scholarly journals Evaluation of rubber tree transcriptome and discovery of SNP and SSR from candidate genes involved in cellulose and lignin biosynthesis

2021 ◽  
Author(s):  
Ahmad Sofiman Othman ◽  
Mohd Fahmi Abu Bakar
Keyword(s):  
Rna Sequencing ◽  
Differential Expression Analysis ◽  
Economic Value ◽  
Rubber Tree ◽  
Lignin Biosynthesis ◽  
Primary Source ◽  
Wood Formation ◽  
Breeding Cycle ◽  
Nucleotide Polymorphisms ◽  
Protein Database

Hevea brasiliensis (the rubber tree) is a well-known species with high economic value, and it is the primary source of natural rubber globally. Increasing demand for furniture and related industries has made rubberwood production as important as latex production. Molecular markers such as Single Nucleotide Polymorphisms (SNPs) and Simple Sequence Repeats (SSRs) are widely used for Marker Assisted Selection (MAS) which can be detected in large quantity by transcriptome sequencing. MAS is thought to be a useful method for the development of new rubberwood clones for its shorter breeding cycle compared to a conventional breeding procedure. In this study we performed RNA sequencing (RNA-seq) on four H. brasiliensis clones (RRIM 712, RRIM 2025, RRIM 3001 and PB 314) from three tissues including bark, latex and leaf samples to identify SSRs and SNPs associated with wood-formation related genes. The RNA sequencing using the Illumina NextSeq 500 v2 platform, generated 1,697,491,922 raw reads. A total of 101,269 transcripts over 400 bp in size were obtained and similarity search of the non-redundant (nr) protein database returned 83,748 (83%) positive BLASTx hits. The transcriptome analysis was annotated using the NCBI NR (National Center for Biotechnology Information Non-Redundant), UniProtKB/Swiss-Prot, gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Differential expression analysis between later-timber rubber clone and non-later-timber rubber clone on wood-formation related genes, showed genes encoding phenylalanine ammonia-lyase (PAL), caffeic acid O-methyltransferase (COMT) and cinnamoyl-CoA reductase (CCR) were highly up-regulated in a latex-timber rubber clone. In total, about 3,210,629 SNPs and 14,956 SSRs were detected with 1,786 SNPs and 31 SSRs were found for wood-formation biosynthesis of H. brasilensis from 11 lignin and cellulose gene toolboxes. After filtering and primer selection, 103 SNPs and 18 SSR markers were successfully amplified and could be useful as molecular tool for marker assisted breeding to produce new timber rubber clones.

scholarly journals RNA Sequencing Reveals Phenylpropanoid Biosynthesis Genes and Transcription Factors for Hevea brasiliensis Reaction Wood Formation

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiangxu Meng ◽  
Yue Wang ◽  
Jia Li ◽  
Nanbo Jiao ◽  
Xiujie Zhang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Rna Sequencing ◽  
Hevea Brasiliensis ◽  
Rubber Tree ◽  
Lignin Biosynthesis ◽  
Wood Formation ◽  
Industrial Applications ◽  
Normal Wood ◽  
Reaction Wood ◽  
Phenylpropanoid Biosynthesis

Given the importance of wood in many industrial applications, much research has focused on wood formation, especially lignin biosynthesis. However, the mechanisms governing the regulation of lignin biosynthesis in the rubber tree (Hevea brasiliensis) remain to be elucidated. Here, we gained insight into the mechanisms of rubber tree lignin biosynthesis using reaction wood (wood with abnormal tissue structure induced by gravity or artificial mechanical treatment) as an experimental model. We performed transcriptome analysis of rubber tree mature xylem from tension wood (TW), opposite wood (OW), and normal wood (NW) using RNA sequencing (RNA-seq). A total of 214, 1,280, and 32 differentially expressed genes (DEGs) were identified in TW vs. NW, OW vs. NW, and TW vs. OW, respectively. GO and KEGG enrichment analysis of DEGs from different comparison groups showed that zeatin biosynthesis, plant hormone signal transduction, phenylpropanoid biosynthesis, and plant–pathogen interaction pathways may play important roles in reaction wood formation. Sixteen transcripts involved in phenylpropanoid biosynthesis and 129 transcripts encoding transcription factors (TFs) were used to construct a TF–gene regulatory network for rubber tree lignin biosynthesis. Among them, MYB, C2H2, and NAC TFs could regulate all the DEGs involved in phenylpropanoid biosynthesis. Overall, this study identified candidate genes and TFs likely involved in phenylpropanoid biosynthesis and provides novel insights into the mechanisms regulating rubber tree lignin biosynthesis.

