Mining and comparative survey of EST–SSR markers among members of Euphorbiaceae family

Sen, Surojit; Dehury, Budheswar; Sahu, Jagajjit; Rathi, S. S.; Yadav, Rajkumar

doi:10.1007/s11033-018-4181-0

Cited by 6 publications

(3 citation statements)

References 55 publications

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“…Advances in next-generation (i.e., high-throughput) sequencing technology have improved the efficiency and reliability of transcriptome sequencing experiments[18]. Consequently, many expressed sequence tag (EST)-SSR markers exhibiting cross-species transferability have been developed via the transcriptome sequencing of various plant species, such as Euphorbiaceae family members [19], Lolium multiflorum [20], and Saccharina japonica [21]. The frequent introduction of A .…”

Section: Introductionmentioning

confidence: 99%

Mining of simple sequence repeats (SSRs) loci and development of novel transferability-across EST-SSR markers from de novo transcriptome assembly of Angelica dahurica

Chen

Wen-juan

et al. 2019

PLoS ONE

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Angelica dahurica is a widely grown plant species with multiple uses, especially in the medical field. However, the frequent introduction of A . dahurica to new areas has made it difficult to distinguish between varieties. Simple sequence repeats (SSRs) detected based on transcriptome analyses are very useful for constructing genetic maps and analyzing genetic diversity. They are also relevant for the molecular marker-assisted breeding of A . dahurica . We identified 33,724 genic SSR loci based on transcriptome sequencing data. A total of 114 primer pairs were designed for the SSR loci and were tested for their specificity and diversity. Ten SSR loci in untranslated regions were ultimately selected. Subsequently, 56 A . dahurica ecotypes collected from different regions were analyzed. The SSR loci comprised 2–8 alleles, with a mean of 5.2 alleles per locus. The polymorphic information content value and Shannon’s information index were 0.6274–0.2702 (average of 0.4091) and 1.3040–0.5618 (average of 0.8475), respectively. Thus, the 10 novel SSRs identified in this study were almost in accordance with Harvey-Weinberg equilibrium and will be useful for analyzing A . dahurica genetic relationships. The results of this study confirm the potential value of transcriptome databases for the development of new SSR markers.

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Section: Introductionmentioning

confidence: 99%

Mining of simple sequence repeats (SSRs) loci and development of novel transferability-across EST-SSR markers from de novo transcriptome assembly of Angelica dahurica

Chen

Wen-juan

et al. 2019

PLoS ONE

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“…The candidate coding region in UniGenes was identified by TransDecoder v2.0.1 software, and then the PFAM protein homologous sequence was examined by BLAST alignment SwissProt database and Hmmscan 3.0 ( http://hmmer.org ), thus predicting the coding region CDSs. MISA ( http://pgrc.ipk-gatersleben.de/misa ) was used to detect simple sequence repeats (SSR) in UniGene with the parameters set as default ( Sen et al, 2018 ).…”

Section: Methodsmentioning

confidence: 99%

Transcriptome analysis of diploid and triploid Populus tomentosa

Wen

Liu

Zhang

et al. 2020

PeerJ

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Triploid Chinese white poplar (Populus tomentosa Carr., Salicaceae) has stronger advantages in growth and better stress resistance and wood quality than diploid P. tomentosa. Using transcriptome sequencing technology to identify candidate transcriptome-based markers for growth vigor in young tree tissue is of great significance for the breeding of P. tomentosa varieties in the future. In this study, the cuttings of diploid and triploid P. tomentosa were used as plant materials, transcriptome sequencing was carried out, and their tissue culture materials were used for RT-qPCR verification of the expression of genes. The results showed that 12,240 differentially expressed genes in diploid and triploid P. tomentosa transcripts were annotated and enriched into 135 metabolic pathways. The top six pathways that enriched the most significantly different genes were plant-pathogen interaction, phenylpropanoid biosynthesis, MAPK signalling pathway-plant, ascorbate and aldarate metabolism, diterpenoid biosynthesis, and the betalain biosynthesis pathway. Ten growth-related genes were selected from pathways of plant hormone signal transduction and carbon fixation in photosynthetic organisms for RT-qPCR verification. The expression levels of MDH and CYCD3 in tissue-cultured and greenhouse planted triploid P. tomentosa were higher than those in tissue-cultured diploid P. tomentosa, which was consist ent with the TMM values calculated by transcriptome.

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“…Quanto aos aspectos químicos, a família é conhecida pela riqueza em metabólitos especiais, como terpenos, flavonoides, taninos, alcaloides e esteróis, com vários estudos comprovando suas atividades antifúngica, antibacteriana, antioxidante, entre outras. [1][2][3][4] Jatropha multifida L. (sinônimo Manihot multifida (L.) Crantz) é destacada pelo seu uso medicinal contra a infecção fúngica causada pelas leveduras do gênero Candida, a candidíase. Seu látex, utilizado para aplicação em feridas com o objetivo de auxiliar na cicatrização, também é ingerido para o tratamento de úlceras gastrointestinais.…”

Section: Introductionunclassified

Antifungal Activity of Latex and Lupenonefrom Jatropha multifida L. (Euphorbiaceae)

Oliveira¹,

Lemos²,

Pereira³

et al. 2019

Rev. Virtual Quim.

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Jatropha multifida L. belongs to the family Euphorbiaceae, being popularly used in Brazil for treatment and healing of infected wounds, gastrointestinal ulcers and candidiasis. Lupenone, isolated from the hexane extract of its leaves, was submitted to the synergism test for Candida tropicalis and evaluation of its possible mechanism of antifungal action. Lupenone was able to halve the minimum inhibitory capacity (MIC) of fluconazole against C. tropicalis with possible action on the cell wall and ergosterol of the fungal membrane. The fraction derived from successive fractions of the aqueous latex residue, was analyzed by HPLC-DAD and tested in the antifungal assay against the following yeasts: Candida albicans, Candida albicans Serology A and B, Candida grablata, Candida krusei, Candida tropicalis and Cryptococcus neoformans. This fraction showed a probable catechin with moderate activity against C. tropicalis and C. grablata. The presence of triterpene and polyphenols in J. multifida may be responsible for the antifungal and cicatrizant activities presented by the species. Lupenone may be used in combination with fluconazole in the development of a new antifungal.

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Mining and comparative survey of EST–SSR markers among members of Euphorbiaceae family

Cited by 6 publications

References 55 publications

Mining of simple sequence repeats (SSRs) loci and development of novel transferability-across EST-SSR markers from de novo transcriptome assembly of Angelica dahurica

Mining of simple sequence repeats (SSRs) loci and development of novel transferability-across EST-SSR markers from de novo transcriptome assembly of Angelica dahurica

Transcriptome analysis of diploid and triploid Populus tomentosa

Antifungal Activity of Latex and Lupenonefrom Jatropha multifida L. (Euphorbiaceae)

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