scholarly journals Candidate genes associated with red colour formation revealed by comparative genomic variant analysis of red- and green-skinned fruits of Japanese apricot (Prunus mume)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4625 ◽  
Author(s):  
Xiaopeng Ni ◽  
Song Xue ◽  
Shahid Iqbal ◽  
Wanxu Wang ◽  
Zhaojun Ni ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Quantitative Polymerase Chain Reaction ◽  
Expression Patterns ◽  
Regulatory Gene ◽  
Anthocyanin Synthesis ◽  
Comparative Genomic ◽  
Prunus Mume ◽  
Sequencing Data ◽  
Japanese Apricot ◽  
Wide Range

The red-skinned fruit of Japanese apricot (Prunus mumeSieb. et Zucc) appeals to customers due to its eye-catching pigmentation, while the mechanism related to its colour formation is still unclear. In this study, genome re-sequencing of six Japanese apricot cultivars was carried out with approximately 92.2 Gb of clean bases using next-generation sequencing. A total of 32,004 unigenes were assembled with an average of 83.1% coverage rate relative to reference genome. A wide range of genetic variation was detected, including 7,387,057 single nucleotide polymorphisms, 456,222 insertions or deletions and 129,061 structural variations in all genomes. Comparative sequencing data revealed that 13 candidate genes were involved in biosynthesis of anthocyanin. Significantly higher expression patterns were observed in genes encoding three anthocyanin synthesis structural genes (4CL,F3HandUFGT), five transcription factors (MYB–bHLH–WD40 complexes and NAC) and five anthocyanin accumulation related genes (GST1,RT1,UGT85A2, ABC and MATE transporters) in red-skinned than in green-skinned Japanese apricots using reverse transcription-quantitative polymerase chain reaction. Eight main kinds of anthocyanin s were detected by UPLC/MS, and cyanidin 3-glucoside was identified as the major anthocyanin (124.2 mg/kg) in red-skinned cultivars. The activity of UDP-glucose flavonoid-3-O-glycosyltransferase enzyme determined by UPLC was significantly higher in all red-skinned cultivars, suggesting that it is the potential vital regulatory gene for biosynthesis of anthocyanin in Japanese apricot.

scholarly journals Genome-wide characterization, evolutionary analysis of WRKY genes in Cucurbitaceae species and assessment of its roles in resisting to powdery mildew disease

2018 ◽  
Author(s):  
Zigao Jiao ◽  
Jianlei Sun ◽  
Chongqi Wang ◽  
Yumei Dong ◽  
Shouhua Xiao ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Genomic Analysis ◽  
Large Family ◽  
Comparative Genomic ◽  
Evolutionary Analysis ◽  
Multiple Sequence ◽  
Wide Range ◽  
Wrky Proteins

AbstractThe WRKY proteins constitute a large family of transcription factors that have been known to play a wide range of regulatory roles in multiple biological processes. Over the past few years, many reports have focused on analysis of evolution and biological function of WRKY genes at the whole genome level in different plant species. However, little information is known about WRKY genes in melon (Cucumis melo L.). In the present study, a total of 56 putative WRKY genes were identified in melon, which were randomly distributed on their respective chromosomes. A multiple sequence alignment and phylogenetic analysis using melon, cucumber and watermelon predicted WRKY domains indicated that melon WRKY proteins could be classified into three main groups (I-III). Our analysis indicated that no recent duplication events of WRKY genes were detected in melon, and strong purifying selection was observed among the 85 orthologous pairs of Cucurbitaceae species. Expression profiles of CmWRKY derived from RNA-seq data and quantitative RT-PCR (qRT-PCR) analyses showed distinct expression patterns in various tissues, and the expression of 16 CmWRKY were altered following powdery mildew infection in melon. Besides, we also found that a total of 24 WRKY genes were co-expressed with 11 VQ family genes in melon. Our comparative genomic analysis provides a foundation for future functional dissection and understanding the evolution of WRKY genes in cucurbitaceae species, and will promote powdery mildew resistance study in melon.