scholarly journals TheEucalyptuslinker histone variant EgH1.3 cooperates with the transcription factor EgMYB1 to control lignin biosynthesis during wood formation

2016 ◽  
Vol 213 (1) ◽  
pp. 287-299 ◽  
Author(s):  
Marçal Soler ◽  
Anna Plasencia ◽  
Romain Larbat ◽  
Cécile Pouzet ◽  
Alain Jauneau ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Lignin Biosynthesis ◽  
Wood Formation ◽  
Histone Variant

scholarly journals Molecular cloning, functional characterization, tissue expression and polymorphism analysis of buffalo PRDX6 gene

2021 ◽  
Author(s):  
Shengnan Sun ◽  
Gongxuan Chen ◽  
Zhenping Hou ◽  
Xuelei Zhang ◽  
Guitao Jiang ◽  
...  
Keyword(s):  
Small Intestine ◽  
Mammary Gland ◽  
Differential Expression Analysis ◽  
Functional Characterization ◽  
Tissue Expression ◽  
Functional Domain ◽  
Polymorphism Analysis ◽  
River Buffalo ◽  
Nucleotide Polymorphisms ◽  
Lactating Mammary Gland

PRDX6 is a bifunctional protein involved in antioxidant regulation and phospholipid metabolism. Previous studies have shown that PRDX6 is involved in some biological pathways and networks related to lactation. The aim of this study was to explore the characteristics, function, tissue expression and variation of buffalo PRDX6 gene. We cloned and characterized the complete coding sequence (CDS) of buffalo PRDX6. The CDS of PRDX6 for swamp and river buffalo is the same, which consists of 675 nucleotides and encodes a protein of 224 amino acids. Buffalo PRDX6 contains one PRX_1cys functional domain (AA 7–222), which is probably related to the regulation of oxidative stress. Multi-tissue differential expression analysis showed that buffalo PRDX6 was highly expressed in the muscle, brain, lung and small intestine during non-lactation and lactation, and there were significant differences in expression in all the tissues except the small intestine between the two periods. It is worth noting that the mRNA abundance of buffalo PRDX6 in non-lactating mammary gland is higher than that in lactating mammary gland. Among the two single nucleotide polymorphisms (SNPs) identified in the CDS in this study, c.261C>T is shared by the two types of buffalo with different allelic frequencies, and c.426T>G is found only in river buffalo. The c.426T>G is non-synonymous, resulting in the amino acid substitution p.Asn142Lys. Only one nucleotide differential site is identified in PRDX6 gene between buffalo and other species of Bovidae. Phylogenetic analysis indicated that buffalo PRDX6 has a closer genetic relationship with that of the species in Bovidae. These results indicate that PRDX6 probably plays a crucial role in the mammary gland of buffalo. This study provides the foundation for further functional studies of PRDX6 in buffalo.

scholarly journals The genome and transcriptome of the Phalaenopsis yield insights into floral organ development and flowering regulation

2016 ◽  
Author(s):  
Jian-Zhi Huang ◽  
Chih-Peng Lin ◽  
Ting-Chi Cheng ◽  
Ya-Wen Huang ◽  
Yi-Jung Tsai ◽  
...  
Keyword(s):  
Economic Value ◽  
Draft Genome ◽  
Floral Organ ◽  
Cool Temperature ◽  
Organ Development ◽  
Nucleotide Polymorphisms ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
Genome Data ◽  
Expression Of Genes

