Transcriptome analysis of mistletoe (Viscum album) haustorium development

Ko, Suk Min; Kwon, Yong Kook; Kim, Jong Hyun; Song, In-Ja; Lee, Hyo-Yeon; Choi, Dong-Woog; Liu, Jang R.; Kim, Suk Weon

doi:10.1007/s13580-014-0033-6

Cited by 11 publications

(15 citation statements)

References 55 publications

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“…Next generation sequencing (NGS) is a widely used, powerful technique that provides insights into plant development through genome-wide transcriptome analysis. NGS, accompanied by sophisticated bioinformatics tools for data analysis, including high performance de novo transcriptome assembly, has emerged to facilitate transcriptome analysis in uncharacterized model plants [ 12 – 16 ]. Recently, de novo assembly and analysis of the transcriptomes of parasitic plants have provided important insights into the process of plant parasitism [ 14 , 16 – 21 ].…”

Section: Introductionmentioning

confidence: 99%

“…NGS, accompanied by sophisticated bioinformatics tools for data analysis, including high performance de novo transcriptome assembly, has emerged to facilitate transcriptome analysis in uncharacterized model plants [ 12 – 16 ]. Recently, de novo assembly and analysis of the transcriptomes of parasitic plants have provided important insights into the process of plant parasitism [ 14 , 16 – 21 ]. For example, transcriptome analysis of the obligate plant stem parasite dodder ( Cuscuta pentagona ) at diverse tissue and developmental stages shed light on transcriptional dynamics during dodder development and parasitism and the categories of key genes involved in plant parasitism [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

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De novo assembly and transcriptome characterization of spruce dwarf mistletoe Arceuthobium sichuanense uncovers gene expression profiling associated with plant development

Wang

Zhou³

et al. 2016

BMC Genomics

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BackgroundThe parasitic flowering plant dwarf mistletoe (Arceuthobium spp., Viscaceae) is one of the most destructive forest pests, posing a major threat to numerous conifer species worldwide. Arceuthobium sichuanense (spruce dwarf mistletoe, SDM) infects Qinghai spruce (Picea crassifolia) and causes severe damage to spruce forests in Northwest China. SDM is a Chinese native parasitic plant and acquires carbohydrates and mineral nutrition from its hosts. However, underlying molecular basis of the physiological development is largely unknown. Investigations of these physiological traits have been hampered by the lack of genomic resources for this species.ResultsIn this study, to investigate the transcriptomic processes underlying physiological traits and development in SDM, we used RNA from four major tissues (i.e., shoots, flowers, fruits, and seeds) for de novo assembly and to annotate the transcriptome of this species. We uncovered the annotated transcriptome and performed whole genome expression profiling to uncover transcriptional dynamics during physiological development, and we identified key gene categories involved in the process of sexual development. The assembled SDM transcriptome reported in this work contains 331,347 assembled transcripts; 226,687 unigenes were functionally annotated by Gene Ontology analysis. RNA-Seq analysis using this reference transcriptome identified 22,641 differentially expressed genes from shoots, flowers, fruits, and seeds. These genes are enriched in processes including organic substance metabolism, cellular metabolism, biosynthesis, and cellular component. In addition, genes related to transport, transcription, hormone biosynthesis and signaling, carbohydrate metabolism, and photosynthesis were differentially expressed between tissues.ConclusionThis work reveals tissue-specific gene expression patterns and pathways of SDM and implied to a difference between photosynthetic and non-photosynthetic tissues in plants. The data can potentially be used for future investigations on endophytic parasitism and SDM-spruce interaction, and it dramatically increases the available genomic resources for Arceuthobium and dwarf mistletoe communities. This preliminary study of the Arceuthobium transcriptome provides excellent opportunities for characterizing plant parasitic genes with unknown functions.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3127-y) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

De novo assembly and transcriptome characterization of spruce dwarf mistletoe Arceuthobium sichuanense uncovers gene expression profiling associated with plant development

Wang

Zhou³

et al. 2016

BMC Genomics

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“…Advances in transcriptome sequencing technology and data mining platforms have led to rapid progress in comparative transcriptomics for non-model, non-crop plants, such as parasitic plants [ 32 , 33 , 34 , 35 , 36 , 37 , 38 ]. Here, transcriptomes were generated and compared for T. nigrans plants parasitizing four different host species.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome Profiling of a Common Mistletoe Species Parasitizing Four Typical Host Species in Urban Southwest China