scholarly journals Positive selection of skeleton-related genes during duck domestication revealed by whole genome sequencing

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Tao Zhu ◽  
Xin Qi ◽  
Yu Chen ◽  
Liang Wang ◽  
Xueze Lv ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Skeletal Development ◽  
Expression Patterns ◽  
Fixation Index ◽  
Transcriptome Data ◽  
Domestic Ducks ◽  
Genetic Changes ◽  
Phenotypic Differences ◽  
Genome Data ◽  
Wide Range

Abstract Background Domestication alters several phenotypic, neurological, and physiological traits in domestic animals compared to those in their wild ancestors. Domestic ducks originated from mallards, and some studies have shown that spot-billed ducks may have also made minor genetic contributions to domestication. Compared with the two ancestral species, domestic ducks generally differ in body size and bone morphology. In this study, we performed both genomic and transcriptomic analyses to identify candidate genes for elucidating the genetic mechanisms underlying phenotypic variation. Methods In this study, the duck genome data from eight domestic breeds and two wild species were collected to study the genetic changes during domestication. And the transcriptome data of different tissues from wild ducks and seven domestic ducks were used to reveal the expression difference between wild and domestic ducks. Results Using fixation index (Fst) algorithm and transcriptome data, we found that the genes related to skeletal development had high Fst values in wild and domestic breeds, and the differentially expressed genes were mainly enriched in the ossification pathway. Our data strongly suggest that the skeletal systems of domestic ducks were changed to adapt to artificial selection for larger sizes. In addition, by combining the genome and transcriptome data, we found that some Fst candidate genes exhibited different expression patterns, and these genes were found to be involved in digestive, immune, and metabolic functions. Conclusions A wide range of phenotypic differences exists between domestic and wild ducks. Through both genome and transcriptome analyses, we found that genes related to the skeletal system in domestic ducks were strongly selected. Our findings provide new insight into duck domestication and selection effects during the domestication.

scholarly journals Mechanism Underlying Color Variation in Calla Lily Spathes Based on Transcriptomic Analysis

2021 ◽  
pp. 1-16
Author(s):  
Ying Fang ◽  
Ting Lei ◽  
Yanmei Wu ◽  
Xuehua Jin
Keyword(s):  
Quantitative Polymerase Chain Reaction ◽  
Expression Patterns ◽  
Flower Color ◽  
Transcriptomic Analysis ◽  
Color Variation ◽  
Anthocyanin Synthesis ◽  
Helix Loop Helix ◽  
Calla Lily ◽  
Unique Shape ◽  
Glutathione S Transferases

The calla lily (Zantedeschia hybrida) is a valued ornamental plant due to its unique shape and color variations. To determine the mechanisms responsible for color development in the calla lily spathe, we conducted a comparative transcriptomic analysis of the spathes of the black [Black Girl (B)], pink [Romantic (P)], and white [Ventura (W)] cultivars. The gene expression patterns in six spathe colors, including the preceding three colors as well as the amaranth [Promise (N)], red [Figo (F)], and yellow [Sun Club (Y)] cultivars were analyzed by real-time quantitative polymerase chain reaction (PCR). Transcriptomic analysis identified 25,165 differentially expressed genes. The transcription abundance and expression level of genes annotated as anthocyanidin reductase (ANR1, ANR2), basic-helix-loop-helix (bHLH1), and glutathione S-transferases (GST1) were significantly upregulated in B, and the expression of anthocyanidin synthase (ANS) was highest in B except for N. However, chalcone isomerase (CHI2) and dihydroflavonol 4-reductase (DFR1, DFR2) were expressed at significantly lower levels in P, W, and Y. Correlation analysis revealed that bHLH1 might act as a positive regulator of ANS expression, promoting anthocyanin synthesis. Moreover, GST1-encoded proteins may be related to the accumulation and transport of both anthocyanin and procyanidin in the calla lily spathe. It is speculated that the formation of the black spathe is related to the accumulation of anthocyanins and procyanidins. However, the low expression of CHI2, DFR1, and DFR2 may result in the inhibition of anthocyanin synthesis, which may lead to lightening of the spathe color. This preliminary study revealed the mechanism responsible for calla lily spathe color, identifying the key genes involved, thus providing effective gene resources and a theoretical basis for flower color molecular breeding.

