Leaf Transcriptome Assembly of Protium copal (Burseraceae) and Annotation of Terpene Biosynthetic Genes

Damasco, Gabriel; Shivakumar, Vikram; Misciewicz, Tracy M.; Daly, Douglas C.; Fine, Paul V. A.

doi:10.3390/genes10050392

Cited by 7 publications

(4 citation statements)

References 47 publications

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“…Instead, it is much more plausible that long distance dispersal into novel habitats and geographic areas was likely the catalyst for initial population isolation followed by lineage 29 divergence. This hypothesis is in line with other studies of diversification of Amazonian taxa, including studies of within species diversification (Damasco et al, 2019;Dexter et al, 2017;Roncal et al, 2015;and discussed in Dick and Pennington, 2019). For instance, a phylogeographic study by Roncal et al (2015) suggested that Astrocaryum sect.…”

Section: Lineage Diversification In Common and Widespread Amazonian T...supporting

confidence: 90%

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Parallel evolution and cryptic diversification in the common and widespread Amazonian tree, Protium subserratum

Misiewicz

Simmons

Carter

et al. 2022

Preprint

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The lowland Amazon rainforest houses some of the greatest tree diversity on earth. While the vast majority of these species are rare, a small number are common and widespread and thus considered to play a disproportionate role in many of the global ecosystem services provided by the Amazon. However, the extent to which dominant Amazonian tree species actually include multiple clades, each on their own unique evolutionary trajectory, is unknown. Here we investigate the extent to which lineage divergence may be occurring within Protium subserratum (Burseraceae), a common and widespread tree species that is monophyletic with populations exhibiting genotypic and phenotypic differences associated with soil and geography. Utilizing a combination of phylogenomic and population genomic methods with sampling from across the range, we found that P. subserratum contains at least eight distinct clades. Specialization onto white-sand soils has evolved independently at least two times within the species; however, phenotype is not correlated with soil type. Finally, cryptic diversity at the base of the Andes is associated with elevational shifts. Together these results lend support to the hypothesis that common and widespread Amazon tree species may not represent evolutionary cohesive units. Instead, these dominant species may more commonly represent species complexes, undergoing evolutionary transitions on a trajectory to become multiple range restricted, specialist species.

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Section: Lineage Diversification In Common and Widespread Amazonian T...supporting

confidence: 90%

“…Engl. (Damasco et al, 2019) et al, 2014). Detailed methods are provided in the Supplementary Materials.…”

Section: Bait Designmentioning

confidence: 99%

Parallel evolution and cryptic diversification in the common and widespread Amazonian tree, Protium subserratum

Misiewicz

Simmons

Carter

et al. 2022

Preprint

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“…In this study, in total, 21 terpenoids were detected ( Table 1 ). Although the genes involved in terpenoid biosynthesis are widely studied in different plants [ 20 , 27 , 28 , 29 , 30 , 31 , 32 , 33 ], genes related to the synthesis of terpenoids in sacred lotus have not been studied so far. The precursors of monoterpenes and diterpenes come from the MEP pathway in plastids, while the precursors of sesquiterpenes and triterpenes come from the MVA pathway in the cytoplasm [ 34 ].…”

Section: Discussionmentioning

confidence: 99%

Transcriptome Analyses Revealed the Key Metabolic Genes and Transcription Factors Involved in Terpenoid Biosynthesis in Sacred Lotus

Qin

Yang

et al. 2022

Molecules

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As the largest group of structurally diverse metabolites, terpenoids are versatile natural compounds that act as metabolism mediators, plant volatiles, and ecological communicators. However, few terpenoid compounds have been identified in plant parts of sacred lotus (Nelumbo nucifera Gaertn.). To elucidate the molecular genetic basis of the terpene biosynthetic pathway, terpenes from different parts of the plant, including seeds (S), young leaves (YL), mature leaves (ML), white flowers (WF), yellow flowers (YF), and red flowers (RF), were identified by LC-MS/MS and the relative contents of the same terpenes in different parts were compared. The results indicate that all plant parts primarily consist of triterpenes, with only minor quantities of sesquiterpenes and diterpenes, and there were differences in the terpene content detected in different plant parts. To illustrate the biosynthesis of various terpenoids, RNA sequencing was performed to profile the transcriptomes of various plant parts, which generated a total of 126.95 GB clean data and assembled into 29,630 unigenes. Among these unigenes, 105 candidate unigenes are involved in the mevalonate (MVA) pathway, methyl-erythritol phosphate (MEP) pathway, terpenoid backbone biosynthesis pathway, and terpenoid synthases pathway. Moreover, the co-expression network between terpene synthase (TPS) and WRKY transcription factors provides new information for the terpene biosynthesis pathway.

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“…The clean reads were used to determine alignment counts and to quantify transcript abundance by the RSEM (RNA-seq by Expectation Maximizattion, http://deweylab.github.io/RSEM/) package [37]. The unigene and transcript abundance levels were analyzed by TPM (transcripts per million reads) [38].…”

Section: Differential Transcript Abundance Analysismentioning

confidence: 99%

Transcriptome Assembly and Gene Expression Analysis of Leaf and Rhizome tissues of Dioscorea opposita

DianYun¹,

Cheng²,

Li³

et al. 2020

Preprint

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Background: Dioscorea opposita is a monocotyledonous plant in the Dioscoreaceae family. The rhizome of D. opposita, known as “dioscoreae rhiaoma” or “Chinese yam”, is not only a well-known traditional Chinese medicine, but also a popular health food.Methods:In this study, the leaf and rhizome tissues of D. opposita were collected. Their transcriptome sequenceand were obtained using an Illumina Hiseq 4000 platform. The data was analyzed by bioinformatics software. Likewise, the consistent expression pattern of DEGs was validated with qRT-PCR analysis.Results: A total of 46,982,031 and 53,689,620 clean reads from leaf and rhizome tissues were acquired, respectively (SRP: PRJNA628588). 50,765 unigenes were obtained with an average length of 1050 base pairs (bp). A total of 13,259 significant differentially expressed genes (DEGs) were obtained from leaf versus rhizome tissues, including 5536 up-regulated and 7723 down-regulated unigenes. In addition, 20,607 simple sequence repeats (SSRs) were identified in this study. Conclusions:This study not only enriched the transcriptomic data of D. opposita, but also laid a foundation for the analysis of terpenoid synthesis pathway.

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Leaf Transcriptome Assembly of Protium copal (Burseraceae) and Annotation of Terpene Biosynthetic Genes

Cited by 7 publications

References 47 publications

Parallel evolution and cryptic diversification in the common and widespread Amazonian tree, Protium subserratum

Parallel evolution and cryptic diversification in the common and widespread Amazonian tree, Protium subserratum

Transcriptome Analyses Revealed the Key Metabolic Genes and Transcription Factors Involved in Terpenoid Biosynthesis in Sacred Lotus

Transcriptome Assembly and Gene Expression Analysis of Leaf and Rhizome tissues of Dioscorea opposita

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