Kuang

Wang

Mao

et al. 2022

Genes

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Comparing gene expression among parasitic plants infecting different host species can have significant implications for understanding host-parasite interactions. Taxillus nigrans is a common hemiparasitic species in Southwest China that parasitizes a variety of host species. However, a lack of nucleotide sequence data to date has hindered transcriptome-level research on T. nigrans. In this study, the transcriptomes of T. nigrans individuals parasitizing four typical host species (Broussonetia papyrifera [Bpap] a broad-leaved tree species; Cryptomeria fortunei [Cfor] a coniferous tree species; Cinnamomum septentrionale [Csep] an evergreen tree species; and Ginkgo biloba [Gbil] a deciduous-coniferous tree species) were sequenced, and the expression profiles and metabolic pathways compared among hosts. A total of 40.06 Gb of clean sequence data were generated in nine cDNA libraries. These were de novo assembled into 293,823 transcripts with an N50 value of 1790 bp. A large number of differentially expressed genes (DEGs) were identified when comparing T. nigrans individuals on different host species: Bpap vs. Cfor (713 DEGs), Bpap vs. Csep (1219), Bpap vs. Gbil (1514), Cfor vs. Csep (1639), Cfor vs. Gbil (1722), and Csep vs. Gbil (1723). Three hundred and eighty-one unigenes were common to all six pairwise comparisons; these were primarily associated with carbohydrate metabolism and energy metabolism, as determined in a KEGG enrichment analysis. Specific involvements included: the TCA cycle, biosynthesis of secondary metabolites, carbon metabolism, biosynthesis of amino acids and glyoxylate/dicarboxylate metabolism. A total of 251 unique unigenes were also identified, specific to either the Bpap vs. Cfor (249 unigenes) or Csep vs. Gbil (two unigenes) comparisons; partial unigenes were associated with the plasma membrane, response to endogenous stimuli, ion binding, and organic hydroxy compound metabolic processes. These results provide a foundation for further explorations of the detailed molecular mechanisms involved in plant parasitism.

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“…The GC content is in the range of 39%, which is about average for flowering plants (Nov ak et al, 2020). An initial transcriptome analysis of V. album haustorium tissue has been performed and yielded sequences of 3044 open reading frames (Ko et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

The gene space of European mistletoe (Viscum album)

et al. 2021

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European mistletoe (Viscum album) is a hemiparasitic flowering plant that is known for its very special life cycle and extraordinary biochemical properties. Particularly, V. album has an unusual mode of cellular respiration that takes place in the absence of mitochondrial complex I. However, insights into the molecular biology of V. album so far are very limited. Since the genome of V. album is extremely large (estimated 600 times larger than the genome of the model plant Arabidopsis thaliana) it has not been sequenced up to now. We here report sequencing of the V. album gene space (defined as the space including and surrounding genic regions, encompassing coding as well as 5 0 and 3 0 non-coding regions). mRNA fractions were isolated from different V. album organs harvested in summer or winter and were analyzed via single-molecule real-time sequencing. We determined sequences of 39 092 distinct open reading frames encoding 32 064 V. album proteins (designated V. album protein space). Our data give new insights into the metabolism and molecular biology of V. album, including the biosynthesis of lectins and viscotoxins. The benefits of the V. album gene space information are demonstrated by re-evaluating mass spectrometry-based data of the V. album mitochondrial proteome, which previously had been evaluated using the A. thaliana genome sequence. Our re-examination allowed the additional identification of nearly 200 mitochondrial proteins, including four proteins related to complex I, which all have a secondary function not related to respiratory electron transport. The V. album gene space sequences are available at the NCBI.

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Transcriptome analysis of mistletoe (Viscum album) haustorium development

Cited by 11 publications

References 55 publications

De novo assembly and transcriptome characterization of spruce dwarf mistletoe Arceuthobium sichuanense uncovers gene expression profiling associated with plant development

De novo assembly and transcriptome characterization of spruce dwarf mistletoe Arceuthobium sichuanense uncovers gene expression profiling associated with plant development

Transcriptome Profiling of a Common Mistletoe Species Parasitizing Four Typical Host Species in Urban Southwest China

The gene space of European mistletoe (Viscum album)

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