scholarly journals Identifying Molecular Pathways and Candidate Genes Associated With Knob Traits by Transcriptome Analysis in the Goose (Anser Cygnoides)

2021 ◽  
Author(s):  
Wangyang Ji ◽  
Qi Xu ◽  
Wenming Zhao ◽  
li E Hou ◽  
Xiaoya Yuan ◽  
...  
Keyword(s):  
Growth And Development ◽  
Consumer Preferences ◽  
Transcriptome Profiling ◽  
Hormone Synthesis ◽  
Kegg Pathways ◽  
Large Size ◽  
Go Enrichment ◽  
Stratum Spinosum ◽  
Molecular Determinants ◽  
Length Width

Abstract Anser cygnoides has a spherical crest on the beak roof, which is described as knob. However, the mechanisms affecting knob morphology are unclear. Here, we investigated the phenotypic characteristics and molecular basis of knob-size differences in Yangzhou geese. The bony crest of konb was found in the frontal area of the skull, rather than hump of upper beak. Although the knob length, width, and height varied greatly in geese with different knob phenotypes, growth of the bony crest was mainly reflected in the length and height, but not the width. Histological analysis showed that knob skin in large-size knobs geese have a greater length in the stratum corneum, stratum spinosum, and stratum reticular. Transcriptome profiling revealed 415 differentially expressed genes involved in knob growth and development. In addition, GO enrichment and KEGG pathway analysis revealed 455 significant GO terms and 210 enriched KEGG pathways. We focused on the TGF-β-signaling and thyroid hormone synthesis-signaling KEGG pathways. Geese with larger knobs had increased ADCY3, TSHR, DCN, and BMP5 mRNA-expression levels, suggesting that both pathways (and the associated genes) mediate knob growth and development. Our data provide comprehensive molecular determinants of knob size, which can potentially be used to promote the genetic improvement of goose knobs to meet consumer preferences.

scholarly journals Identifying molecular pathways and candidate genes associated with knob traits by transcriptome analysis in the goose (Anser cygnoides)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wangyang Ji ◽  
li E Hou ◽  
Xiaoya Yuan ◽  
Tiantian Gu ◽  
ZhuoYu Chen ◽  
...  
Keyword(s):  
Transcriptome Profiling ◽  
Phenotypic Characteristics ◽  
Hormone Synthesis ◽  
Kegg Pathways ◽  
Large Size ◽  
Kegg Pathway Analysis ◽  
Go Enrichment ◽  
Stratum Spinosum ◽  
Molecular Determinants ◽  
Go Terms

AbstractAnser cygnoides has a spherical crest on the beak roof, which is described as knob. However, the mechanisms affecting knob morphology are unclear. Here, we investigated the phenotypic characteristics and molecular basis of knob-size differences in Yangzhou geese. Anatomically, the knob was identified as frontal hump in the frontal area of the skull, rather than hump of upper beak. Although the frontal hump length, and height varied greatly in geese with different knob phenotypes, little was changed in the width. Histologically, knob skin in large-size knobs geese have a greater length in the stratum corneum, stratum spinosum, and stratum reticular than that in small-size knobs geese. Moveover, the 415 differentially expressed genes were found between the large knobs and small ones through transcriptome profiling. In addition, GO enrichment and KEGG pathway analysis revealed 455 significant GO terms and 210 KEGG pathways were enriched, respectively. Among these, TGF-β signaling and thyroid hormone synthesis-signaling pathways were identified to determine knob-size phenotype. Furthermore, BMP5, DCN, TSHR and ADCY3 were recognized to involve in the growth and development of knob. Our data provide comprehensive molecular determinants of knob size phenotype, which can potentially promote the genetic improvement of goose knobs.

scholarly journals Identification of Differentially Expressed Genes in Porcine Ovaries at Proestrus and Estrus Stages Using RNA-Seq Technique

2018 ◽  
Vol 2018 ◽  
pp. 1-8 ◽  
Author(s):  
Songbai Yang ◽  
Xiaolong Zhou ◽  
Yue Pei ◽  
Han Wang ◽  
Ke He ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Hormone Secretion ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
The Novel ◽  
Kegg Pathways ◽  
Go Enrichment ◽  
Single Organism

