Fig 2 - available from: BMC Genomics
This content is subject to copyright. Terms and conditions apply.
Phylogenetic tree of nine Allium species, constructed on the basis of their transcriptomes  

Phylogenetic tree of nine Allium species, constructed on the basis of their transcriptomes  

Source publication
Article
Full-text available
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 c...

Contexts in source publication

Context 1
... to our phylogenetic tree (Fig. 2), TUB was lo- cated at the root of the tree, and had far phylogenetic distance with the others, suggesting that TUB was more ancestral than the other species. This finding was con- sistent with the result of previous study [29]. The other eight species were split into four clades. Interestingly, the classification based on the ...
Context 2
... with that based on leaf morphology, i.e., the spe- cies with flat, solid leaves (SAT and POR) were grouped together, the species with cylindrical, fistular leaves (ASC, FIS, CEP, and AGR) were placed in a monophy- letic clade, and the species with small-gapped and tri- angular fistular leaves (MAC and CHI) were placed in a single branch, as well (Fig. ...

Citations

... Transcriptome data have recently been shown to be useful in defining the diverse lineages of eukaryotes by extracting sequences of a large number of single-copy nuclear genes from transcriptomes of the taxa (Wen et al. , 2020. Zhu et al. (2017) revealed that Allium tuberosum was the most ancestral of the nine Allium species using a comparative transcriptome approach based on phylogenetic analysis. Furthermore, an analysis of orthologous genes between A. tuberosum and the other 8 species revealed that 149 genes that have been positively selected and are potentially involved in programmed cell death may play important roles in the formation of fistular leaf cavities in Allium, and that different selection patterns in fistular-and solid-leaved species may be responsible for the evolution of fistular leaves. ...
Article
Full-text available
Medicinal plants of the NorthWestern Himalayan region are known for their unprecedented biodiversity and valuable secondary metabolites that are unique to this dynamic geo-climatic region. From ancient times these medicinal herbs have been used traditionally for their therapeutic potentials. But from the last 2 decades increasing pharmaceutical demand, illegal and unorganized trade of these medicinal plants have accelerated the rate of over-exploitation in a non-scientific manner. In addition, climate change and anthropogenic activities also affected their natural habitat and driving most of these endemic plant species to critically endangered that foresee peril of mass extinction from this eco-region. Hence there is an urgent need for developing alternative sustainable approaches and policies to utilize this natural bioresource ensuring simultaneous conservation. Hither, arise the advent of sequencing-based transcriptomic studies significantly contributes to better understand the background of important metabolic pathways and related genes/enzymes of high-value medicinal herbs, in the absence of genomic information. The use of comparative transcriptomics in conjunction with biochemical techniques in NorthWestern Himalayan medicinal plants has resulted in significant advances in the identification of the molecular players involved in the production of secondary metabolic pathways over the last decade. This information could be used to further engineer metabolic pathways and breeding programs, ultimately leading to the development of in vitro systems dedicated to the production of pharmaceutically important secondary metabolites at the industrial level. Collectively, successful adoption of these approaches can certainly ensure the sustainable utilization of Himalayan bioresource by reducing the pressure on the wild population of these critically endangered medicinal herbs. This review provides novel insight as a transcriptome-based bioresource repository for the understanding of important secondary metabolic pathways genes/enzymes and metabolism of endangered high-value NorthWestern Himalayan medicinal herbs, so that researchers across the globe can effectively utilize this information for devising effective strategies for the production of pharmaceutically important compounds and their scale-up for sustainable usage and take a step forward in omics-based conservation genetics.
... Recently, next-generation sequencing (NGS) technology has been widely used as an important tool in the research of plant genetics. Unlike genome analysis, transcriptome analysis by NGS technology is rapid, inexpensive, and unconstrained by genomic complexity (Zhu et al. 2017). Additionally, this technique has been effectively applied to several Allium species, including onion (Rajkumar et al. 2015;Han et al. 2016), garlic (Sun et al. 2012;Chen et al. 2018), and Chinese chive (Zhou et al. 2015). ...