Phalaenopsis orchid is an important potted flower with high economic value around the world. We report the 3.1 Gb draft genome assembly of an important winter flowering Phalaenopsis ‘KHM190’ cultivar. We generated 89.5 Gb RNA-seq and 113 million sRNA-seq reads to use these data to identify 41,153 protein-coding genes and 188 miRNA families. We also generated a draft genome for Phalaenopsis pulcherrima ‘B8802’, a summer flowering species, via resequencing. Comparison of genome data between the two Phalaenopsis cultivars allowed the identification of 691,532 single-nucleotide polymorphisms. In this study, we reveal the key role of PhAGL6b in the regulation of flower organ development involves alternative splicing. We also show gibberellin pathways that regulate the expression of genes control flowering time during the stage in reproductive phase change induced by cool temperature. Our work should contribute a valuable resource for the flowering control, flower architecture development, and breeding of the Phalaenopsis orchids.

scholarly journals Cloning and Functional Analysis of Lignin Biosynthesis Genes Cf4CL and CfCCoAOMT in Cryptomeria fortunei

Genes ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 619 ◽  
Author(s):  
Zhenhao Guo ◽  
Hui Hua ◽  
Jin Xu ◽  
Jiaxing Mo ◽  
Hui Zhao ◽  
...  
Keyword(s):  
Gene Editing ◽  
Bioinformatics Analysis ◽  
Southern China ◽  
Lignin Biosynthesis ◽  
Wood Formation ◽  
Primary Component ◽  
Vascular Cambium ◽  
Timber Species ◽  
Wood Production ◽  
Lignin Synthesis

Cryptomeria fortunei, also known as the Chinese cedar, is an important timber species in southern China. The primary component of its woody tissues is lignin, mainly present in secondary cell walls. Therefore, continuous lignin synthesis is crucial for wood formation. In this study, we aimed to discover key genes involved in lignin synthesis expressed in the vascular cambium of C. fortunei. Through transcriptome sequencing, we detected expression of two genes, 4CL and CCoAOMT, known to be homologous to enzymes involved in the lignin synthesis pathway. We studied the function of these genes through bioinformatics analysis, cloning, vascular cambium expression analysis, and transgenic cross-species functional validation studies. Our results show that Cf4CL and CfCCoAOMT do indeed function in the pathway of lignin synthesis and likely perform this function in C. fortunei. They are prime candidates for future (gene-editing) studies aimed at optimizing C. fortunei wood production.

scholarly journals Global Transcriptomic Profile Analysis of Genes Involved in Lignin Biosynthesis and Accumulation Induced by Boron Deficiency in Poplar Roots

Biomolecules ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 156 ◽  
Author(s):  
Wan-Long Su ◽  
Na Liu ◽  
Li Mei ◽  
Jie Luo ◽  
Yi-Jie Zhu ◽  
...  
Keyword(s):  
Histidine Kinase ◽  
Theoretical Basis ◽  
Reference Data ◽  
Profile Analysis ◽  
Expression Patterns ◽  
Lignin Biosynthesis ◽  
Wood Formation ◽  
Boron Deficiency ◽  
Rna Seq ◽  
Lignin Accumulation