Estrus is an important factor for the fecundity of sows, and it is involved in ovulation and hormone secretion in ovaries. To better understand the molecular mechanisms of porcine estrus, the expression patterns of ovarian mRNA at proestrus and estrus stages were analyzed using RNA sequencing technology. A total of 2,167 differentially expressed genes (DEGs) were identified (P≤0.05, log2  Ratio≥1), of which 784 were upregulated and 1,383 were downregulated in the estrus compared with the proestrus group. Gene Ontology (GO) enrichment indicated that these DEGs were mainly involved in the cellular process, single-organism process, cell and cell part, and binding and metabolic process. In addition, a pathway analysis showed that these DEGs were significantly enriched in 33 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including cell adhesion molecules, ECM-receptor interaction, and cytokine-cytokine receptor interaction. Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) confirmed the differential expression of 10 selected DEGs. Many of the novel candidate genes identified in this study will be valuable for understanding the molecular mechanisms of the sow estrous cycle.

scholarly journals Comparative Transcriptome Profiling of High and Low oil yielding Santalum album L.

2021 ◽  
Author(s):  
Tanzeem Fatima ◽  
Rangachari Krishnan ◽  
Ashutosh Srivastava ◽  
Vageeshbabu S. Hanur ◽  
M. Srinivasa Rao
Keyword(s):  
Transcriptome Profiling ◽  
Santalum Album ◽  
Rna Seq ◽  
Improvement Program ◽  
East Indian ◽  
Kegg Pathways ◽  
Oil Biosynthesis ◽  
Genome Wide ◽  
A Genome ◽  
Santalum Album L

East Indian Sandalwood (Santalum album L.) is highly valued for its heartwood and its oil. There have been no efforts to comparative study of high and low oil yielding genetically identical sandalwood trees grown in similar climatic condition. Thus we intend to study a genome wide transcriptome analysis to identify the corresponding genes involved in high oil biosynthesis in S. album. In this study, 15 years old S. album (SaSHc and SaSLc) genotypes were targeted for analysis to understand the contribution of genetic background on high oil biosynthesis in S. album. A total of 28,959187 and 25,598869 raw PE reads were generated by the Illumina sequencing. 2.12 million and 1.811 million coding sequences were obtained in respective accessions. Based on the GO terms, functional classification of the CDS 21262, & 18113 were assigned into 26 functional groups of three GO categories; (4,168; 3,641) for biological process (5,758;4,971) cellular component and (5,108;4,441) for molecular functions. Total 41,900 and 36,571 genes were functionally annotated and KEGG pathways of the DEGs resulted 213 metabolic pathways. In this, 14 pathways were involved in secondary metabolites biosynthesis pathway in S. album. Among 237 cytochrome families, nine groups of cytochromes were participated in high oil biosynthesis. 16,665 differentially expressed genes were commonly detected in both the accessions (SaHc and SaSLc). The results showed that 784 genes were upregulated and 339 genes were downregulated in SaHc whilst 635 upregulated 299 downregulated in SaSLc S. album. RNA-Seq results were further validated by quantitative RT-PCR. Maximum Blast hits were found to be against Vitis vinifera. From this study we have identified additional number of cytochrome family in SaHc. The accessibility of a RNA-Seq for high oil yielding sandalwood accessions will have broader associations for the conservation and selection of superior elite samples/populations for further genetic improvement program.

scholarly journals Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition

2020 ◽  
Author(s):  
Luis Enrique Cabrera Quio ◽  
Alexander Schleiffer ◽  
Karl Mechtler ◽  
Andrea Pauli
Keyword(s):  
Regulation Of Gene Expression ◽  
Physiological Role ◽  
Transcriptome Profiling ◽  
Time Frame ◽  
Rna Degradation ◽  
Developmental Transitions ◽  
Mrna Targets ◽  
Go Enrichment ◽  
Normal Adults

