Reference-based assembly of chloroplast genome from leaf transcriptome data of Pterocarpus santalinus

Coconut palms are categorized into two forms, viz., ‘talls’ and ‘dwarfs’ which are being utilized to produce hybrids through the process of inter-varietal or intra-varietal crosses. Hybrid coconut seedlings are generally identified and selected based on morphological traits by plant breeders, which is quite difficult and requires expertise. Even minor errors in identification may adversely affect breeding programs in coconut, which is spread over many decades. In this study, we have utilized thirty EST-SSR markers, derived from existing coconut leaf transcriptome data, for screening polymorphism between eighteen coconut parental lines. The polymorphic primers capable of differentiating the parental palms were then utilized successfully for assessment of purity of hybrids derived from these parents. Thus, the current study demonstrates the utility of EST-SSR markers in determining the genetic purity of hybrids in coconut.

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Leaf transcriptome data of two tropical medicinal plants: Sterculia lanceolata and Clausena excavata

Data in Brief ◽

10.1016/j.dib.2019.104297 ◽

2019 ◽

Vol 25 ◽

pp. 104297 ◽

Cited By ~ 1

Author(s):

Seok Hyun Eom ◽

Jong-Kuk Na

Keyword(s):

Medicinal Plants ◽

Transcriptome Data ◽

Leaf Transcriptome

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An integrated analysis of mRNA-miRNA transcriptome data revealed hub regulatory networks in three genitourinary cancers

BIOCELL ◽

10.32604/biocell.2017.00019 ◽

2018 ◽

Vol 41 (1) ◽

pp. 19-26 ◽

Cited By ~ 7

Author(s):

M. Liu ◽

X. Zhang

Keyword(s):

Regulatory Networks ◽

Integrated Analysis ◽

Transcriptome Data ◽

Genitourinary Cancers

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Integrated Quantitative Analysis of the Phosphoproteome and Transcriptome in Tamoxifen-resistant Breast Cancer*

10.31234/osf.io/wtxu7 ◽

2020 ◽

Author(s):

Lungwani Muungo

Keyword(s):

Breast Cancer ◽

High Rate ◽

System Level ◽

Clinical Samples ◽

Transcriptome Data ◽

Data Set ◽

Reporter Assays ◽

Treated Breast ◽

Mcf 7 ◽

Resistant Cells

Quantitative phosphoproteome and transcriptome analysisof ligand-stimulated MCF-7 human breast cancer cells wasperformed to understand the mechanisms of tamoxifen resistanceat a system level. Phosphoproteome data revealed thatWT cells were more enriched with phospho-proteins thantamoxifen-resistant cells after stimulation with ligands.Surprisingly, decreased phosphorylation after ligand perturbationwas more common than increased phosphorylation.In particular, 17?-estradiol induced down-regulation inWT cells at a very high rate. 17?-Estradiol and the ErbBligand heregulin induced almost equal numbers of up-regulatedphospho-proteins in WT cells. Pathway and motifactivity analyses using transcriptome data additionallysuggested that deregulated activation of GSK3? (glycogensynthasekinase 3?) and MAPK1/3 signaling might be associatedwith altered activation of cAMP-responsive elementbindingprotein and AP-1 transcription factors intamoxifen-resistant cells, and this hypothesis was validatedby reporter assays. An examination of clinical samples revealedthat inhibitory phosphorylation of GSK3? at serine 9was significantly lower in tamoxifen-treated breast cancerpatients that eventually had relapses, implying that activationof GSK3? may be associated with the tamoxifen-resistantphenotype. Thus, the combined phosphoproteomeand transcriptome data set analyses revealed distinct signal

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Faculty Opinions recommendation of Analysis of the Amborella trichopoda chloroplast genome sequence suggests that amborella is not a basal angiosperm.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1014262.195385 ◽

2003 ◽

Author(s):

David Smyth

Keyword(s):

Chloroplast Genome ◽

Genome Sequence ◽

Basal Angiosperm ◽

Chloroplast Genome Sequence

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Faculty Opinions recommendation of The chloroplast genome of Nymphaea alba: whole-genome analyses and the problem of identifying the most basal angiosperm.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1019893.225486 ◽

2004 ◽

Author(s):

David Smyth

Keyword(s):

Chloroplast Genome ◽

Basal Angiosperm ◽

Whole Genome ◽

Nymphaea Alba ◽

Genome Analyses

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Faculty Opinions recommendation of Reference-free population genomics from next-generation transcriptome data and the vertebrate-invertebrate gap.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718022014.793479111 ◽

