De novo transcriptome assembly of Zanthoxylum bungeanum using Illumina sequencing for evolutionary analysis and simple sequence repeat marker development

Feng, Shijing; Zhao, Lili; Liu, Zhenshan; Liu, Yulin; Wei, Anzhi

doi:10.1038/s41598-017-15911-7

Cited by 38 publications

(43 citation statements)

References 49 publications

(47 reference statements)

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“…Among the mononucleotide repeats, A/T repeats (95.08%) were far more prevalent than G/C repeats (4.92%), which was consistent with most plants (Gao et al, 2013;Yue et al, 2016;Feng et al, 2017;Taheri et al, 2019). The most abundant dinucleotide repeat was the AC/GT motif (65.37%), followed by AG/CT (22.93%) and AT/TA (10.73%), which was similar to previous findings in other Chrysanthemum species Chrysanthemum indicum (Han et al, 2018).…”

Section: Figure 4 | Results Of the Bayesian Clustering Analysis Condusupporting

confidence: 87%

Genetic Divergence and Relationship Among Opisthopappus Species Identified by Development of EST-SSR Markers

Chai

Wang

et al. 2020

Front. Genet.

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Opisthopappus Shih is an endemic and endangered genus restricted to the Taihang Mountains that has important ornamental and economic value. According to the Flora Reipublicae Popularis Sinicae (FRPS, Chinese version), this genus contains two species (Opisthopappus longilobus and Opisthopappus taihangensis), whereas in the Flora of China (English version) only one species O. taihangensis is present. The interspecific phylogenetic relationship remains unclear and undefined, which might primarily be due to the lack of specific molecular markers for phylogenetic analysis. For this study, 2644 expressed sequence tag-simple sequence repeats (EST-SSRs) from 33,974 unigenes using a de novo transcript assembly of Opisthopappus were identified with a distribution frequency of 7.78% total unigenes. Thereinto, mononucleotides (1200, 45.39%) were the dominant repeat motif, followed by trinucleotides (992, 37.52%), and dinucleotides (410, 15.51%). The most dominant trinucleotide repeat motif was ACC/GGT (207, 20.87%). Based on the identified EST-SSRs, 245 among 1444 designed EST-SSR primers were selected for the development of potential molecular markers. Among these markers, 63 pairs of primers (25.71%) generated clear and reproducible bands with expected sizes. Eventually, 11 primer pairs successfully amplified all individuals from the studied populations. Through the EST-SSR markers, a high level of genetic diversity was detected between Opisthopappus populations. A significant genetic differentiation between the O. longilobus and O. taihangensis populations was found. All studied populations were divided into two clusters by UPGMA, NJ, STRUCTURE, and PCoA. These results fully supported the view of the FRPS, namely, that O. longilobus and O. taihangensis should be regarded as two distinct species. Our study demonstrated that transcriptome sequences, as a valuable tool for the quick and cost-effective development of molecular markers, was helpful toward obtaining comprehensive EST-SSR markers that could contribute to an in-depth assessment of the genetic and phylogenetic relationships between Opisthopappus species.

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Section: Figure 4 | Results Of the Bayesian Clustering Analysis Condusupporting

confidence: 87%

Genetic Divergence and Relationship Among Opisthopappus Species Identified by Development of EST-SSR Markers

Chai

Wang

et al. 2020

Front. Genet.

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“…In fact, both Citrus and Zanthoxylum belong to Rutaceae [25]. The consistent results indicated that Zanthoxylum is a relatively recent species that is predicted to have diverged from Citrus 36.5-37.7 million years ago [1,26].…”

Section: Discussionmentioning

confidence: 67%

“…In summary, a large number of molecular markers were detected in the present study, indicating that high variation might exist in Z. armatum. In a previous study, 11 pairs of primers were used to clearly distinguish Zanthoxylum bungeanum (red Sichuan pepper) from Zanthoxylum armatum (green Sichuan pepper), even differentiating various cultivars [1]. The molecular markers screened in the present study provide rich information and could contribute to the improvement of a molecular marker database that can be used for revealing high polymorphism and multiple alleles and for markerassisted selection breeding in Zanthoxylum species.…”