... Additionally, this technique has been effectively applied to several Allium species, including onion (Rajkumar et al. 2015;Han et al. 2016), garlic (Sun et al. 2012;Chen et al. 2018), and Chinese chive (Zhou et al. 2015). Transcriptome sequencing can provide a wealth of biological information and is an effective method for gene functional annotation (Sun et al. 2012), gene expression analysis (Khosa et al. 2016), molecular marker development , and interspecific genetic diversity analysis (Zhu et al. 2017). However, studies that apply transcriptome analysis to improve the understanding of the interspecific genetic relationships of A. victorialis are still lacking. ...
... We also compared the domain annotations of six A. victorialis samples with that of the other eight Allium species, including A. tuberosum, A. sativum, A. ampeloprasum, A. macrostemon, A. chinense, A. ascalonicum, A. cepa, and A. fistulosum (Zhu et al. 2017;Chen et al. 2018). A total of 3765 Pfam families were conserved among the nine species. ...
Article
Full-text available
The Changbai Mountains comprise one of the main distribution areas of A. victorialis in China, and this species is endangered owing to habitat changes and overexploitation. However, A. victorialis germplasms have not been systematically collected and studied. The aims of this study were to obtain some detailed genetic information, analyze the genetic diversity, and further promote the protection of A. victorialis germplasms from the Changbai Mountains. Transcriptomic analysis was performed with six A. victorialis samples collected from the Changbai Mountains. At least 146,759 genes for each sample were obtained after performing de novo assembly of the RNA-seq data, and at least 92% of these genes were found to have only one mRNA isoform. These sequences and their functional annotations provided a large-scale genetic resource of this species. Phylogenetic analysis showed that A. victorialis was genetically distant from some related species, e.g. Allium sativum, Allium fistulosum, and Allium cepa, but genetically close to Allium tuberosum. The two A. victorialis var. listera samples were phylogenetically separated from the other four samples, and these two samples should be regarded as Allium listera. In addition, two KASP markers for discriminating the Dongfeng samples from the other four A. victorialis samples were successfully developed. This study lays the foundation for future studies on the genetic diversity and evolution of Allium species, as well as for the conservation of A. victorialis germplasms from the Changbai Mountains and other populations of this species.
... Such pattern seemingly suggests that the leaf shape might be not related with the formation of fistular or solid leaves. It has been documented that the process of fistular leaf formation involves programmed cell death (Wang 2010;Zhu et al. 2017). The vascular bundles in Asian sect. ...
Article
Full-text available
The disjunctive distribution (Europe-Caucasus-Asia) and species diversification across Eurasia for the genus Allium sect. Daghestanica has fascinating attractions for researchers aiming to understanding the development and history of the modern Eurasia flora. However, no any studies have been carried out to address the evolutionary history of this section. Based on the nrITS and cpDNA fragments (trnL-trnF and rpl32-trnL), the evolutionary history of the third evolutionary line (EL3) of the genus Allium was reconstructed and we further elucidate the evolutionary line of sect. Daghestanica under this background. Our molecular phylogeny recovered two highly supported clades in sect. Daghestanica: the Clade I includes Caucasian-European species and Asian A. maowenense, A. xinlongense and A. carolinianum collected in Qinghai; the Clade II comprises Asian yellowish tepal species, A. chrysanthum, A. chrysocephalum, A. herderianum, A. rude and A. xichuanense. The divergence time estimation and biogeography inference indicated that Asian ancestor located in the QTP and the adjacent region could have migrated to Caucasus and Europe distributions around the Late Miocene and resulted in further divergence and speciation; Asian ancestor underwent the rapid radiation in the QTP and the adjacent region most likely due to the heterogeneous ecology of the QTP resulted from the orogeneses around 4–3 Mya. Our study provides a picture to understand the origin and species diversification across Eurasia for sect. Daghestanica.
... 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. ...
Article
Full-text available
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.
... 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. ...
Article
Full-text available
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.
... Although sequencing technologies have advanced rapidly in terms of higher throughput and longer read lengths, analysis of the complex and huge genome of Allium species, the non-model plant, has remained a herculean task (Schatz, 2012;Nagarajan and Pop, 2013). Currently, only a few transcriptome resources of Allium species are available in GenBank (Zhou et al., 2015;Zhang et al., 2016a;Zhu et al., 2017). Therefore, little is known about the evolution and genetic adaptation of Allium species. ...
