Tissue-specific transcriptome for Rheum tanguticum reveals candidate genes related to the anthraquinones biosynthesis

AbstractPheromones known as cuticular hydrocarbons are a major component of reproductive isolation in Drosophila. Individuals from morphologically similar sister species produce different sets of hydrocarbons that allow potential mates to identify them as a suitable partner. In order to explore the molecular mechanisms underlying speciation, we performed RNA-seq in F1 hybrids to measure tissue-specific cis-regulatory divergence between the sister species D. simulans and D. sechellia. By focusing on cis-regulatory changes specific to female oenocytes, we rapidly identified a small number of candidate genes. We found that one of these, the fatty acid elongase eloF, broadly affects both the complement of hydrocarbons present on D. sechellia females and the propensity of D. simulans males to mate with those females. In addition, knockdown of eloF in the more distantly related D. melanogaster led to a similar shift in hydrocarbons as well as lower interspecific mate discrimination by D. simulans males. Thus, cis-regulatory changes in eloF appear to be a major driver in the sexual isolation of D. simulans from multiple other species. More generally, our RNA-seq approach proved to be far more efficient than QTL mapping in identifying candidate genes; the same framework can be used to pinpoint cis-regulatory drivers of divergence in a wide range of traits differing between any interfertile species.

Download Full-text

Genetic and Transcription Profile Analysis of Tissue-Specific Anthocyanin Pigmentation in Carrot Root Phloem

Genes ◽

10.3390/genes12101464 ◽

2021 ◽

Vol 12 (10) ◽

pp. 1464

Author(s):

Florencia Bannoud ◽

Sofia Carvajal ◽

Shelby Ellison ◽

Douglas Senalik ◽

Sebastian Gomez Talquenca ◽

...

Keyword(s):

Candidate Genes ◽

Profile Analysis ◽

Phylogenetic Analyses ◽

Cellular Transport ◽

Mads Box ◽

Anthocyanin Pigmentation ◽

Carrot Root ◽

Tissue Specific ◽

F2 Population ◽

Genomic Regions

In purple carrots, anthocyanin pigmentation can be expressed in the entire root, or it can display tissue specific-patterns. Within the phloem, purple pigmentation can be found in the outer phloem (OP) (also called the cortex) and inner phloem (IP), or it can be confined exclusively to the OP. In this work, the genetic control underlying tissue-specific anthocyanin pigmentation in the carrot root OP and IP tissues was investigated by means of linkage mapping and transcriptome (RNA-seq) and phylogenetic analyses; followed by gene expression (RT-qPCR) evaluations in two genetic backgrounds, an F2 population (3242) and the inbred B7262. Genetic mapping of ‘root outer phloem anthocyanin pigmentation’ (ROPAP) and inner phloem pigmentation (RIPAP) revealed colocalization of ROPAP with the P1 and P3 genomic regions previously known to condition pigmentation in different genetic stocks, whereas RIPAP co-localized with P3 only. Transcriptome analysis of purple OP (POP) vs. non-purple IP (NPIP) tissues, along with linkage and phylogenetic data, allowed an initial identification of 28 candidate genes, 19 of which were further evaluated by RT-qPCR in independent root samples of 3242 and B7262, revealing 15 genes consistently upregulated in the POP in both genetic backgrounds, and two genes upregulated in the POP in specific backgrounds. These include seven transcription factors, seven anthocyanin structural genes, and two genes involved in cellular transport. Altogether, our results point at DcMYB7, DcMYB113, and a MADS-box (DCAR_010757) as the main candidate genes conditioning ROPAP in 3242, whereas DcMYB7 and MADS-box condition RIPAP in this background. In 7262, DcMYB113 conditions ROPAP.

Download Full-text

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

International Journal of Molecular Sciences ◽

10.3390/ijms22168835 ◽

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.

