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

Zhu, Siyuan; Tang, Shouwei; Tan, Zhijian; Yu, Yongting; Dai, Qiuzhong; Liu, Touming

doi:10.1186/s12864-016-3474-8

Cited by 23 publications

(19 citation statements)

References 44 publications

(50 reference statements)

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“…Cellular studies have revealed that fistular leaves arise from a solid precursor by PCD ( Ni et al, 2015 ) . A molecular evidence for this finding was provided using transcriptome analyses of nine important species of Allium with different leaf morphologies ( Zhu et al, 2017 ) . Phylogenetic analyses of transcriptome revealed that genes associated with PCD presented rapid diversification in fistular leaf species or showed conserved nature in solid leaf species in evolutionary history.…”

Section: Survey Methodologymentioning

confidence: 99%

Omics approaches inAlliumresearch: Progress and way ahead

Khandagale

Krishna

Roylawar

et al. 2020

PeerJ

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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.

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Section: Survey Methodologymentioning

confidence: 99%

Omics approaches inAlliumresearch: Progress and way ahead

Khandagale

Krishna

Roylawar

et al. 2020

PeerJ

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“… 12 Only the transcripts that did not pass the protein-coding-score test were classified as long non-coding RNAs (lncRNAs), and the others were subjected to functional annotation by searching against seven public databases, including the National Center for Biotechnology Information (NCBI) non-redundant (NR) protein sequences, NCBI nucleotide sequences (NT), eukaryotic ortholog groups (KOG), Kyoto Encyclopedia of Genes and Genomes ortholog (KO), Swiss-Prot protein, Gene Ontology (GO), and protein family (PFAM) databases, as described previously. 13 The coding sequence (CDS) of each transcript was predicted by BLAST search against the NCBI non-redundant protein sequence database ( https://blast.ncbi.nlm.nih.gov/Blast.cgi ) and the SwissProt protein database ( http://www.uniprot.org/uniprot/ ), as well as by using the ESTscan program. 14…”

Section: Methodsmentioning

confidence: 99%

Transcriptome-referenced association study of clove shape traits in garlic

et al. 2018

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Genome-wide association studies are a powerful approach for identifying genes related to complex traits in organisms, but are limited by the requirement for a reference genome sequence of the species under study. To circumvent this problem, we propose a transcriptome-referenced association study (TRAS) that utilizes a transcriptome generated by single-molecule long-read sequencing as a reference sequence to score population variation at both transcript sequence and expression levels. Candidate transcripts are identified when both scores are associated with a trait and their potential interactions are ascertained by expression quantitative trait loci analysis. Applying this method to characterize garlic clove shape traits in 102 landraces, we identified 22 candidate transcripts, most of which showed extensive interactions. Eight transcripts were long non-coding RNAs (lncRNAs), and the others were proteins involved mainly in carbohydrate metabolism, protein degradation, etc. TRAS, as an efficient tool for association study independent of a reference genome, extends the applicability of association studies to a broad range of species.

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“…Because it is impossible to determine the CDS regions of some ESTs, the location of 748 SSRs on their respective ESTs was uncertain. Of the 2476 SSR-containing ESTs, 1326 had already been annotated by Zhu et al (2017a , Table S2), and 179 those had been annotated as transcription factors. GO functional classification also matched the 2476 SSR-containing sequences to known proteins in the GO database, with a total of 4332 functional terms.…”

Section: Annotation Of Ssr-containing Estsmentioning

confidence: 99%

“…Given recent developments in sequencing technology, large numbers of EST-derived SSR markers have been developed de novo assembly of species transcriptomes (Ding et al, 2015), and these makers have been used extensively in the genetic and breeding studies of crops (Zhu et al, 2016). however, even though the Chinese chive transcriptome has been de novo assembled (Zhu et al, 2017a) and various SSRs have been developed (Zhou et al, 2015), the number of available SSR marker is insufficient. Therefore, to improve the resources available for genetic and breeding studies of Chinese chive, the aim of the present study was to complete the large-scale development of transcriptome-based SSR markers for Chinese chive.…”

Section: Introductionmentioning

confidence: 99%

Research Article Large-scale development, characterization, and cross-amplification of EST–SSR markers in Chinese chive

Tang¹,

Yi²,

Yuan³

et al. 2017

Genet. Mol. Res.

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Chinese chive (Allium tuberosum Rottler ex Spr.) is an important vegetable crop. However, genetic and breeding studies of the species have been restricted by the lack of simple sequence repeat markers (SSRs). In the present study, a total of 2553 Chinese chive SSRs were developed from the species' transcriptome, with 626, 643, and 536 of the makers located in coding sequences, 5' untranslated regions and 3' untranslated region, respectively. The annotation of SSR-containing expressed sequence tags revealed that the transcripts were enriched for several Gene Ontology (GO) categories, including 'protein binding', 'regulation of transcription', and 'integral to membrane'. Among the 2,553 SSRs, di-and tri-nucleotide repeat motifs were the most abundant (52.3 and 45.6%, respectively), and AC/GT and GAA/TTC were the most frequent di-and tri-nucleotide motifs, respectively. PCR amplification, using 100 SSR primer pairs, revealed that 94% of the markers were of good quality and that 83-88 of the makers could be amplified in six other Allium species. This suggests that the markers had high cross-species transferability. The substantial number of SSRs developed will provide a valuable resource for future genetic and breeding studies in Chinese chive.

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

Cited by 23 publications

References 44 publications

Omics approaches inAlliumresearch: Progress and way ahead

Omics approaches inAlliumresearch: Progress and way ahead

Transcriptome-referenced association study of clove shape traits in garlic

Research Article Large-scale development, characterization, and cross-amplification of EST–SSR markers in Chinese chive

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