with ATP in the presence of the ATP sulfurylase enzyme to form APS (adenosine-5-phosphosulfate) or APSe (adenosine-5-phosphoselenate) [ 66 ]; subsequently, a reduction process is carried out to selenide (Se 2− ) or sulfide (S 2− ) [ 45 ], giving rise to the organic incorporation that can take two paths, the first consists of the synthesis of the amino acid cysteine (Cys) or Se cysteine (Secys), and is called the primary path which has been described for both Se and S [ 67 ]. The second pathway is carried out for the synthesis of secondary metabolites, resulting in the synthesis of PAPS (3-phosphoadenosine-5-phosphosulfate) from APS, has been confirmed only for sulfur, and is called secondary or sulfation path.…”

“…In the primary pathway, following APS or APSe synthesis, these compounds are reduced to sulfite (SO 3 2− ) or selenite (SeO 3 2− ) ( Figure 2 ) by the enzyme APS reductase [ 66 , 68 ]. Subsequently, the enzyme sulfite reductase reduces sulfite to sulfide (S 2− ) and selenite to selenide (Se 2− ) [ 68 , 69 ], whose protonated forms (H 2 S and H 2 Se) are incorporated into the skeleton of acetyl serine by the cysteine synthase complex (serine acetyltransferase + O -acetyl serine (thiol) lyase) to obtain the amino acids cysteine or selenocysteine [ 70 , 71 ].…”