scholarly journals Identification of Salt-Stress-Induced Genes from the RNA-Seq Data ofReaumuria trigynaUsing Differential-Display Reverse Transcription PCR

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Zhen-hua Dang ◽  
Qi Qi ◽  
Hui-rong Zhang ◽  
Hao-yu Li ◽  
Shu-Biao Wu ◽  
...  
Keyword(s):  
Salt Stress ◽  
Differential Display ◽  
Reverse Transcription ◽  
Expression Patterns ◽  
Digital Gene Expression ◽  
Rna Seq ◽  
Sequencing Data ◽  
Reverse Transcription Pcr ◽  
Wide Range ◽  
Differential Display Reverse Transcription

Next generation sequencing (NGS) technologies have been used to generate huge amounts of sequencing data from many organisms. However, the correct choice of candidate genes and prevention of false-positive results computed from digital gene expression (DGE) of RNA-seq data are vital when using these genetic resources. We indirectly identified 18 salt-stress-inducedReaumuria trigynatranscripts from the transcriptome sequencing data using differential-display reverse transcription PCR (DDRT-PCR) combined with local BLAST searches. Highly consistent with the DGE results, the quantitative real-time PCR expression patterns of these transcripts showed strong upregulation by salt stress, suggesting that these genes may play important roles inR. trigyna’s survival under high-salt environments. The method presented here successfully identified responsive genes from the massive amount of RNA-seq data. Thus, we suggest that DDRT-PCR could be employed to mine NGS data in a wide range of applications in transcriptomic studies. In addition, the genes identified in the present study are promising candidates for further elucidation of the salt tolerance mechanisms inR. trigyna.

Candidate Genes on Chromosome 9q33-34 Involved in the Progression of Childhood Ependymomas

2009 ◽  
Vol 27 (11) ◽  
pp. 1884-1892 ◽  
Author(s):  
Stéphanie Puget ◽  
Jacques Grill ◽  
Alexander Valent ◽  
Ivan Bieche ◽  
Carmela Dantas-Barbosa ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Posterior Fossa ◽  
Target Genes ◽  
Quantitative Polymerase Chain Reaction ◽  
Notch Pathway ◽  
Comparative Genomic ◽  
Missense Mutations ◽  
Tenascin C ◽  
Genomic Imbalances

Purpose The molecular pathogenesis of pediatric ependymoma remains unclear. Our study was designed to identify genetic changes implicated in ependymoma progression. Patients and Methods We characterized 59 ependymoma samples (33 at diagnosis and 26 at relapse) using array-comparative genomic hybridization (aCGH). Specific chromosomal imbalances were confirmed by fluorescent in situ hybridization, and candidate genes were assessed by real-time quantitative polymerase chain reaction (qPCR), immunohistochemistry, sequencing, and in vitro functional studies. Results aCGH analysis revealed a significant increase in genomic imbalances on relapse compared with diagnosis, such as gain of 9qter and 1q (54% v 21% and 12% v 0%, respectively) and loss of 6q (27% v 6%). Supervised tumor classification showed that gain of 9qter was associated with tumor recurrence, age older than 3 years, and posterior fossa location. Using a candidate-gene strategy, we found an overexpression of two potential oncogenes at the locus 9qter: Tenascin-C and Notch1. Moreover, Notch pathway analysis (qPCR) revealed overexpression of Notch ligands, receptors, and target genes (Hes-1, Hey2, and c-Myc), and downregulation of Notch repressor Fbxw7. We confirmed by immunohistochemistry the overexpression of Tenascin-C and Hes-1. We detected Notch1 missense mutations in 8.3% of the tumors (only in the posterior fossa location and in case of 9q33-34 gain). Furthermore, inhibition of Notch pathway with a γ-secretase inhibitor impaired the growth of ependymoma stem cell cultures. Conclusion The activation of the Notch pathway and Tenascin-C seem to be important events in ependymoma progression and may represent future targets for therapy. We report, to our knowledge for the first time, recurrent oncogenic mutations in pediatric posterior fossa ependymomas.