Section: Discussionmentioning

confidence: 86%

“…Zanthoxylum armatum (Rutaceae), commonly known as green Sichuan pepper, is one of the most economically important trees in Sichuan Province and is widely distributed in most parts of southwest China and some parts of southeast Asia [1]. The production of Z. armatum is currently a billions of dollars commercially, and this species has a long history of cultivation in China because it is one of the eight main spices used in Chinese cuisine and is an essential ingredient in Sichuan hot-pot, with a special numbing taste [2].…”

Section: Introductionmentioning

confidence: 99%

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De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism

et al. 2020

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De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism Abstract Background: Zanthoxylum armatum (Z. armatum) is a highly economically important tree that presents a special numbing taste. However, the underlying regulatory mechanism of the numbing taste remains poorly understood. Thus, the elucidation of the key genes associated with numbing taste biosynthesis pathways is critical for providing genetic information on Z. armatumand the breeding of high-quality germplasms of this species.Results: Here, de novo transcriptome assembly was performed for the five major organs of Z. armatum, including the roots, stems, leaf buds, mature leaves and fruits. A total of 111,318 unigenes were generated with an average length of 1014 bp. Additionally, a large number of SSRs were obtained to improve our understanding of the phylogeny and genetics of Z. armatum. The organ-specific unigenes of the five major samples were screened and annotated via GO and KEGG enrichment analysis. A total of 53 and 34 unigenes that were exclusively upregulated in fruit samples were identified as candidate unigenes for terpenoid biosynthesis or fatty acid biosynthesis, elongation and degradation pathways, respectively. Moreover, 40 days after fertilization (Fr4 stage) could be an important period for the accumulation of terpenoid compounds during the fruit development and maturation of Z. armatum. The Fr4 stage could be a key point at which the first few steps of the fatty acid biosynthesis process are promoted, and the catalysis of subsequent reactions could be significantly induced at 62 days after fertilization (Fr6 stage). Conclusions: The present study realized de novo transcriptome assembly for the five major organs of Z. armatum. To the best of our knowledge, this study provides the first comprehensive analysis revealing the genes underlying the special numbing taste of Z. armatum. The assembled transcriptome profiles expand the available genetic information on this species and will contribute to gene functional studies, which will aid in the engineering of high-quality cultivars of Z. armatum.

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“…Of the 123 567 unigenes, 75.65% were between 201 and 500 bp and 3.04% (4971) of the unigenes were longer than 2000 bp ( Table 2). The data size and unigene number were much larger than a previous study 31 , which generated a more comprehensive transcriptome of Z. bungeanum pericarps.…”

Section: Sequencing and De Novo Assemblymentioning

confidence: 98%

Identification of the candidate genes related to sanshool biosynthesis in Zanthoxylum bungeanum by comparative RNA sequencing analysis

Li¹,

Sun²,

Li³

et al. 2019

ScienceAsia

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Zanthoxylum bungeanum is an edible and medicinal plant with great economic value in East Asia due to high sanshool content in its pericarp. Sanshools not only provide a unique pungency in cuisine, but also have potential for use in anaesthetics, anticancer drugs, and botanical safeners. In this study, to identify the candidate genes related to sanshool biosynthesis, the transcriptomes of pericarps from three developmental stages were comparatively analysed. According to differentially expressed gene (DEG) analysis, 2322 unigenes were upregulated or downregulated significantly among the three types of pericarps and 176 of the DEGs were putative transcription factors (TFs) belonging to 40 TF families. Furthermore, based on the chemical structure of sanshools and unigene annotation, DEGs involved in the pathways of fatty acid biosynthesis and metabolism and amino acid transport were predicted. These DEGs were related to sanshool biosynthesis and 12 candidate enzymes encoded by 18 unigenes were related to the biosynthesis and metabolism of sanshools and identified and classified into three groups. This study provides a global survey of gene expression patterns in pericarp development of Z. bungeanum, which offers clues regarding important regulatory mechanisms, especially with respect to sanshool biosynthesis in the pericarp of Z. bungeanum.

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De novo transcriptome assembly of Zanthoxylum bungeanum using Illumina sequencing for evolutionary analysis and simple sequence repeat marker development

Cited by 38 publications

References 49 publications

Genetic Divergence and Relationship Among Opisthopappus Species Identified by Development of EST-SSR Markers

Genetic Divergence and Relationship Among Opisthopappus Species Identified by Development of EST-SSR Markers

De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism

Identification of the candidate genes related to sanshool biosynthesis in Zanthoxylum bungeanum by comparative RNA sequencing analysis

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