Identification of tissue-specific gene clusters and orthologues of nodulation-related genes in Vigna angularis

2014 ◽  
Vol 12 (S1) ◽  
pp. S21-S26 ◽  
Author(s):  
Yang Jae Kang ◽  
Jayern Lee ◽  
Yong Hwan Kim ◽  
Suk-Ha Lee
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Lotus Japonicus ◽  
Gene Clusters ◽  
Specific Gene ◽  
Vigna Angularis ◽  
Model Legume ◽  
Tissue Specific ◽  
Autoregulation Of Nodulation ◽  
Species Specific

Nitrogen fixation in legumes is an important agricultural trait that results from symbiosis between the root and rhizobia. To understand the molecular basis of nodulation, recent research has been focused on the identification of nodulation-related genes by functional analysis using two major model legumes, Medicago truncatula and Lotus japonicus. Thus far, three important processes have been discovered, namely Nod factor (NF) perception, NF signalling and autoregulation of nodulation. Nevertheless, application of the results of these studies is limited for non-model legume crops because a reference genome is unavailable. However, because the cost of whole-transcriptome analysis has dropped dramatically due to the Next generation sequencer (NGS) technology, minor crops for which reference sequences are yet to be constructed can still be studied at the genome level. In this study, we sequenced the leaf and root transcriptomes of Vigna angularis (accession IT213134) and de novo assembled. Our results demonstrate the feasibility of using the transcriptome assembly to effectively identify tissue-specific peptide clusters related to tissue-specific functions and species-specific nodulation-related genes.

scholarly journals Mosaic Genes and Mosaic Chromosomes: Intra- and Interspecies Genomic Variation of Streptococcus pneumoniae

2001 ◽  
Vol 69 (4) ◽  
pp. 2477-2486 ◽  
Author(s):  
Regine Hakenbeck ◽  
Nadège Balmelle ◽  
Beate Weber ◽  
Christophe Gardès ◽  
Wolfgang Keck ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Gene Pool ◽  
Reference Strain ◽  
Gene Clusters ◽  
Genomic Variation ◽  
Smooth Transition ◽  
Oligonucleotide Array ◽  
Specific Gene ◽  
Antibiotic Resistant ◽  
Species Specific

ABSTRACT Streptococcus pneumoniae remains a major causative agent of serious human diseases. The worldwide increase of antibiotic resistant strains revealed the importance of horizontal gene transfer in this pathogen, a scenario that results in the modulation of the species-specific gene pool. We investigated genomic variation in 20S. pneumoniae isolates representing major antibiotic-resistant clones and 10 different capsular serotypes. Variation was scored as decreased hybridization signals visualized on a high-density oligonucleotide array representing 1,968 genes of the type 4 reference strain KNR.7/87. Up to 10% of the genes appeared altered between individual isolates and the reference strain; variability within clones was below 2.1%. Ten gene clusters covering 160 kb account for half of the variable genes. Most of them are associated with transposases and are assumed to be part of a flexible gene pool within the bacterial population; other variable loci include mosaic genes encoding antibiotic resistance determinants and gene clusters related to bacteriocin production. Genomic comparison between S. pneumoniae and commensal Streptococcus mitis andStreptococcus oralis strains indicates distinct antigenic profiles and suggests a smooth transition between these species, supporting the validity of the microarray system as an epidemiological and diagnostic tool.

scholarly journals De novo transcriptome assembly of two Vigna angularis varieties collected from Korea

Genomics Data ◽  
2016 ◽  
Vol 8 ◽  
pp. 119-120 ◽  
Author(s):  
Yeonhwa Jo ◽  
Sen Lian ◽  
Jin Kyong Cho ◽  
Hoseong Choi ◽  
Sang-Min Kim ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
De Novo Transcriptome Assembly ◽  
Vigna Angularis ◽  
De Novo Transcriptome

scholarly journals Comparative transcriptomics of seven Impatiens species

2021 ◽  
Author(s):  
Mária Šurinová ◽  
Štepán Stočes ◽  
Tomáš Dostálek ◽  
Andrea Jarošová ◽  
Zuzana Münzbergová
Keyword(s):  
De Novo ◽  
Protein Structures ◽  
Natural Populations ◽  
Gene Families ◽  
Single Species ◽  
Distinct Species ◽  
Species Group ◽  
Specific Gene ◽  
Flowering Regulation ◽  
Species Specific

