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

Transcriptome of the pygmy grasshopper Formosatettix qinlingensis (Orthoptera: Tetrigidae)

Formosatettix qinlingensis (Zheng, 1982) is a tiny grasshopper endemic to Qinling in China. For further study of its transcriptomic features, we obtained RNA-Seq data by Illumina HiSeq X Ten sequencing platform. Firstly, transcriptomic analysis showed that transcriptome read numbers of two female and one male samples were 25,043,314, 24,429,905, and 25,034,457, respectively. We assembled 65,977 unigenes, their average length was 1,072.09 bp, and the length of N50 was 2,031 bp. The average lengths of F. qinlingensis female and male unigenes were 911.30 bp, and 941.82 bp, and the N50 lengths were 1,745 bp and 1,735 bp, respectively. Eight databases were used to annotate the functions of unigenes, and 23,268 functional unigenes were obtained. Besides, we also studied the body color, immunity and insecticide resistance of F. qinlingensis. Thirty-nine pigment-related genes were annotated. Some immunity genes and signaling pathways were found, such as JAK-STAT and Toll-LIKE receptor signaling pathways. There are also some insecticide resistance genes and signal pathways, like nAChR, GST and DDT. Further, some of these genes were differentially expressed in female and male samples, including pigment, immunity and insecticide resistance. The transcriptomic study of F. qinlingensis will provide data reference for gene prediction and molecular expression study of other Tetrigidae species in the future. Differential genetic screening of males and females provides a basis for studying sex and immune balance in insects.

Welsh Onion (Allium fistulosum L.) Seed Physiology, Breeding, Production and Trade

In the coming years, it is expected that the European Union countries will increase their interest in the use of the Welsh onion (Allium fistulosum L.). It is a little-known vegetable from the Far East. Consequently, growers might be asking their extension advisors increasingly about its seed physiology and commercial production. This article provides basic information on the origin of the species, its botanical characteristics, the main breeding directions and achievements, seed production methods and areas, main plant breeding and seed production companies, seed dormancy and the best methods for seed storage, use of the crop and market responses to promotion activities.

Effects of nitrogen levels on gene expression and amino acid metabolism in Welsh onion

Background

Welsh onion constitutes an important crop due to its benefits in traditional medicine. Nitrogen is an important nutrient for plant growth and yield; however, little is known about its influence on the mechanisms of Welsh onion regulation genes. In this study, we introduced a gene expression and amino acid analysis of Welsh onion treated with different concentrations of nitrogen (N0, N1, and N2 at 0 kg/ha, 130 kg/ha, and 260 kg/ha, respectively).

Results

Approximately 1,665 genes were differentially regulated with different concentrations of nitrogen. Gene ontology enrichment analysis revealed that the genes involved in metabolic processes, protein biosynthesis, and transportation of amino acids were highly represented. KEGG analysis indicated that the pathways were related to amino acid metabolism, cysteine, beta-alanine, arginine, proline, and glutathione. Differential gene expression in response to varying nitrogen concentrations resulted in different amino acid content. A close relationship between gene expression and the content of amino acids was observed.

Conclusions

This work examined the effects of nitrogen on gene expression and amino acid synthesis and provides important evidence on the efficient use of nitrogen in Welsh onion.

Transcriptome landscapes of multiple tissues highlight the genes involved in the flavor metabolic pathway in Chinese chive (Allium tuberosum)

The unique flavor of Allium tuberosum is primarily associated with the hydrolysis of a series of organosulfur compounds, S-alk(en)yl cysteine sulphoxides (CSOs), upon tissue bruising or maceration. To obtain the tissue-specific transcriptomes, 18 RNA-Seq libraries representing leaf, root, stem, mature flower, inflorescence, and seed tissues of A. tuberosum were sequenced, finally yielding 133.7 Gb clean reads. The de novo assembled transcriptomes enabled the identification of 223,529 unigenes, which were functionally annotated and analyzed for the gene ontology and metabolic pathways. Furthermore, to reveal the flavor metabolic pathways, a total of 205 unigenes involved in the sulfur assimilation and CSO biosynthesis were identified, and their expression profiles were analyzed by RNA-Seq and qRT-PCR. Collectively, this study provides a valuable resource for in-depth molecular and functional researches especially on flavor formation, as well as for the development of molecular markers, and other genetic studies in A. tuberosum.

Transcriptome and phytochemical analyses provide insights into the organic sulfur pathway in Allium hirtifolium

Allium is one of the well-known genera of the Amaryllidaceae family, which contains over 780 species. Onions, garlic, leeks, and shallots are the most important species of this genus. Allium hirtifolium (shallot) is a rich source of proteins, carbohydrates, lipids, amino acids, and bioactive compounds such as organic sulfur compounds with an expansive range of biological activities and medicinal attributes. To identify the putative compounds and genes involved in the organic sulfur pathway, we applied GC-MS and RNA-seq techniques for the bulb, stem, and flower tissues of A. hirtifolium. The essential oil analysis revealed the maximum amount of sulfur compounds in stem against flower and bulb tissues. Transcriptome profiling showed 6155, 6494, and 4259 DEGs for bulb vs. flower, bulb vs. stem, and flower vs. stem, respectively. Overall, more genes were identified as being up-regulated rather than down-regulated in flower tissue compared to the stem and bulb tissues. Our findings in accordance with other results from different papers, suggest that carbohydrates are vital to bulb formation and development because a high number of identified DEGs (586 genes) were mapped to carbohydrate metabolism. This study has detected the genes in the organic sulfur pathway and indicated that the alliinase gene shows a high variability among different tissues. In general, this study formed a useful genomic resource data to explore tissue-specific sulfur pathway in A. hirtifolium, which is helpful for functional breeding.