scholarly journals A genomic portrait of zebrafish transposable elements and their spatiotemporal embryonic expression

2021 ◽  
Author(s):  
Ni-Chen Chang ◽  
Quirze Rovira ◽  
Jonathan N Wells ◽  
Cédric Feschotte ◽  
Juan M Vaquerizas
Keyword(s):  
Transposable Elements ◽  
Single Cell ◽  
Expression Patterns ◽  
Endogenous Retroviruses ◽  
Gene Promoters ◽  
Vertebrate Development ◽  
Sequencing Data ◽  
Dna Transposons ◽  
Wide Range ◽  
The Impact

There is considerable interest in understanding the effect of transposable elements (TEs) on embryonic development. Studies in humans and mice are limited by the difficulty of working with mammalian embryos, and by the relative scarcity of active TEs in these organisms. Zebrafish is an outstanding model for the study of vertebrate development and over half of its genome consists of diverse TEs. However, zebrafish TEs remain poorly characterized. Here we describe the demography and genomic distribution of zebrafish TEs and their expression throughout embryogenesis using bulk and single-cell RNA sequencing data. These results reveal a highly dynamic genomic ecosystem comprising nearly 2,000 distinct TE families, which vary in copy number by four orders of magnitude and span a wide range of ages. Longer retroelements tend to be retained in intergenic regions, whilst short interspersed nuclear elements (SINEs) and DNA transposons are more frequently found nearby or within genes. Locus-specific mapping of TE expression reveals extensive TE transcription during development. While two thirds of TE transcripts are likely driven by nearby gene promoters, we still observe stage and tissue-specific expression patterns in self-regulated TEs. Long terminal repeat (LTR) retroelements are most transcriptionally active immediately following zygotic genome activation, whereas DNA transposons are enriched amongst transcripts expressed in later stages of development. Single-cell analysis reveals several endogenous retroviruses expressed in specific somatic cell lineages. Overall, our study provides an important resource for using zebrafish as a model to study the impact of TEs on vertebrate development.

scholarly journals Genome-Wide Identification and Characterization of Amino Acid Polyamine Organocation Transporter Family Genes Reveal Their Role in Fecundity Regulation in a Brown Planthopper Species (Nilaparvata lugens)

2021 ◽  
Vol 12 ◽  
Author(s):  
Lei Yue ◽  
Ziying Guan ◽  
Mingzhao Zhong ◽  
Luyao Zhao ◽  
Rui Pang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Gene Family ◽  
Quantitative Polymerase Chain Reaction ◽  
Expression Patterns ◽  
Regulatory Gene ◽  
Brown Planthopper ◽  
Nilaparvata Lugens ◽  
Functional Domain ◽  
Common Amino Acid