... The length of N50 ranged from 886 to 1209 bp in flowers, as well as 819 bp to 1184 bp in leaves, and the relevant sequence information are summarized in Table 1. In the present assembled results, the mean length of unigenes were slightly larger than previous publications (Zhou et al., 2015;Zhu et al., 2017 ...
... Despite fundamental studies on the phylogenetic taxonomy of genus Allium by Friesen et al. (2006) and Li et al. (2010), there are still many poorly described Allium groups or sections available in different regions of the world. Particularly, studies regarding the evolutionary relationships and adaption mechanisms of Allium species are still scarce, although some transcriptome analyses or plastid genomes have been conducted (Kamenetsky et al., 2015;Filyushin et al., 2016Filyushin et al., , 2018Lee et al., 2017;Zhu et al., 2017;Jin et al., 2018). Our present study provides the first phylogenomic analysis to resolve the interspecies relationships of Chinese section Daghestanica and discuss the adaptive evolution of several highland species in this section. ...
... Лук-порей -популярный объект для биохимических исследований (Bernaert et al., 2013(Bernaert et al., , 2014Soininen et al., 2014), однако генные и геномные исследования этой культуры ранее практически не проводили. Так, был определен транскриптом листа лука-порея, который использовали для сравнительного анализа экспрессии генов у видов Allium с различной морфологией листа (Zhu et al., 2017). Методами AFLP и ISSR изучены геномный полиморфизм 16 образцов лука-порея и внутрисортовая вариабельность (Филюшин и др., 2011; Филюшин, Агафонов, 2015). ...
Article
Full-text available
The genus Allium L. (Amaryllidaceae), the most numerous among monocotyledonous plants, includes such economically important vegetable crops as onion (A. cepa), garlic (A. sativum) and leek (A. porrum). Leek has a high taste and proven valuable dietary properties and is one of the most popular vegetable crops in Western Europe. Despite a high importance of leek as a vegetable, this species is rarely the subject of molecular genetic studies. The genetic diversity of leeks has never been studied before. Therefore, in this work, we studied the nuclear variability (AFLP) and the chloroplast (nucleotide sequence analysis) genomes using a broad sample. For this work, 65 leek accessions were selected from the collection of the Scientific Center of Vegetable Crops, which included varieties of domestic and foreign breeding. As a result of an AFLP analysis and processing of the DNA spectra obtained, 760 fragments were identified, of which 716 were polymorphic for the leek accessions being analyzed. The calculated genetic distances between the leek samples varied from 0.4 to 0.76, which is comparable to the intraspecific polymorphism of related Allium species (onions, garlic). Analysis of the genomic structure with STRUCTURE 2.3.4 divided the leek samples into seven groups, which generally coincides with the clustering of these samples. To assess the variability of the chloroplast genome, nine sites of the chloroplast genome were sequenced in the leek samples, both non-coding (intergenic spacers rpl32-trnL, ndhJ-trnL, and intron rps16 gene), and protein coding genes (psaA, psaB, psbA, psbB, psbE, petB). The analysis of the sites of the leek chloroplast genome revealed an extremely low level of their polymorphism, only six SNPs were detected in the studied sequences with a total length of about 10,500 bp. Thus, as a result of this work, a high level of polymorphism of the leek nuclear genome was revealed, while the polymorphism of the chloroplast genome was extremely low.
... Transcripts were subjected to functional annotation by searching against six public databases, including the National Center for Biotechnology Information (NCBI) non-redundant protein sequences (NR), eukaryotic ortholog groups (KOG), Kyoto Encyclopedia of Genes and Genomes ortholog (KEGG), Swiss-Prot protein, Gene Ontology (GO), and Interpro databases [28]. The E-value cutoff for the annotated search was set to 10 − 5 . ...
