Dataset Information

Leaf tissue specific transcriptome sequence and de novo assembly datasets of Asiatic mangrove Rhizophora mucronata Lam.

ABSTRACT: Transcriptome data is beneficial to explore molecular mechanisms of extreme adaptations in non- model organisms like mangroves. In this data article, five major datasets and two data sub sets of a salt secreting mangrove, Rhizophora mucronata Lam. were described. A combination of Illumina HiSeq 2500, Trinity, BLAST X, Bowtie 2 and BLAST 2GO was used for RNA Seq, de novo assembly, transcript annotation, gene expression estimation and gene ontology annotation respectively. The RNA Sequence (Read 1 and Read 2) in Sequence Read Archive amounting to 46,366,348 paired end raw reads is the first data set made open for de novo or comparative transcript assembly. Assembled sequences of 93960 gene transcripts constitute the second data set in Transcriptome Shotgun Assembly. The gene/protein annotations to the assembled transcripts give two sub data sets containing 93960 each of GenBank and GenPept entries with comprehensive cDNA and translated protein sequences of genes. Of these, predicted proteins for 87768 coding sequences, mapped to UniProtKB serve as the third data set. The gene expression levels of the annotated transcripts comprise the fourth data set in Gene Expression Omnibus. The fifth data set in Figshare includes 44,028 gene ontology terms extracted for 21,073 confident transcripts. The data sets provide a valuable resource for further analyses including transcriptomic changes in response to environmental stresses.

SUBMITTER: Meera SP

PROVIDER: S-EPMC7262405 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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Leaf tissue specific transcriptome sequence and de novo assembly datasets of Asiatic mangrove Rhizophora mucronata Lam.

Meera S P SP Sreeshan Anusha A Augustine Anu A

Data in brief 20200522

Transcriptome data is beneficial to explore molecular mechanisms of extreme adaptations in non- model organisms like mangroves. In this data article, five major datasets and two data sub sets of a salt secreting mangrove, Rhizophora mucronata Lam. were described. A combination of Illumina HiSeq 2500, Trinity, BLAST X, Bowtie 2 and BLAST 2GO was used for RNA Seq, de novo assembly, transcript annotation, gene expression estimation and gene ontology annotation respectively. The RNA Se ...[more]

PMID: 32490096

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Project description:Currently, there is a renewed interest towards the development of plant-based pharmacophores. In this work, 16 extracts prepared from the leaves, twigs, roots and fruits of a hydro-halophyte, Rhizophora mucronata Lam. (Family: Rhizophoraceae), were studied for possible antioxidant activity and the phenolic profiles established. Thereafter, enzymatic inhibitory activities (?-amylase, ?-glucosidase, tyrosinase, acetyl- (AChE), butyrylcholinesterase (BChE), lipase, and elastase) were assessed. The total phenolic, flavonoid, phenolic acid, tannin, flavanol and triterpenoid content were estimated using standard assays. An untargeted metabolomics-based approach, based on ultra-high-pressure liquid chromatography coupled to quadrupole-time-of-flight mass spectrometry (UHPLC-QTOF-MS) followed by multivariate statistics, was then used to comprehensively profile and describe the phenolics present. UHPLC-QTOF-MS allowed for putatively annotating 104 phenolic acids, 103 flavonols, 94 flavones, 71 anthocyanins, 66 tyrosols, 29 lignans, 15 alkylphenols and 10 stilbenes in the extracts. Nine strains (Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Methicillin-resistant Staphylococcus aureus (MRSA), Salmonella enteritidis, Sarcina lutea, Proteus mirabilis, Bacillus cereus and Candida albicans) were then used to investigate the antimicrobial properties. The methanolic twig extract exhibited significant reducing potential towards Cu (II)/Cu (I) and Fe (III)/Fe (II) (1336.88 ± 15.70 and 710.18 ± 21.04 mg TE/g, respectively) and was the most potent DPPH radical scavenger (807.07 ± 6.83 mg TE/g). Additionally, the methanolic twig extract showed significant inhibition against most targeted enzymes. Anti-microbial results showed that all extracts were active against MRSA. Multivariate analysis demonstrated that the phenolic profile of ethyl acetate extracts and leaves were the two most discriminative parameters in terms of solvents and organs, respectively. The present findings indicated that R. mucronata may be further explored for the management/prevention of oxidative stress, neurodegenerative complications and hyperpigmentation.

Project description:BACKGROUND:Mangrove forests are ecologically important but globally threatened intertidal plant communities. Effective mangrove conservation requires the determination of species identity, management units, and genetic structure. Here, we investigate the genetic distinctiveness and genetic structure of an iconic but yet taxonomically confusing species complex Rhizophora mucronata and R. stylosa across their distributional range, by employing a suite of 20 informative nuclear SSR markers. RESULTS:Our results demonstrated the general genetic distinctiveness of R. mucronata and R. stylosa, and potential hybridization or introgression between them. We investigated the population genetics of each species without the putative hybrids, and found strong genetic structure between oceanic regions in both R. mucronata and R. stylosa. In R. mucronata, a strong divergence was detected between populations from the Indian Ocean region (Indian Ocean and Andaman Sea) and the Pacific Ocean region (Malacca Strait, South China Sea and Northwest Pacific Ocean). In R. stylosa, the genetic break was located more eastward, between populations from South and East China Sea and populations from the Southwest Pacific Ocean. The location of these genetic breaks coincided with the boundaries of oceanic currents, thus suggesting that oceanic circulation patterns might have acted as a cryptic barrier to gene flow. CONCLUSIONS:Our findings have important implications on the conservation of mangroves, especially relating to replanting efforts and the definition of evolutionary significant units in Rhizophora species. We outlined the genetic structure and identified geographical areas that require further investigations for both R. mucronata and R. stylosa. These results serve as the foundation for the conservation genetics of R. mucronata and R. stylosa and highlighted the need to recognize the genetic distinctiveness of closely-related species, determine their respective genetic structure, and avoid artificially promoting hybridization in mangrove restoration programmes.

Dataset Information

Leaf tissue specific transcriptome sequence and de novo assembly datasets of Asiatic mangrove Rhizophora mucronata Lam.

Publications

Leaf tissue specific transcriptome sequence and <i>de novo</i> assembly datasets of Asiatic mangrove <i>Rhizophora mucronata</i> Lam.

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