2013 ◽

Author(s):

Julin Maloof

Keyword(s):

Population Genomics ◽

Transcriptome Data ◽

Next Generation

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Recombinant Protein Production in Microalgae: Emerging Trends

Protein and Peptide Letters ◽

10.2174/0929866526666191014124855 ◽

2020 ◽

Vol 27 (2) ◽

pp. 105-110 ◽

Cited By ~ 4

Author(s):

Niaz Ahmad ◽

Muhammad Aamer Mehmood ◽

Sana Malik

Keyword(s):

Chloroplast Genome ◽

Recombinant Proteins ◽

Large Scale ◽

Higher Plants ◽

Scale Up ◽

Chloroplast Transformation ◽

Point Of View ◽

Nuclear Transformation ◽

Scale Production ◽

Algal Chloroplast

: In recent years, microalgae have emerged as an alternative platform for large-scale production of recombinant proteins for different commercial applications. As a production platform, it has several advantages, including rapid growth, easily scale up and ability to grow with or without the external carbon source. Genetic transformation of several species has been established. Of these, Chlamydomonas reinhardtii has become significantly attractive for its potential to express foreign proteins inexpensively. All its three genomes – nuclear, mitochondrial and chloroplastic – have been sequenced. As a result, a wealth of information about its genetic machinery, protein expression mechanism (transcription, translation and post-translational modifications) is available. Over the years, various molecular tools have been developed for the manipulation of all these genomes. Various studies show that the transformation of the chloroplast genome has several advantages over nuclear transformation from the biopharming point of view. According to a recent survey, over 100 recombinant proteins have been expressed in algal chloroplasts. However, the expression levels achieved in the algal chloroplast genome are generally lower compared to the chloroplasts of higher plants. Work is therefore needed to make the algal chloroplast transformation commercially competitive. In this review, we discuss some examples from the algal research, which could play their role in making algal chloroplast commercially successful.

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Complete Chloroplast Genome of Japanese Larch (Larix kaempferi): Insights into Intraspecific Variation with an Isolated Northern Limit Population

Forests ◽

10.3390/f11080884 ◽

2020 ◽

Vol 11 (8) ◽

pp. 884

Author(s):

Shufen Chen ◽

Wataru Ishizuka ◽

Toshihiko Hara ◽

Susumu Goto

Keyword(s):

Chloroplast Genome ◽

Intraspecific Variation ◽

Japanese Larch ◽

Monophyletic Group ◽

Phylogenetic Position ◽

Larix Kaempferi ◽

Northern Limit ◽

Complete Chloroplast Genome ◽

Intraspecific Variations ◽

Cpdna Markers

Research Highlights: The complete chloroplast genome for eight individuals of Japanese larch, including from the isolated population at the northern limit of the range (Manokami larch), revealed that Japanese larch forms a monophyletic group, within which Manokami larch can be phylogenetically placed in Japanese larch. We detected intraspecific variation for possible candidate cpDNA markers in Japanese larch. Background and Objectives: The natural distribution of Japanese larch is limited to the mountainous range in the central part of Honshu Island, Japan, with an isolated northern limit population (Manokami larch). In this study, we determined the phylogenetic position of Manokami larch within Japanese larch, characterized the chloroplast genome of Japanese larch, detected intraspecific variation, and determined candidate cpDNA markers. Materials and Methods: The complete genome sequence was determined for eight individuals, including Manokami larch, in this study. The genetic position of the northern limit population was evaluated using phylogenetic analysis. The chloroplast genome of Japanese larch was characterized by comparison with eight individuals. Furthermore, intraspecific variations were extracted to find candidate cpDNA markers. Results: The phylogenetic tree showed that Japanese larch forms a monophyletic group, within which Manokami larch can be phylogenetically placed, based on the complete chloroplast genome, with a bootstrap value of 100%. The value of nucleotide diversity (π) was calculated at 0.00004, based on SNP sites for Japanese larch, suggesting that sequences had low variation. However, we found three hyper-polymorphic regions within the cpDNA. Finally, we detected 31 intraspecific variations, including 19 single nucleotide polymorphisms, 8 simple sequence repeats, and 4 insertions or deletions. Conclusions: Using a distant genotype in a northern limit population (Manokami larch), we detected sufficient intraspecific variation for the possible candidates of cpDNA markers in Japanese larch.

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