Article
Full-text available
Background: The redundancy of genomic resources, including transcript and molecular markers, and their uncertain position in the genome have dramatically hindered the study of traits in ramie, an important natural fiber crop. Results: We obtained a high-quality transcriptome consisting of 30,591 non-redundant transcripts using single-molecule long-read sequencing and proposed it as a universal ramie transcriptome. Additionally, 55,882 single nucleotide polymorphisms (SNPs) were identified and a high-density genetic map was developed. Based on this genetic map, 181.7 Mb ramie genome sequences were assembled into 14 chromosomes. For the convenient use of these resources, 29,286 (~ 95.7%) of the transcripts and all 55,882 SNPs, along with 1827 previously reported sequence repeat markers (SSRs), were mapped into the ramie genome, and 22,343 (~ 73.0%) transcripts, 50,154 (~ 89.7%) SNPs, and 1466 (~ 80.3%) SSRs were assigned to a specific location in the corresponding chromosome. Conclusion: This is the first study to characterize the ramie transcriptome by long-read sequencing, and the substantial number of transcripts of significant length obtained will accelerate our understanding of ramie growth and development. This integration of genome sequences, expressed transcripts, and genetic markers will provide an extremely useful resource for genetic, molecular, and breeding studies of ramie.
... Allium L. is the single genus of Allieae and belongs to the subfamily Allioideae (Amaryllidaceae) as per update APG IV (Chase et al., 2016). It is one of the largest genera of the monocotyledons (∼ 920 species) and includes many economically important crops (Herden et al., 2016;Zhu et al., 2017). The new classification of Allium was made by Friesen et al. (2006), who first suggested that the genus Allium is monophyletic. ...
Article
Full-text available
The genus Allium (Amaryllidaceae, Allioideae) is one of the largest monocotyledonous genera and it includes many economically important crops that are cultivated for consumption or medicinal uses. Recent advances in molecular phylogenetics have revolutionized our understanding of Allium taxonomy and evolution. However, the phylogenetic relationships in some Allium sections (such as the Allium section Daghestanica) and the genetic bases of adaptative evolution, remain poorly understood. Here, we newly assembled six chloroplast genomes from Chinese endemic species in Allium section Daghestanica and by combining these genomes with another 35 allied species, we performed a series of analyses including genome structure, GC content, species pairwise Ka/Ks ratios, and the SSR component, nucleotide diversity and codon usage. Positively selected genes (PSGs) were detected in the Allium lineage using the branch-site model. Comparison analysis of Bayesian and ML phylogeny on CCG (complete chloroplast genome), SCG (single copy genes) and CDS (coding DNA sequences) produced a well-resolved phylogeny of Allioideae plastid lineages, which illustrated several novel relationships with the section Daghestanica. In addition, six species in section Daghestanica showed highly conserved structures. The GC content and the GC3s content in Allioideae species exhibited lower values than studied non-Allioideae species, along with elevated pairwise Ka/Ks ratios. The rps2 gene was lost in all examined Allioideae species, and 10 genes with significant posterior probabilities for codon sites were identified in the positive selection analysis, seven of them are associated with photosynthesis. Our study uncovered a new species relationship in section Daghestanica and suggested that the selective pressure has played an important role in Allium adaptation and evolution, these results will facilitate our further understanding of evolution and adaptation of species in the genus Allium.
... Some of the key genes involved in regulation of bulb and flower formation were identified by tra- ditional methods ( Taylor et al. 2010) but RNA-SEQ methods have enabled a rapid expan- sion in the knowledge of key gene families and variation underlying development and adaptation in garlic ( Kamenetsky et al. 2015) and onion ( Lee et al. 2013;Manoharan et al. 2016). In contrast to these transcriptome approa- ches within a single species, Zhu et al. (2017) used a comparative approach to identify candidate genes for the fistular leaf phenotype. With the growing availability of such catalogs in Allium species such as those reported by Han et al. (2016) and Sun et al. (2015), and bioinformatics tools to support comparative transcriptomics, this kind of evolutionary approach deserves wider usage. ...
Chapter
Ability to conduct molecular analyses in Allium species was previously limited by the power of available technologies to sample very large heterozygous genomes in a cost-effective manner. The emergence of third-generation long-read sequencing technologies, coupled with maturing strategies for population genomics in non-model systems provides exciting opportunities for Allium crops. Now that these technical advances have removed major barriers to progress, it is necessary to consider the horticultural resources to which we can apply such technologies. This will hasten delivery of genetics tools that will ultimately benefit breeders, farmers, and consumers of Allium vegetables. Here, we describe progress to date in Allium mapping, with an emphasis on onion, and review approaches used on other non-model systems that could be applied. We also present strategies we have developed over the past decade to establish genetic stocks for onion suited to modern population genomics analyses.