Transcriptome sequencing and comparative analysis reveal long-term flowing mechanisms in Hevea brasiliensis latex

Wei, Fang; Luo, Senlin; Zheng, Qiankun; Qiu, Jian; Yang, Wei‐Cai; Wu, Ming; Xianzhou, Xiao

doi:10.1016/j.gene.2014.11.048

Cited by 21 publications

(14 citation statements)

References 52 publications

(2 reference statements)

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“…About 70 antioxidant activity genes were expressed in the bark of healthy and TPD-affected trees ( Mantello et al 2014 , Liu et al 2015 ). However, only seven antioxidant activity genes were predicted in latex ( Wei et al 2015 ).…”

Section: Ros-associated Tpd Affects Latex Productionmentioning

confidence: 99%

Reactive oxygen species in Hevea brasiliensis latex and relevance to Tapping Panel Dryness

2016

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Environmental stress can lead to oxidative stress resulting from an increase in reactive oxygen species (ROS) and involves redox adjustments. Natural rubber is synthesized in laticifers, which is a non-photosynthetic tissue particularly prone to oxidative stress. This paper reviews the current state of knowledge on the ROS production and ROS-scavenging systems in laticifers. These regulations have been the subject of intense research into a physiological syndrome, called Tapping Panel Dryness (TPD), affecting latex production in Hevea brasiliensis. In order to prevent TPD occurrence, monitoring thiol content appeared to be a crucial factor of latex diagnosis. Thiols, ascorbate and γ-tocotrienol are the major antioxidants in latex. They are involved in membrane protection from ROS and likely have an effect on the quality of raw rubber. Some transcription factors might play a role in the redox regulatory network in Hevea, in particular ethylene response factors, which have been the most intensively studied given the role of ethylene on rubber production. Current challenges for rubber research and development with regard to redox systems will involve improving antioxidant capacity using natural genetic variability.

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Section: Ros-associated Tpd Affects Latex Productionmentioning

confidence: 99%

Reactive oxygen species in Hevea brasiliensis latex and relevance to Tapping Panel Dryness

2016

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“…In recent years, transcriptome sequencing has emerged as an efficient method to generate genomic-level data, large expressed sequence tag (EST) sequences, and molecular markers. Next generation sequencing (NGS) technologies are providing cutting-edge approaches for high-throughput sequence generation [22], allowing rapid and comprehensive analyses of plant genomes and cost-effective means of analyzing transcripts [23, 24]. Transcriptome sequencing has been successfully used for marker development in many underutilized legume plants, such as faba bean [25], adzuki bean [26], rice bean [27], hyacinth bean, grass pea and Bambara groundnut [28], and winged bean [28, 29], but has not yet been applied to research on Mucuna .…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic resources for the medicinal legume Mucuna pruriens: de novo transcriptome assembly, annotation, identification and validation of EST-SSR markers

et al. 2017

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BackgroundThe medicinal legume Mucuna pruriens (L.) DC. has attracted attention worldwide as a source of the anti-Parkinson’s drug L-Dopa. It is also a popular green manure cover crop that offers many agronomic benefits including high protein content, nitrogen fixation and soil nutrients. The plant currently lacks genomic resources and there is limited knowledge on gene expression, metabolic pathways, and genetics of secondary metabolite production. Here, we present transcriptomic resources for M. pruriens, including a de novo transcriptome assembly and annotation, as well as differential transcript expression analyses between root, leaf, and pod tissues. We also develop microsatellite markers and analyze genetic diversity and population structure within a set of Indian germplasm accessions.ResultsOne-hundred ninety-one million two hundred thirty-three thousand two hundred forty-two bp cleaned reads were assembled into 67,561 transcripts with mean length of 626 bp and N50 of 987 bp. Assembled sequences were annotated using BLASTX against public databases with over 80% of transcripts annotated. We identified 7,493 simple sequence repeat (SSR) motifs, including 787 polymorphic repeats between the parents of a mapping population. 134 SSRs from expressed sequenced tags (ESTs) were screened against 23 M. pruriens accessions from India, with 52 EST-SSRs retained after quality control. Population structure analysis using a Bayesian framework implemented in fastSTRUCTURE showed nearly similar groupings as with distance-based (neighbor-joining) and principal component analyses, with most of the accessions clustering per geographical origins. Pair-wise comparison of transcript expression in leaves, roots and pods identified 4,387 differentially expressed transcripts with the highest number occurring between roots and leaves. Differentially expressed transcripts were enriched with transcription factors and transcripts annotated as belonging to secondary metabolite pathways.ConclusionsThe M. pruriens transcriptomic resources generated in this study provide foundational resources for gene discovery and development of molecular markers. Polymorphic SSRs identified can be used for genetic diversity, marker-trait analyses, and development of functional markers for crop improvement. The results of differential expression studies can be used to investigate genes involved in L-Dopa synthesis and other key metabolic pathways in M. pruriens.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3780-9) contains supplementary material, which is available to authorized users.

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“…In recent years, next-generation sequencing technology has emerged as a cutting-edge approach for high-throughput sequence determination 22 . Additionally, it not only allows rapid and comprehensive analyses of the plant genome but also offers a cost-effective means of analysing gene transcripts 23 . Next-generation sequencing has been successfully and increasingly used in most plants, such as rice 24 , alfalfa 13 25 , V. sativa 26 , and barley 27 , but it has not yet been applied to research on E .…”

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confidence: 99%

Development and cross-species transferability of EST-SSR markers in Siberian wildrye (Elymus sibiricus L.) using Illumina sequencing

Zhou

Luo

et al. 2016

Sci Rep

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Siberian wildrye (Elymus sibiricus L.) is a perennial, self-fertilizing grass that plays an important role in animal husbandry and environmental sustenance. However, the transcriptomic and genomic information on this species is very limited, which hinders genetic and breeding studies. In the present study, 76,686,804 clean reads were generated from 11 different tissue samples of E. sibiricus by Illumina paired-end sequencing, and the reads were deposited into the NCBI SRA database (SRX574376). A total of 8,769 EST-SSRs were identified from 94,458 unigene sequences, which were obtained by de novo assembly. Moreover, 1,078 primer pairs were successfully designed, and 500 pairs were randomly selected to assess polymorphisms in 15 E. sibiricus accessions. A total of 112 primer pairs were polymorphic, and the polymorphism information content (PIC) values ranged from 0.39 to 0.81, indicating a high level of informativeness. Furthermore, these 112 polymorphic primer pairs were used to evaluate the transferability to 13 other related species, and 55 EST-SSR markers were found to be polymorphic among these 13 Elymus species. This study collected the global sequence data for E. sibiricus, and the newly developed markers will prove valuable in facilitating genetic diversity in E. sibiricus and related Elymus species.

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Transcriptome sequencing and comparative analysis reveal long-term flowing mechanisms in Hevea brasiliensis latex

Cited by 21 publications

References 52 publications

Reactive oxygen species in Hevea brasiliensis latex and relevance to Tapping Panel Dryness

Reactive oxygen species in Hevea brasiliensis latex and relevance to Tapping Panel Dryness

Transcriptomic resources for the medicinal legume Mucuna pruriens: de novo transcriptome assembly, annotation, identification and validation of EST-SSR markers

Development and cross-species transferability of EST-SSR markers in Siberian wildrye (Elymus sibiricus L.) using Illumina sequencing

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