Unraveling vascular development-related genes in laticifer-containing tissue of rubber tree by high-throughput transcriptome sequencing

Tropical rainforests in Southeast Asia are enriched by multifarious biota dominated by Dipterocarpaceae. In this family, Shorea robusta is an ecologically sensitive and economically important timber species whose genomic diversity and phylogeny remain understudied due to lack of datasets on genetic resources. Smattering availability of molecular markers impedes population genetic studies indicating a necessity to develop genomic databases and species-specific markers in S. robusta . Accordingly, the present study focused on fostering de novo low-depth genome sequencing, identification of reliable microsatellites markers, and their validation in various populations of S. robusta in Uttarakhand Himalayas. With 69.88 million raw reads assembled into 1,97,489 contigs (read mapped to 93.2%) and a genome size of 357.11 Mb (29 × coverage), Illumina paired-end sequencing technology arranged a library of sequence data of ~ 10 gigabases (Gb). From 57,702 microsatellite repeats, a total of 35,049 simple sequence repeat (SSR) primer pairs were developed. Afterward, among randomly selected 60 primer pairs, 50 showed successful amplification and 24 were found as polymorphic. Out of which, nine polymorphic loci were further used for genetic analysis in 16 genotypes each from three different geographical locations of Uttarakhand (India). Prominently, the average number of alleles per locus ( N a), observed heterozygosity ( H o), expected heterozygosity ( H e), and the polymorphism information content (PIC) were recorded as 2.44, 0.324, 0.277 and 0.252, respectively. The accessibility of sequence information and novel SSR markers potentially enriches the current knowledge of the genomic background for S. robusta and to be utilized in various genetic studies in species under tribe Shoreae. Supplementary Information The online version contains supplementary material available at 10.1007/s10142-023-00975-8.

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“… 2014 ; Sae-Lim et al. 2019 ); and in angiosperms, such as rose, peony, and olive (Gao et al. 2013 ; Yan et al.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide characterization leading to simple sequence repeat (SSR) markers development in Shorea robusta

Mishra

Meena

Kant

et al. 2023

Funct Integr Genomics

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“…The auxin transporter gene is likely involved in the development of laticifers and other tissues. Previous research has shown that ARF5 and WOX13 , which are associated with the auxin signaling pathway, are highly expressed in newly developed stem tissues of high latex–yield rubber tree clones, suggesting that increased expression of ARF5 and WOX13 may promote laticifer differentiation ( Sae-Lim et al., 2019 ). Most of these genes were expressed in the embryonic axis, where laticifer cells exist.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome analysis reveals the molecular mechanisms of rubber biosynthesis and laticifer differentiation during rubber seed germination

Hu,

Yang,

Zhou

et al. 2024

Front. Plant Sci.

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The molecular mechanisms underlying the initiation of natural rubber synthesis and laticifer differentiation have not been fully elucidated. In this study, we conducted a time-series transcriptome analysis of five rubber tree tissues at four stages of seed germination. A total of 161,199 DEGs were identified between the two groups, including most 16,673 DEGs (A3 vs B3 and A3 vs C3) and lest 1,210 DEGs (C2 vs D2). We found that the maturation of the seed is accompanied by the formation of laticifer cells in cotyledon. Meanwhile, the analysis of hormones related genes expression may provide effective clues for us to promote the differentiation of laticifer cells in seeds by hormones in the future. In this study, hormone-related gene enrichment analyses revealed that IAA, GA, and CTK were activated in laticifer containing tissues. Similarly, GO and GEGG analysis showed that hormone pathways, especially the auxin pathway, are enriched. Gene expression clustering was analyzed using the short time-series expression miner (STEM), and the analysis revealed four distinct trends in the gene expression profiles. Moreover, we enriched transcription factor (TF) enrichment in cotyledon and embryonic axis tissues, and the MYB type exhibited the most significant difference. Furthermore, our findings revealed that genes related to rubber synthesis exhibited tissue-specific expression patterns during seed germination. Notably, key genes associated with rubber biosynthesis, specifically small rubber particle protein (SRPP) and cis-prenyltransferase (CPT), exhibited significant changes in expression in cotyledon and embryonic axis tissues, suggesting synchronous rubber synthesis with seed germination. Our staining results reveled that laticifer cells were exits in the cotyledon before seed imbibition stage. In conclusion, these results lay the foundation for exploring the molecular mechanisms underlying laticifer differentiation and rubber synthesis during seed germination, deepening our understanding of the initiation stages of rubber biosynthesis and laticifer differentiation.

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“…In the trunk bark of tapped Hevea trees, the number of laticifer rings is one to three times more than that observed in un-tapped trees, indicating the stimulating effect of tapping on laticifer differentiation ( Hao and Wu, 1982 ). Meanwhile, both mechanical injury and jasmonic acid induce laticifer differentiation, latex regeneration and production ( Hao and Wu, 2000 ; Sae-Lim et al, 2019 ). Cytologically, latex is the cytoplasm of the laticifers, 90% of the dry weight as rubber hydrocarbon (NR) ( Chrestin et al, 1997 ).…”

Section: Introductionmentioning

confidence: 99%

Transcript and Protein Profiling Provides Insights Into the Molecular Mechanisms of Harvesting-Induced Latex Production in Rubber Tree

Fan

Xiao

et al. 2022

Front. Genet.

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Natural rubber, an important industrial raw material with wide applications, is harvested in the form of latex (cytoplasm of rubber-producing laticifers) from Hevea brasiliensis (para rubber tree) by the way of tapping. Conspicuous stimulation on latex production is observed for the first few tappings conducted on virgin (untapped before) or resting (tapped before but no tapping for a period) rubber trees. To understand the underlying mechanisms, an integrative analysis of the latex transcriptome and proteome was conducted on virgin or resting Hevea trees for the first five tappings. A total of 505 non-redundant differentially expressed (DE) transcript-derived fragments (TDFs) were identified by silver-staining cDNA-AFLP, with 217 exhibiting patterns of upregulated, 180 downregulated and 108 irregularly-regulated. Meanwhile, 117 two dimensional gel electrophoresis DE-protein spots were isolated and subjected to mass spectrometry analysis, with 89 and 57 being successfully identified by MALDI-TOF and MALDI-TOF/TOF, respectively. About 72.5% DE-TDFs and 76.1% DE-proteins were functionally annotated and categorized. Noteworthily, most of the DE-TDFs implicated in sugar transport and metabolism as well as rubber biosynthesis were upregulated by the tapping treatment. The importance of sugar metabolism in harvesting-induced latex production was reinforced by the identification of abundant relevant DE-protein spots. About 83.8% of the randomly selected DE-TDFs were validated for expression patterns by semi-quantitative RT-PCR, and an 89.7% consistency for the 29 latex regeneration-related DE-TDFs examined by quantitative RT-PCR analysis. In brief, our results reveal extensive physiological and molecular changes in Hevea laticifers incurred by the tapping treatment, and the vast number of DE genes and proteins identified here contribute to unraveling the gene regulatory network of tapping-stimulated latex production.

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Unraveling vascular development-related genes in laticifer-containing tissue of rubber tree by high-throughput transcriptome sequencing

Cited by 10 publications

References 98 publications

Genome-wide characterization leading to simple sequence repeat (SSR) markers development in Shorea robusta

Genome-wide characterization leading to simple sequence repeat (SSR) markers development in Shorea robusta

Transcriptome analysis reveals the molecular mechanisms of rubber biosynthesis and laticifer differentiation during rubber seed germination

Transcript and Protein Profiling Provides Insights Into the Molecular Mechanisms of Harvesting-Induced Latex Production in Rubber Tree

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