Omics approaches in Allium research: Progress and way ahead

BACKGROUND

The genus Allium (Family: Amaryllidaceae) is an economically important group of crops cultivated worldwide for their use as a vegetable and spices. Alliums are also well known for their nutraceutical properties. Among alliums, onion, garlic, leek, and chives cultivated worldwide. Despite their substantial economic and medicinal importance, the genome sequence of any of the Allium is not available, probably due to their large genome sizes. Recently evolved omics technologies are highly efficient and robust in elucidating molecular mechanisms of several complex life processes in plants. Omics technologies, such as genomics, transcriptomics, proteomics, metabolomics, metagenomics, etc. have the potential to open new avenues in research and improvement of allium crops where genome sequence information is limited. A significant amount of data has been generated using these technologies for various Allium species; it will help in understanding the key traits in Allium crops such as flowering, bulb development, flavonoid biosynthesis, male sterility and stress tolerance at molecular and metabolite level. This information will ultimately assist us in speeding up the breeding in Allium crops.

METHOD

In the present review, major omics approaches, and their progress, as well as potential applications in Allium crops, could be discussed in detail.

RESULTS

Here, we have discussed the recent progress made in Allium research using omics technologies such as genomics, transcriptomics, micro RNAs, proteomics, metabolomics, and metagenomics. These omics interventions have been used in alliums for marker discovery, the study of the biotic and abiotic stress response, male sterility, organ development, flavonoid and bulb color, micro RNA discovery, and microbiome associated with Allium crops. Further, we also emphasized the integrated use of these omics platforms for a better understanding of the complex molecular mechanisms to speed up the breeding programs for better cultivars.

CONCLUSION

All the information and literature provided in the present review throws light on the progress and potential of omics platforms in the research of Allium crops. We also mentioned a few research areas in Allium crops that need to be explored using omics technologies to get more insight. Overall, alliums are an under-studied group of plants, and thus, there is tremendous scope and need for research in Allium species.

Comparative transcriptome analyses in contrasting onion (Allium cepa L.) genotypes for drought stress

Onion (Allium cepa L.) is an important vegetable crop widely grown for diverse culinary and nutraceutical properties. Being a shallow-rooted plant, it is prone to drought. In the present study, transcriptome sequencing of drought-tolerant (1656) and drought-sensitive (1627) onion genotypes was performed to elucidate the molecular basis of differential response to drought stress. A total of 123206 and 139252 transcripts (average transcript length: 690 bases) were generated after assembly for 1656 and 1627, respectively. Differential gene expression analyses revealed upregulation and downregulation of 1189 and 1180 genes, respectively, in 1656, whereas in 1627, upregulation and downregulation of 872 and 1292 genes, respectively, was observed. Genes encoding transcription factors, cytochrome P450, membrane transporters, and flavonoids, and those related to carbohydrate metabolism were found to exhibit a differential expression behavior in the tolerant and susceptible genotypes. The information generated can facilitate a better understanding of molecular mechanisms underlying drought response in onion.

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

The physiological functions of insect foregut, especially in xenobiotic detoxification, are scarcely reported because of unimportance in appearance and insufficient molecular information. The cockroach Periplaneta americana, an entomological model organism, provides perfect material to study physiological functions of foregut tissue due to its architectural feature. Through Illumina sequencing of foregut tissue from P. americana individuals (control) or insects treated with cycloxaprid, as a novel neonicotinoid insecticide, 54 193 166 clean reads were obtained and further assembled into 53 853 unigenes with an average length of 366 bp. Furthermore, the number of unigenes involved in xenobiotic detoxification was analyzed, mainly including 70 cytochrome P450s, 12 glutathione S-transferases (GSTs), seven carboxylesterases (CarEs) and seven adenosine triphosphate-binding cassette (ABC) transporters. Compared to control, the expression of 22 xenobiotic detoxification unigenes was up-regulated after cycloxaprid application, mainly containing 18 P450s, one GST, two CarEs and one ABC adenosine triphosphate transporter, indicating that the oxidation-reduction was the major reactive process to cycloxaprid application. Through quantitative real-time polymerase chain reaction analysis, the expression of selected unigenes (six P450s, one GST and one CarE) was up-regulated at least two-fold following cycloxaprid treatment, and was generally in agreement with transcriptome data. Compared to the previous midgut transcriptome of P. americana, it looks like the expressive abundance of the xenobiotic detoxification unigenes might be important factors to the detoxifying functional differences between foregut and midgut. In conclusion, insect foregut would also play important roles in the physiological processes related to xenobiotic detoxification.