AbstractPost-transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte-to-embryo transition, which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions, changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified, it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte-to-embryo transition. Here, we focused on the auxiliary 3’-to-5’ degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults, yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte-to-embryo transition, transcriptome profiling identified stage-specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type, suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis-regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall, our results provide first insights into the physiological role of vertebrate Ski7 as an important post-transcriptional regulator during the oocyte-to-embryo transition.

scholarly journals Comparative Transcriptome Profiling Analysis to Unravel the Potential Mechanism of Seed Abortion in Lumnitzera littorea

2021 ◽  
Vol 25 (02) ◽  
pp. 420-426
Author(s):  
Jingwen Zhang
Keyword(s):  
High Throughput Sequencing ◽  
Transcriptome Profiling ◽  
Seed Abortion ◽  
Sequencing Data ◽  
Mangrove Plant ◽  
Kegg Pathways ◽  
High Throughput Sequencing Data ◽  
Natural Reproduction ◽  
The Family ◽  
Profiling Analysis

Lumnitzera littorea (Jack) Voigt. is a species of mangrove plant belonging to the family Combretaceae. Natural reproduction of L. littorea is extremely difficult due to its seed abortion in China. To reveal the molecular mechanism of seed abortion, we performed transcriptome to analyze the seeds of L. littorea-T (normal seeds) and L. littorea-S (abortive seeds). After analysis of the raw data, 64,868 transcripts (mean length = 658 bp) were assembled. Among these transcripts, 39,779 were functionally annotated. Then, differentially expressed genes (DEGs) were screened, and 23,513 transcripts were identified that were likely involved in seed abortion. About 207 DEGs assigned to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and approximately 12.1% fell into reproduction categories. Genes involved in response to sucrose and starch metabolism, and phytohormone biosynthesis showed significant different expression levels between normal and abortive seeds of L. littorea. Further expressions patterns of key genes contribute to seed development were analyzed using quantitative real-time PCR, and the results were consistent with high-throughput sequencing data. The information obtained in this study will aid in the research of the mechanism of seed abortion in further molecular studies of L. littorea. © 2021 Friends Science Publishers

scholarly journals Study of Terpenoid Synthesis and Prenyltransferase in Roots of Rehmannia glutinosa Based on iTRAQ Quantitative Proteomics

2021 ◽  
Vol 12 ◽  
Author(s):  
Peilei Chen ◽  
Xiaoyan Wei ◽  
Qianting Qi ◽  
Wenjing Jia ◽  
Mingwei Zhao ◽  
...  
Keyword(s):  
Tca Cycle ◽  
Maturation Stage ◽  
Rehmannia Glutinosa ◽  
Active Components ◽  
Kegg Pathways ◽  
Medicinal Value ◽  
Go Enrichment ◽  
Expansion Stage ◽  
Proteasome Pathway ◽  
Ggpp Synthase

Rehmannia glutinosa has important medicinal value; terpenoid is one of the main active components in R. glutinosa. In this study, iTRAQ technique was used to analyze the relative abundance of proteins in roots of R. glutinosa, and 6,752 reliable proteins were quantified. GO enrichment results indicated that most proteins were involved in metabolic process or cellular process, 57.63% proteins had catalytic activity, and 65.80% proteins were enriched in membrane-bounded organelle. In roots of R. glutinosa, there were 38 KEGG enrichments with significance, more DEPs were found in some pathways, especially the proteasome pathway and TCA cycle with 15.0% DEPs between elongation stage and expansion stage of roots. Furthermore, five KEGG pathways of terpenoid synthesis were found. Most prenyltransferases belong to FPP/GGPP synthase family, involved in terpenoid backbone biosynthesis, and all interacted with biotin carboxylase CAC2. Compared with that at the elongation stage, many prenyltransferases exhibited higher expression at the expansion stage or maturation stage of roots. In addition, eight FPP/GGPP synthase encoding genes were cloned from R. glutinosa, namely FPPS, FPPS1, GGPS, GGPS3, GGPS4, GGPS5, GPPS and GPPS2, introns were also found in FPPS, FPPS1, GGPS5 and GGPS2, and FPP/GPP synthases were more conservative in organisms, especially in viridiplantae, in which the co-occurrence of GPPS or GPPS2 was significantly higher in plants. Further analysis found that FPP/GGPP synthases of R. glutinosa were divided into three kinds, GGPS, GPPS and FPPS, and their gene expression was significantly diverse in different varieties, growth periods, or tissues of R. glutinosa. Compared with that of GGPS, the expression of GPPS and FPPS was much higher in R. glutinosa, especially at the expansion stage and maturation stage. Thus, the synthesis of terpenoids in roots of R. glutinosa is intricately regulated and needs to be further studied.