The brown planthopper (BPH), Nilaparvata lugens Stål (Hemiptera:Delphacidae), is one of the most destructive pests of rice worldwide. As a sap-feeding insect, the BPH is incapable of synthesizing several amino acids which are essential for normal growth and development. Therefore, the insects have to acquire these amino acids from dietary sources or their endosymbionts, in which amino acid transporters (AATs) play a crucial role by enabling the movement of amino acids into and out of insect cells. In this study, a common amino acid transporter gene family of amino acid/polyamine/organocation (APC) was identified in BPHs and analyzed. Based on a homology search and conserved functional domain recognition, 20 putative APC transporters were identified in the BPH genome. Molecular trait analysis showed that the verified BPH APC family members were highly variable in protein features, conserved motif distribution patterns, and exon/intron organization. Phylogenetic analysis of five hemipteran species revealed an evolutionary pattern of interfamily conservation and lineage-specific expansion of this gene family. Moreover, stage- and tissue-specific expression analysis revealed diverse expression patterns in the 20 BPH APC transporter genes. Lastly, a potential BPH fecundity regulatory gene of NlAPC09 was identified and shown to participate in the fecundity regulation through the use of quantitative polymerase chain reaction (qPCR) and RNA inference experiments. Our results provide a basis for further functional investigations of APC transporters in BPH.

scholarly journals Anthocyanin Synthesis and the Expression Patterns of bHLH Transcription Factor Family during Development of the Chinese Jujube Fruit (Ziziphus jujuba Mill.)

Forests ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 346 ◽  
Author(s):  
Qianqian Shi ◽  
Xi Li ◽  
Jiangtao Du ◽  
Xingang Li
Keyword(s):  
Transcription Factor ◽  
Biological Activities ◽  
Expression Patterns ◽  
Protein Sequences ◽  
Anthocyanin Synthesis ◽  
Bhlh Transcription Factor ◽  
Helix Loop Helix ◽  
Jujube Fruit ◽  
Wide Range ◽  
Changing Patterns

The basic helix–loop–helix (bHLH) family is an important transcription factor for eukaryotes and is involved in a wide range of biological activities. Among these, bHLH can interaction with WD repeat (WD40 or WDR) and V-myb avian myeloblastosis viral oncogene homolog (MYB) form a ternary complex to promote the efficient synthesis of anthocyanins. In this study, a total of 138 jujube bHLH (ZjbHLH) family members were screened from the transcriptome of the two jujube cultivars, ‘Junzao’ (JZ) and ‘Tailihong’ (TLH). Of these, 95 ZjbHLH genes were mapped to 12 chromosomes. A phylogenetic tree was constructed using 27 arabidopsis bHLH (AtbHLH) protein sequences of Arabidopsis thaliana (L.) Heynh. and 138 ZjbHLH protein sequences of jujube. The results show that the ZjbHLH family of jujube can be divided into 12 subfamilies. The three candidate genes, ZjGL3a, ZjGL3b and ZjTT8, related to anthocyanin synthesis, were classified into subgroup III. Meanwhile, ZjGL3a, ZjGL3b and ZjTT8 have high homology with the bHLH transcription factors involved in anthocyanin synthesis in other plants. In addition, it was found that the jujube ZjbHLH transcript family showed changing patterns of expression during fruit development. The relative expression levels of ZjGL3a, ZjGL3 and ZjTT8 were consistent with the changes of the anthocyanin contents in the two jujube cultivars examined. To better understand the anthocyanin synthesis pathway involved in ZjbHLH, a regulatory pathway model for anthocyanin synthesis was constructed. This model involves the processes of anthocyanin signal transduction, synthesis and transport.

Insights into the heat-responsive transcriptional network of tomato contrasting genotypes

2021 ◽  
Vol 19 (1) ◽  
pp. 44-57
Author(s):  
Sirine Werghi ◽  
Charfeddine Gharsallah ◽  
Nishi Kant Bhardwaj ◽  
Hatem Fakhfakh ◽  
Faten Gorsane
Keyword(s):  
Heat Stress ◽  
Heat Shock ◽  
Candidate Genes ◽  
Expression Patterns ◽  
Response Strategies ◽  
Transcriptional Reprogramming ◽  
Genes Encoding ◽  
Breeding Programmes ◽  
Gene Transcripts ◽  
Resource Data