Download Full-text

Comparative molecular analyses of select pH- and osmoregulatory genes in three freshwater crayfishCherax quadricarinatus,C. destructorandC. cainii

PeerJ ◽

10.7717/peerj.3623 ◽

2017 ◽

Vol 5 ◽

pp. e3623

Author(s):

Muhammad Y. Ali ◽

Ana Pavasovic ◽

Lalith K. Dammannagoda ◽

Peter B. Mather ◽

Peter J. Prentis

Keyword(s):

Candidate Genes ◽

Molecular Analysis ◽

Expression Analysis ◽

Sequence Conservation ◽

Neutral Evolution ◽

Tissue Type ◽

Specific Expression ◽

Tissue Specific ◽

Tissue Specific Expression ◽

High Level

Systemic acid-base balance and osmotic/ionic regulation in decapod crustaceans are in part maintained by a set of transport-related enzymes such as carbonic anhydrase (CA), Na+/K+-ATPase (NKA), H+-ATPase (HAT), Na+/K+/2Cl−cotransporter (NKCC), Na+/Cl−/HCO${}_{3}^{-}$ cotransporter (NBC), Na+/H+exchanger (NHE), Arginine kinase (AK), Sarcoplasmic Ca+2-ATPase (SERCA) and Calreticulin (CRT). We carried out a comparative molecular analysis of these genes in three commercially important yet eco-physiologically distinct freshwater crayfish, Cherax quadricarinatus, C. destructorandC. cainii, with the aim to identify mutations in these genes and determine if observed patterns of mutations were consistent with the action of natural selection. We also conducted a tissue-specific expression analysis of these genes across seven different organs, including gills, hepatopancreas, heart, kidney, liver, nerve and testes using NGS transcriptome data. The molecular analysis of the candidate genes revealed a high level of sequence conservation across the threeCherax sp.Hyphy analysis revealed that all candidate genes showed patterns of molecular variation consistent with neutral evolution. The tissue-specific expression analysis showed that 46% of candidate genes were expressed in all tissue types examined, while approximately 10% of candidate genes were only expressed in a single tissue type. The largest number of genes was observed in nerve (84%) and gills (78%) and the lowest in testes (66%). The tissue-specific expression analysis also revealed that most of the master genes regulating pH and osmoregulation (CA, NKA, HAT, NKCC, NBC, NHE) were expressed in all tissue types indicating an important physiological role for these genes outside of osmoregulation in other tissue types. The high level of sequence conservation observed in the candidate genes may be explained by the important role of these genes as well as potentially having a number of other basic physiological functions in different tissue types.

Download Full-text

Tissue-Specific Transcriptome Analysis Reveals Candidate Genes for Terpenoid and Phenylpropanoid Metabolism in the Medicinal Plant Ferula assafoetida

G3 Genes|Genome|Genetics ◽

10.1534/g3.118.200852 ◽

2019 ◽

pp. g3.200852.2018 ◽

Cited By ~ 1

Author(s):

Hajar Amini ◽

Mohammad Reza Naghavi ◽

Tong Shen ◽

Yanhong Wang ◽

Jaber Nasiri ◽

...

Keyword(s):

Medicinal Plant ◽

Candidate Genes ◽

Transcriptome Analysis ◽

Phenylpropanoid Metabolism ◽

Tissue Specific ◽

Ferula Assafoetida

Download Full-text

A tissue-specific collaborative mixed model for jointly analyzing multiple tissues in transcriptome-wide association studies

Nucleic Acids Research ◽

10.1093/nar/gkaa767 ◽

2020 ◽

Vol 48 (19) ◽

pp. e109-e109

Author(s):

Xingjie Shi ◽

Xiaoran Chai ◽

Yi Yang ◽

Qing Cheng ◽

Yuling Jiao ◽

...