scholarly journals RNA seq analyses of chicken reveals biological pathways involved in acclimation into different geographical locations

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Himansu Kumar ◽  
Hyojun Choo ◽  
Asankadyr U. Iskender ◽  
Krishnamoorthy Srikanth ◽  
Hana Kim ◽  
...  
Keyword(s):  
Enrichment Analysis ◽  
Mapk Signaling ◽  
Climatic Conditions ◽  
Rna Seq ◽  
Kegg Pathways ◽  
Go Enrichment ◽  
Commercial Chicken ◽  
Pathways Analysis ◽  
Ppar Signaling ◽  
Transcriptome Expression

Abstract Transcriptome expression reflects genetic response in diverse conditions. In this study, RNA sequencing was utilized to profile multiple tissues such as liver, breast, caecum, and gizzard of Korean commercial chicken raised in Korea and Kyrgyzstan. We analyzed ten samples per tissue from each location to identify candidate genes which are involved in the adaptation of Korean commercial chicken to Kyrgyzstan. At false discovery rate (FDR) < 0.05 and fold change (FC) > 2, we found 315, 196, 167 and 198 genes in liver, breast, cecum, and gizzard respectively as differentially expressed between the two locations. GO enrichment analysis showed that these genes were highly enriched for cellular and metabolic processes, catalytic activity, and biological regulations. Similarly, KEGG pathways analysis indicated metabolic, PPAR signaling, FoxO, glycolysis/gluconeogenesis, biosynthesis, MAPK signaling, CAMs, citrate cycles pathways were differentially enriched. Enriched genes like TSKU, VTG1, SGK, CDK2 etc. in these pathways might be involved in acclimation of organisms into diverse climatic conditions. The qRT-PCR result also corroborated the RNA-Seq findings with R2 of 0.76, 0.80, 0.81, and 0.93 for liver, breast, caecum, and gizzard respectively. Our findings can improve the understanding of environmental acclimation process in chicken.

scholarly journals Triacontanol Promotes the Fruit Development and Retards Fruit Senescence in Strawberry: A Transcriptome Analysis

Plants ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 488
Author(s):  
Qianqian Pang ◽  
Xueqin Chen ◽  
Jinhua Lv ◽  
Teng Li ◽  
Jinggui Fang ◽  
...  
Keyword(s):  
Plant Growth ◽  
Fruit Development ◽  
Growth And Development ◽  
High Efficiency ◽  
Low Cost ◽  
Sugar Content ◽  
Regulation Mechanism ◽  
Cellular Processes ◽  
Go Enrichment ◽  
Related Enzyme

Triacontanol (TA) is a non-toxic, pollution-free, low-cost, high-efficiency, broad-spectrum plant growth regulator that plays an important role in plant growth and development, but its regulation mechanism of strawberry (Sweet charlie, Fragaria × ananassa Duch.) fruit development is still unclear. In this study, we showed that TA treatment (50 μM) could promote fruit development by up-regulating factors related to fruit ripening-related growth and development. TA increased fruit sugar content and anthocyanin accumulation, and many stress-related enzyme activities. In the meantime, Illumina RNA-Seq technology was used to evaluate the effect of TA treatment on strawberry fruit senescence. The results showed that 9338 differentially expressed genes (DEGs) were obtained, including 4520 up-regulated DEGs and 4818 down-regulated DEGs. We performed gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of these DEGs. The results showed that TA treatment caused changes in transcript levels related to cellular processes, hormones and secondary metabolism, such as DNA metabolic processes, flavonoid synthesis, and plant hormone signal transduction. Bioinformatics analysis showed that many transcription factors were related to fruit maturity. Taken together, this study will provide new insights into the mechanism of strawberry development and postharvest response to TA treatment.