AbstractImpatiens is a genus containing more than 1000 species. Thanks to its size, it is a unique system for studying species diversification in natural populations. This study focused on the characterization of novel transcriptomes from seven Impatiens species originating from Nepal. Leave transcriptome of Impatines balsamina L., I. racemosa DC., I. bicornuta Wall, I. falcifer Hook, I. devendrae Pusalkar, I. scullyi Hook and I. scabrida DC were sequenced and compared. Reads were de novo assembled and aligned to 92 035-226 081 contigs. We identified 14 728 orthology groups shared among all the species and 3 020 which were unique to a single species. In single species, 2536-3009 orthology groups were under selection from which 767 were common for all species. Six of the seven investigated species shared 77% of gene families with I. bicornuta being the most distinct species. Specific gene families involved in response to different environmental stimuli were closely described. Impatiens bicornuta selection profile shared selection on zing finger protein structures and flowering regulation and stress response proteins with the other investigated species. Overall, the study showed substantial similarity in patterns of selections on transcribed genes across the species suggesting similar evolutionary pressures. This suggests that the species group may have evolved via adaptive radiation.

scholarly journals Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in Mallotus japonicus

2021 ◽  
Vol 22 (16) ◽  
pp. 8835
Author(s):  
Megha Rai ◽  
Amit Rai ◽  
Tetsuya Mori ◽  
Ryo Nakabayashi ◽  
Manami Yamamoto ◽  
...  
Keyword(s):  
Candidate Genes ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Biological Properties ◽  
Bioactive Metabolites ◽  
Tissue Specific ◽  
Specialized Metabolites ◽  
Manual Curation ◽  
Specific Accumulation ◽  
Mallotus Japonicus

Mallotus japonicus is a valuable traditional medicinal plant in East Asia for applications as a gastrointestinal drug. However, the molecular components involved in the biosynthesis of bioactive metabolites have not yet been explored, primarily due to a lack of omics resources. In this study, we established metabolome and transcriptome resources for M. japonicus to capture the diverse metabolite constituents and active transcripts involved in its biosynthesis and regulation. A combination of untargeted metabolite profiling with data-dependent metabolite fragmentation and metabolite annotation through manual curation and feature-based molecular networking established an overall metabospace of M. japonicus represented by 2129 metabolite features. M. japonicus de novo transcriptome assembly showed 96.9% transcriptome completeness, representing 226,250 active transcripts across seven tissues. We identified specialized metabolites biosynthesis in a tissue-specific manner, with a strong correlation between transcripts expression and metabolite accumulations in M. japonicus. The correlation- and network-based integration of metabolome and transcriptome datasets identified candidate genes involved in the biosynthesis of key specialized metabolites of M. japonicus. We further used phylogenetic analysis to identify 13 C-glycosyltransferases and 11 methyltransferases coding candidate genes involved in the biosynthesis of medicinally important bergenin. This study provides comprehensive, high-quality multi-omics resources to further investigate biological properties of specialized metabolites biosynthesis in M. japonicus.

scholarly journals RNA-Sequencing based gene expression landscape of guava cv. Allahabad Safeda and comparative analysis to colored cultivars

2020 ◽  
Author(s):  
Amandeep Mittal ◽  
Inderjit Singh Yadav ◽  
Naresh Kumar Arora ◽  
Rajbir Singh Boora ◽  
Meenakshi Mittal ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Rna Sequencing ◽  
Fruit Development ◽  
De Novo ◽  
Transcriptome Assembly ◽  
White Pulp ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome ◽  
Tissue Specific

Abstract Background Guava ( Psidium guajava L.) is an important fruit crop of tropical and subtropical areas of the world. Genomics resources in guava are scanty. RNA-Seq based tissue specific expressed genomic information, de novo transcriptome assembly, functional annotation and differential expression among contrasting genotypes has potential to set the stage for the functional genomics for traits of commerce. Results Development of fruit from flower involves orchestration of myriad molecular switches. We did comparative transcriptome sequencing on leaf, flower and fruit tissues of cv. Allahabad Safeda to understand important genes and pathways controlling fruit development. Tissue specific RNA sequencing and de novo transcriptome assembly using Trinity pipeline provided us the first reference transcriptome for guava consisting of 84,206 genes comprising 279,792 total transcripts with N50 of 3,603 bp. Blast2GO assigned annotation to 116,629 transcripts and PFam based HMM profile annotated 140,061 transcripts with protein domains. Differential expression with EdgeR identified 3033 genes in Allahabad Safeda tissues and 68 genes among colored tissue comparisons. Mapping the differentially expressed transcripts over molecular pathways indicate significant hormonal changes during fruit development. Comparisons of red vs green peel in guava cv. Apple Colour, white pulp vs red pulp in Punjab pink and fruit maturation vs ripening in non-coloured Allahabad Safeda indicates up-regulation of ethylene biosynthesis accompanied to secondary metabolism like phenylpropanoid and monolignol pathways. Conclusions Benchmarking Universal Single-Copy Orthologs analysis of de novo transcriptome of guava with eudicots identified 93.7% complete BUSCO genes. In silico differential gene expression among tissue types of Allahabad Safeda and validation of candidate genes with qRT-PCR in contrasting colour genotypes promises the utility of this first guava transcriptome for its potential of tapping the genetic elements from germplasm collections for enhancing fruit traits.