Keyword(s):

Candidate Genes ◽

Complex Traits ◽

Mixed Model ◽

Target Genes ◽

Association Studies ◽

Tissue Specific ◽

Candidate Target ◽

Different Tissues ◽

Trait Associations

Abstract Transcriptome-wide association studies (TWASs) integrate expression quantitative trait loci (eQTLs) studies with genome-wide association studies (GWASs) to prioritize candidate target genes for complex traits. Several statistical methods have been recently proposed to improve the performance of TWASs in gene prioritization by integrating the expression regulatory information imputed from multiple tissues, and made significant achievements in improving the ability to detect gene-trait associations. Unfortunately, most existing multi-tissue methods focus on prioritization of candidate genes, and cannot directly infer the specific functional effects of candidate genes across different tissues. Here, we propose a tissue-specific collaborative mixed model (TisCoMM) for TWASs, leveraging the co-regulation of genetic variations across different tissues explicitly via a unified probabilistic model. TisCoMM not only performs hypothesis testing to prioritize gene-trait associations, but also detects the tissue-specific role of candidate target genes in complex traits. To make full use of widely available GWASs summary statistics, we extend TisCoMM to use summary-level data, namely, TisCoMM-S2. Using extensive simulation studies, we show that type I error is controlled at the nominal level, the statistical power of identifying associated genes is greatly improved, and the false-positive rate (FPR) for non-causal tissues is well controlled at decent levels. We further illustrate the benefits of our methods in applications to summary-level GWASs data of 33 complex traits. Notably, apart from better identifying potential trait-associated genes, we can elucidate the tissue-specific role of candidate target genes. The follow-up pathway analysis from tissue-specific genes for asthma shows that the immune system plays an essential function for asthma development in both thyroid and lung tissues.

Download Full-text

Reproductive tissues-specific meta-QTLs and candidate genes for development of heat-tolerant rice cultivars

10.1101/2020.05.02.073429 ◽

2020 ◽

Author(s):

Qasim Raza ◽

Awais Riaz ◽

Khurram Bashir ◽

Muhammad Sabar

Keyword(s):

Heat Stress ◽

Abiotic Stress ◽

Heat Shock ◽

Candidate Genes ◽

Heat Tolerance ◽

Fast Track ◽

Reproductive Tissue ◽

Rice Cultivars ◽

Tissue Specific ◽

Heat Tolerant

AbstractRice holds the key to future food security. In rice-growing areas, temperature has already reached an optimum level for growth, hence, any further increase due to global climate change could significantly reduce rice yield. Several mapping studies have identified a plethora of reproductive tissue-specific and heat stress associated inconsistent quantitative trait loci (QTL), which could be exploited for improvement of heat tolerance. In this study, we performed a meta-analysis on previously reported QTLs and identified 35 most consistent meta-QTLs (MQTLs) across diverse genetic backgrounds and environments. Genetic and physical intervals of nearly 66% MQTLs were narrower than 5 cM and 2 Mb respectively, indicating hotspot genomic regions for heat tolerance. Comparative analyses of MQTLs underlying genes with microarray and RNA-seq based transcriptomic data sets revealed a core set of 45 heat-responsive genes, among which 24 were reproductive tissue-specific and have not been studied in detail before. Remarkably, all these genes corresponded to various stress associated functions, ranging from abiotic stress sensing to regulating plant stress responses, and included heat-shock genes (OsBiP2, OsMed37_1), transcription factors (OsNAS3, OsTEF1, OsWRKY10, OsWRKY21), transmembrane transporters (OsAAP7A, OsAMT2;1), sugar metabolizing (OsSUS4, α-Gal III) and abiotic stress (OsRCI2-7, SRWD1) genes. Functional data evidences from Arabidopsis heat-shock genes also suggest that OsBIP2 may be associated with thermotolerance of pollen tubes under heat stress conditions. Furthermore, promoters of identified genes were enriched with heat, dehydration, pollen and sugar responsive cis-acting regulatory elements, proposing a common regulatory mechanism might exist in rice for mitigsating reproductive stage heat stress. These findings strongly support our results and provide new candidate genes for fast-track development of heat-tolerant rice cultivars.Key MessageBy integrating genetics and genomics data, reproductive tissues-specific and heat stress responsive 35 meta-QTLs and 45 candidate genes were identified, which could be exploited through marker-assisted breeding for fast-track development of heat-tolerant rice cultivars.

Download Full-text