To uncover the transcriptomic mechanism of lignin accumulation caused by boron deficiency (BD), Nanlin895 (Populus × euramericana “Nanlin895”) was subjected to control (CK, 0.25 mg·L−1) and BD (0 mg·L−1) treatments for 3 days. RNA-Seq was carried out to survey the expression patterns of the lignin-regulated biosynthetic genes in response to BD. The results showed that 5946 genes were identified as differentially expressed genes (DEGs), 2968 (44.2%) of which were upregulated and 3318 (55.8%) of which were downregulated in response to BD. Among them, the expression of lignin monomer biosynthetic (PAL, CCR, CAD, COMT, F5H, PER/LAC) and modulated genes, for example, transcription factors (MYBs) and hormone signal regulating genes (GIDs, histidine kinase 1, coronatine-insensitive protein 1), were upregulated, and some hormone signal regulating genes, such as AUXs and BR-related (sterol methyltransferases), were downregulated under BD treatment. There are also some genes that were screened as candidates for an association with wood formation, which will be used for the further analysis of the function of lignin formation. These results provide an important theoretical basis and reference data in plant for further research on the mechanism of lignin accumulation under BD.

scholarly journals Genetic analysis of the molecular regulation of electric fields-guided glia migration

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Li Yao ◽  
Teresa Shippy ◽  
Yongchao Li
Keyword(s):  
Cell Migration ◽  
Rna Sequencing ◽  
Electric Fields ◽  
Differential Expression Analysis ◽  
Cell Types ◽  
Molecular Regulation ◽  
Sequencing Data ◽  
Oligodendrocyte Precursor ◽  
Go Terms ◽  
Developing Nervous System

Abstract In a developing nervous system, endogenous electric field (EF) influence embryonic growth. We reported the EF-directed migration of both rat Schwann cells (SCs) and oligodendrocyte precursor cells (OPCs) and explored the molecular mechanism using RNA-sequencing assay. However, previous studies revealed the differentially expressed genes (DEGs) associated with EF-guided migration of SCs or OPCs alone. In this study, we performed joint differential expression analysis on the RNA-sequencing data from both cell types. We report a number of significantly enriched gene ontology (GO) terms that are related to the cytoskeleton, cell adhesion, and cell migration. Of the DEGs associated with these terms, nine up-regulated DEGs and 32 down-regulated DEGs showed the same direction of effect in both SCs and OPCs stimulated with EFs, while the remaining DEGs responded differently. Thus, our study reveals the similarities and differences in gene expression and cell migration regulation of different glial cell types in response to EF stimulation.

scholarly journals Transcriptomics in Toxicogenomics, Part II: Preprocessing and Differential Expression Analysis for High Quality Data

Nanomaterials ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 903 ◽  
Author(s):  
Antonio Federico ◽  
Angela Serra ◽  
My Kieu Ha ◽  
Pekka Kohonen ◽  
Jang-Sik Choi ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Differential Expression Analysis ◽  
Enrichment Analysis ◽  
Data Preprocessing ◽  
Functional Enrichment Analysis ◽  
Toxicity Assessment ◽  
Functional Enrichment ◽  
Quality Data ◽  
Chemical Toxicity ◽  
Transcriptomics Data

Preprocessing of transcriptomics data plays a pivotal role in the development of toxicogenomics-driven tools for chemical toxicity assessment. The generation and exploitation of large volumes of molecular profiles, following an appropriate experimental design, allows the employment of toxicogenomics (TGx) approaches for a thorough characterisation of the mechanism of action (MOA) of different compounds. To date, a plethora of data preprocessing methodologies have been suggested. However, in most cases, building the optimal analytical workflow is not straightforward. A careful selection of the right tools must be carried out, since it will affect the downstream analyses and modelling approaches. Transcriptomics data preprocessing spans across multiple steps such as quality check, filtering, normalization, batch effect detection and correction. Currently, there is a lack of standard guidelines for data preprocessing in the TGx field. Defining the optimal tools and procedures to be employed in the transcriptomics data preprocessing will lead to the generation of homogeneous and unbiased data, allowing the development of more reliable, robust and accurate predictive models. In this review, we outline methods for the preprocessing of three main transcriptomic technologies including microarray, bulk RNA-Sequencing (RNA-Seq), and single cell RNA-Sequencing (scRNA-Seq). Moreover, we discuss the most common methods for the identification of differentially expressed genes and to perform a functional enrichment analysis. This review is the second part of a three-article series on Transcriptomics in Toxicogenomics.

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