AbstractDuring recent decades, global warming has intensified, altering crop growth, development and survival. To overcome changes in their environment, plants undergo transcriptional reprogramming to activate stress response strategies/pathways. To evaluate the genetic bases of the response to heat stress, Conserved DNA-derived Polymorphism (CDDP) markers were applied across tomato genome of eight cultivars. Despite scattered genotypes, cluster analysis allowed two neighbouring panels to be discriminate. Tomato CDDP-genotypic and visual phenotypic assortment permitted the selection of two contrasting heat-tolerant and heat-sensitive cultivars. Further analysis explored differential expression in transcript levels of genes, encoding heat shock transcription factors (HSFs, HsfA1, HsfA2, HsfB1), members of the heat shock protein (HSP) family (HSP101, HSP17, HSP90) and ascorbate peroxidase (APX) enzymes (APX1, APX2). Based on discriminating CDDP-markers, a protein functional network was built allowing prediction of candidate genes and their regulating miRNA. Expression patterns analysis revealed that miR156d and miR397 were heat-responsive showing a typical inverse relation with the abundance of their target gene transcripts. Heat stress is inducing a set of candidate genes, whose expression seems to be modulated through a complex regulatory network. Integrating genetic resource data is required for identifying valuable tomato genotypes that can be considered in marker-assisted breeding programmes to improve tomato heat tolerance.

scholarly journals Integrated molecular characterisation of endometrioid ovarian carcinoma identifies opportunities for stratification

2021 ◽  
Vol 5 (1) ◽  
Author(s):  
Robert L. Hollis ◽  
Barbara Stanley ◽  
John P. Thomson ◽  
Michael Churchman ◽  
Ian Croy ◽  
...  
Keyword(s):  
High Risk ◽  
Ovarian Carcinoma ◽  
Expression Patterns ◽  
Parp Inhibitors ◽  
Receptor Expression ◽  
Cancer Type ◽  
Sequencing Data ◽  
Molecular Features ◽  
Endometrioid Ovarian Carcinoma ◽  
Molecular Landscape

AbstractEndometrioid ovarian carcinoma (EnOC) is an under-investigated ovarian cancer type. Recent studies have described disease subtypes defined by genomics and hormone receptor expression patterns; here, we determine the relationship between these subtyping layers to define the molecular landscape of EnOC with high granularity and identify therapeutic vulnerabilities in high-risk cases. Whole exome sequencing data were integrated with progesterone and oestrogen receptor (PR and ER) expression-defined subtypes in 90 EnOC cases following robust pathological assessment, revealing dominant clinical and molecular features in the resulting integrated subtypes. We demonstrate significant correlation between subtyping approaches: PR-high (PR + /ER + , PR + /ER−) cases were predominantly CTNNB1-mutant (73.2% vs 18.4%, P < 0.001), while PR-low (PR−/ER + , PR−/ER−) cases displayed higher TP53 mutation frequency (38.8% vs 7.3%, P = 0.001), greater genomic complexity (P = 0.007) and more frequent copy number alterations (P = 0.001). PR-high EnOC patients experience favourable disease-specific survival independent of clinicopathological and genomic features (HR = 0.16, 95% CI 0.04–0.71). TP53 mutation further delineates the outcome of patients with PR-low tumours (HR = 2.56, 95% CI 1.14–5.75). A simple, routinely applicable, classification algorithm utilising immunohistochemistry for PR and p53 recapitulated these subtypes and their survival profiles. The genomic profile of high-risk EnOC subtypes suggests that inhibitors of the MAPK and PI3K-AKT pathways, alongside PARP inhibitors, represent promising candidate agents for improving patient survival. Patients with PR-low TP53-mutant EnOC have the greatest unmet clinical need, while PR-high tumours—which are typically CTNNB1-mutant and TP53 wild-type—experience excellent survival and may represent candidates for trials investigating de-escalation of adjuvant chemotherapy to agents such as endocrine therapy.

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