Characterization of the Lycium barbarum fruit transcriptome and development of EST-SSR markers

Lycium barbarum, commonly known as goji, is important in Chinese herbal medicine and its fruit is a very important agricultural and biological product. However, the molecular mechanism of formation of its fruit and associated medicinal and nutritional components is unexplored. Moreover, this species lacks SSR markers due to lack of genomic and transcriptomic information. In this study, a total of 139,333 unigenes with average length of 1049 bp and N50 of 1579 bp are obtained by trinity assembly from Illumina sequencing reads. A total of 92,498 (66.38%) unigenes showed similarities in at least one database including Nr (46.15%), Nt (56.56%), KO (15.56%), Swiss-prot (33.34%), Pfam (33.43%), GO (33.62%) and KOG/COG (17.55%). Genes in flavonoid and taurine biosynthesis pathways were found and validated by RT-qPCR. A total of 50,093 EST-SSRs were identified from 38,922 unigenes, and 22,537 EST-SSR primer pairs were designed. Four hundred pairs of SSR markers were randomly selected to validate assembly quality, of which 352 (88%) were successful in PCR amplification of genomic DNA from 11 Lycium accessions and 210 produced polymorphisms. The polymorphic loci showed that the genetic similarity of the 11 Lycium accessions ranged from 0.50 to 0.99 and the accessions could be divided into 4 groups. These results will facilitate investigations of the molecular mechanism of formation of L. barbarum fruit and associated medicinal and nutritional components, and will be of value to novel gene discovery and functional genomic studies. The EST-SSR markers will be useful for genetic diversity evaluation, genetic mapping and marker-assisted breeding.

Selenium and Sulfur to Produce Allium Functional Crops

Selenium is an element that must be considered in the nutrition of certain crops since its use allows the obtaining of biofortified crops with a positive impact on human health. The objective of this review is to present the information on the use of Se and S in the cultivation of plants of the genus Allium. The main proposal is to use Allium as specialist plants for biofortification with Se and S, considering the natural ability to accumulate both elements in different phytochemicals, which promotes the functional value of Allium. In spite of this, in the agricultural production of these species, the addition of sulfur is not realized to obtain functional foods and plants more resistant; it is only sought to cover the necessary requirements for growth. On the other hand, selenium does not appear in the agronomic management plans of most of the producers. Including S and Se fertilization as part of agronomic management can substantially improve Allium crop production. Allium species may be suitable to carry out biofortification with Se; this practice can be combined with the intensive use of S to obtain crops with higher production and sensory, nutritional, and functional quality.

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

BACKGROUND

Fistular leaves frequently appear in Allium species, and previous developmental studies have proposed that the process of fistular leaf formation involves programmed cell death. However, molecular evidence for the role of programmed cell death in the formation of fistular leaf cavities has yet to be reported.

RESULTS

In this study, we characterized the leaf transcriptomes of nine Allium species, including six fistular- and three solid-leaved species. In addition, we identified orthologous genes and estimated their Ka and Ks values, in order to ascertain their selective pattern. Phylogenetic analysis based on the transcriptomes revealed that A. tuberosum was the most ancestral among the nine species, and analysis of orthologous genes between A. tuberosum and the other eight species indicated that 149 genes were subject to positive selection; whereas >3000 had undergone purifying selection in each species.

CONCLUSIONS

We found that many genes that are potentially related to programmed cell death either exhibited rapid diversification in fistular-leaved species, or were conserved in solid-leaved species in evolutionary history. These genes potentially involved in programmed cell death might play important roles in the formation of fistular leaf cavities in Allium, and the differing selection patterns in fistular- and solid-leaved species may be responsible for the evolution of fistular leaves.

Identification of an NAC Transcription Factor Family by Deep Transcriptome Sequencing in Onion (Allium cepa L.)

Although onion has been used extensively in the past for cytogenetic studies, molecular analysis has been lacking because the availability of genetic resources is limited. NAM, ATAF, and CUC (NAC) transcription factors (TFs) are plant-specific proteins, and they play key roles in plant growth, development, and stress tolerance. However, none of the onion NAC (CepNAC) genes had been identified thus far. In this study, the transcriptome of onion leaves was analyzed by Illumina paired-end sequencing. Approximately 102.9 million clean sequence reads were produced and used for de novo assembly, which generated 117,189 non-redundant transcripts. Of these transcripts, 39,472 were annotated for their function. In order to mine the CepNAC TFs, CepNAC genes were searched from the transcripts assembled, resulting in the identification of all 39 CepNAC genes. These 39 CepNAC proteins were subjected to phylogenetic analysis together with 47 NAC proteins of known function that were previously identified in other species. The results showed that they can be divided into five groups (NAC-I–V). Interestingly, the NAC-IV and -V groups were found to be likely related to the processes of secondary wall synthesis and stress response, respectively. The transcriptome analysis generated a substantial amount of transcripts, which will aid immensely in identifying important genes and accelerating our understanding of onion growth and development. Moreover, the discovery of 39 CepNAC TFs and the identification of the sequence conservation between them and NAC proteins published will provide a basis for further characterization and validation of their functions in the future.