scholarly journals De novo transcriptome assembly from the gonads of a scleractinian coral, Euphyllia ancora: Molecular mechanisms underlying scleractinian gametogenesis

2020 ◽  
Author(s):  
Yi-Ling Chiu ◽  
Shinya Shikina ◽  
Yuki Yoshioka ◽  
Chuya Shinzato ◽  
Ching-Fong Chang
Keyword(s):  
Sperm Motility ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Expression Profiles ◽  
Molecular Characteristics ◽  
Specific Gene ◽  
Ecological Data ◽  
Developmental Phases ◽  
Upregulated Genes

Abstract Background: Sexual reproduction of scleractinians has captured the attention of researchers and the general public for decades. Although extensive ecological data has been acquired, underlying molecular and cellular mechanisms remain largely unknown. In this study, to better understand mechanisms underlying gametogenesis, we isolated ovaries and testes at different developmental phases from a gonochoric coral, Euphyllia ancora , and adopted a transcriptomic approach to reveal sex- and phase-specific gene expression profiles. In particular, we explored genes associated with oocyte development and maturation, spermiogenesis, sperm motility / capacitation, and fertilization.Results: 1.6 billion raw reads were obtained from 24 gonadal samples. De novo assembly of trimmed reads, and elimination of contigs derived from symbiotic dinoflagellates (Symbiodiniaceae) and other organisms yielded a reference E. ancora gonadal transcriptome of 35,802 contigs. Analysis of 4 developmental phases identified 2,023 genes that were differentially expressed during oogenesis and 678 during spermatogenesis. In premature/mature ovaries, 631 genes were specifically upregulated, with 538 in mature testes. Upregulated genes included those involved in gametogenesis, gamete maturation, sperm motility / capacitation, and fertilization in other metazoans, including humans. Meanwhile, a large number of genes without homology to sequences in the SWISS-PROT database were also observed among upregulated genes in premature / mature ovaries and mature testes.Conclusions: Our findings show that scleractinian gametogenesis shares many molecular characteristics with that of other metazoans, but it also possesses unique characteristics developed during cnidarian and/or scleractinian evolution. To the best of our knowledge, this study is the first to create a gonadal transcriptome assembly from any scleractinian. This study and associated datasets provide a foundation for future studies regarding gametogenesis and differences between male and female colonies from molecular and cellular perspectives. Furthermore, our transcriptome assembly will be a useful reference for future development of sex-specific and/or stage-specific germ cell markers that can be used in coral aquaculture and ecological studies.

scholarly journals The structure and activity of nodulation-suppressing CLE peptide hormones of legumes

2015 ◽  
Vol 42 (3) ◽  
pp. 229 ◽  
Author(s):  
April H. Hastwell ◽  
Peter M. Gresshoff ◽  
Brett J. Ferguson
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Lotus Japonicus ◽  
Peptide Hormones ◽  
Negative Feedback Loops ◽  
C Terminus ◽  
Cle Peptides ◽  
Autoregulation Of Nodulation ◽  
Cle Peptide ◽  
External Stimuli

Legumes form a highly-regulated symbiotic relationship with specific soil bacteria known as rhizobia. This interaction results in the de novo formation of root organs called nodules, in which the rhizobia fix atmospheric di-nitrogen (N2) for the plant. Molecular mechanisms that regulate the nodulation process include the systemic ‘autoregulation of nodulation’ and the local nitrogen-regulation of nodulation pathways. Both pathways are mediated by novel peptide hormones called CLAVATA/ESR-related (CLE) peptides that act to suppress nodulation via negative feedback loops. The mature peptides are 12–13 amino acids in length and are post-translationally modified from the C-terminus of tripartite-domain prepropeptides. Structural redundancy between the prepropeptides exists; however, variations in external stimuli, timing of expression, tissue specificity and presence or absence of key functional domains enables them to act in a specific manner. To date, nodulation-regulating CLE peptides have been identified in Glycine max (L.) Merr., Medicago truncatula Gaertn., Lotus japonicus (Regel) K.Larsen and Phaseolus vulgaris L. One of the L. japonicus peptides, called LjCLE-RS2, has been structurally characterised and found to be an arabinosylated glycopeptide. All of the known nodulation CLE peptides act via an orthologous leucine rich repeat (LRR) receptor kinase. Perception of the peptide results in the production of a novel, unidentified inhibitor signal that acts to suppress further nodulation events. Here, we contrast and compare the various nodulation-suppressing CLE peptides of legumes.

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