Larval development of the queen scallop, Equichlamys bifrons

1976 ◽  
Vol 27 (3) ◽  
pp. 399 ◽  
Author(s):  
TG Dix
Keyword(s):  
Larval Development ◽  
Geometric Mean ◽  
Shell Growth ◽  
Larval Life ◽  
Large Size ◽  
Pelagic Larvae ◽  
Mean Diameter ◽  
Length Width ◽  
Early Larvae

The smallest length of pelagic larvae of E. bifrons reared from fertilized eggs (mean diameter 119.6 pm) was 150 pm. Shell growth revealed insignificant umbone development, and the length-width relationship is described by the geometric mean regression: w = 0.751l+20.720. Eye spots were conspicuous and common in larvae of 165-175 pm length; metamorphosis generally occurred when larvae were just longer than 200 pm. In cultures maintained between 14 and 18°C juveniles were present 17-20 days after fertilization. Provinicular structure was simple, and there were generally four teeth at each end of the hinge. Unisexuality, the large size of eggs and early larvae, shorter larval life, and the lack of umbone development are the most significant characteristics distinguishing the development of E. bifrons from that of Pecten meridionalis, another local pectinid.

scholarly journals Post-Translational Protein Deimination Signatures in Plasma and Plasma EVs of Reindeer (Rangifer tarandus)

Biology ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 222
Author(s):  
Stefania D’Alessio ◽  
Stefanía Thorgeirsdóttir ◽  
Igor Kraev ◽  
Karl Skírnisson ◽  
Sigrun Lange
Keyword(s):  
Signaling Pathway ◽  
Prion Disease ◽  
Rangifer Tarandus ◽  
Extreme Environments ◽  
Estrogen Signaling ◽  
The Arctic ◽  
Receptor Interaction ◽  
Wild Female ◽  
Hormone Synthesis ◽  
Kegg Pathways

The reindeer (caribou) Rangifer tarandus is a Cervidae in the order Artiodactyla. Reindeer are sedentary and migratory populations with circumpolar distribution in the Arctic, Northern Europe, Siberia and North America. Reindeer are an important wild and domesticated species, and have developed various adaptive strategies to extreme environments. Importantly, deer have also been identified to be putative zoonotic carriers, including for parasites, prions and coronavirus. Therefore, novel insights into immune-related markers are of considerable interest. Peptidylarginine deiminases (PADs) are a phylogenetically conserved enzyme family which causes post-translational protein deimination by converting arginine into citrulline in target proteins. This affects protein function in health and disease. Extracellular vesicles (EVs) participate in cellular communication, in physiological and pathological processes, via transfer of cargo material, and their release is partly regulated by PADs. This study assessed deiminated protein and EV profile signatures in plasma from sixteen healthy wild female reindeer, collected in Iceland during screening for parasites and chronic wasting disease. Reindeer plasma EV profiles showed a poly-dispersed distribution from 30 to 400 nm and were positive for phylogenetically conserved EV-specific markers. Deiminated proteins were isolated from whole plasma and plasma EVs, identified by proteomic analysis and protein interaction networks assessed by KEGG and GO analysis. This revealed a large number of deimination-enriched pathways for immunity and metabolism, with some differences between whole plasma and EVs. While shared KEGG pathways for whole plasma and plasma EVs included complement and coagulation pathways, KEGG pathways specific for EVs were for protein digestion and absorption, platelet activation, amoebiasis, the AGE–RAGE signaling pathway in diabetic complications, ECM receptor interaction, the relaxin signaling pathway and the estrogen signaling pathway. KEGG pathways specific for whole plasma were pertussis, ferroptosis, SLE, thyroid hormone synthesis, phagosome, Staphylococcus aureus infection, vitamin digestion and absorption, and prion disease. Further differences were also found between molecular function and biological processes GO pathways when comparing functional STRING networks for deiminated proteins in EVs, compared with deiminated proteins in whole plasma. This study highlights deiminated proteins and EVs as candidate biomarkers for reindeer health and may provide information on regulation of immune pathways in physiological and pathological processes, including neurodegenerative (prion) disease and zoonosis.

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