scholarly journals Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Sarika Jaiswal ◽  
Samiran Nandi ◽  
Mir Asif Iquebal ◽  
Rahul Singh Jasrotia ◽  
Sunita Patra ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Rna Sequencing ◽  
De Novo ◽  
Clock Genes ◽  
Labeo Rohita ◽  
Monsoon Season ◽  
Biological Clock ◽  
Differentially Expressed ◽  
Freshwater Aquaculture ◽  
Carp Fish

Abstract Background Carp fish, rohu (Labeo rohita Ham.) is important freshwater aquaculture species of South-East Asia having seasonal reproductive rhythm. There is no holistic study at transcriptome level revealing key candidate genes involved in such circannual rhythm regulated by biological clock genes (BCGs). Seasonality manifestation has two contrasting phases of reproduction, i.e., post-spawning resting and initiation of gonadal activity appropriate for revealing the associated candidate genes. It can be deciphered by RNA sequencing of tissues involved in BPGL (Brain-Pituitary-Gonad-Liver) axis controlling seasonality. How far such BCGs of this fish are evolutionarily conserved across different phyla is unknown. Such study can be of further use to enhance fish productivity as seasonality restricts seed production beyond monsoon season. Result A total of ~ 150 Gb of transcriptomic data of four tissues viz., BPGL were generated using Illumina TruSeq. De-novo assembled BPGL tissues revealed 75,554 differentially expressed transcripts, 115,534 SSRs, 65,584 SNPs, 514 pathways, 5379 transcription factors, 187 mature miRNA which regulates candidate genes represented by 1576 differentially expressed transcripts are available in the form of web-genomic resources. Findings were validated by qPCR. This is the first report in carp fish having 32 BCGs, found widely conserved in fish, amphibian, reptile, birds, prototheria, marsupials and placental mammals. This is due to universal mechanism of rhythmicity in response to environment and earth rotation having adaptive and reproductive significance. Conclusion This study elucidates evolutionary conserved mechanism of photo-periodism sensing, neuroendocrine secretion, metabolism and yolk synthesis in liver, gonadal maturation, muscular growth with sensory and auditory perception in this fish. Study reveals fish as a good model for research on biological clock besides its relevance in reproductive efficiency enhancement.

scholarly journals Revelation of candidate genes and molecular mechanism of reproductive seasonality in carp fish (Labeo rohita Ham) by RNA sequencing

2020 ◽  
Author(s):  
Sarika Jaiswal ◽  
Samiran Nandi ◽  
Mir Iquebal ◽  
Rahul Jasrotia ◽  
Sunita Patra ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Rna Sequencing ◽  
De Novo ◽  
Clock Genes ◽  
Labeo Rohita ◽  
Monsoon Season ◽  
Biological Clock ◽  
Differentially Expressed ◽  
Freshwater Aquaculture ◽  
Carp Fish

Abstract BackgroundCarp fish, rohu (Labeo rohita Ham) is important freshwater aquaculture species of South-East Asia having seasonal reproductive rhythm. There is no holistic study at transcriptome level revealing key candidate genes involved in such circannual rhythm regulated by biological clock genes (BCGs). Seasonality manifestation has two contrasting phases of reproduction, i.e., post-spawning regression and initiation of gonadal activity appropriate for discovery of associated candidate genes. It can be deciphered by RNA sequencing of tissues involved in BPGL (Brain-Pituitary-Gonad-Liver) axis controlling seasonality. How far such BCGs of this fish are evolutionarily conserved across different phyla is unknown. Such study can be of further use to enhance fish productivity as seasonality restricts seed production beyond monsoon season.ResultA total of ~150 Gb of transcriptomic data of four tissues viz., BPGL were generated using Illumina TruSeq. De-novo assembled BPGL tissues revealed 75554 differentially expressed transcripts, 115534 SSRs, 65584 SNPs, 514 pathways, 5379 transcription factors, 187 mature miRNA which regulates candidate genes represented by 1576 differentially expressed transcripts which are available in the form of web-genomic resources. Findings were validated by qPCR. This is first report in carp fish having 32 BCGs found widely conserved in fish, amphibian, reptile, birds, prototheria, marsupials and placental mammals. This is due to universal mechanism of rhythmicity in response to environment and earth rotation having adaptive and reproductive significance.ConclusionThis study elucidates evolutionary conserved mechanism of photo-periodism sensing, neuroendocrine secretion, metabolism and yolk synthesis in liver, gonadal maturation, muscular growth with sensory and auditory perception in this fish. Study reveals fish as a good model for research on biological clock besides its relevance in reproductive efficiency enhancement.

scholarly journals Identifying Candidate Genes for Hypoxia Adaptation of Tibet Chicken Embryos by Selection Signature Analyses and RNA Sequencing

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 823
Author(s):  
Xiayi Liu ◽  
Xiaochen Wang ◽  
Jing Liu ◽  
Xiangyu Wang ◽  
Haigang Bao
Keyword(s):  
Candidate Genes ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Gallus Gallus ◽  
Differentially Expressed ◽  
Tibet Plateau ◽  
Embryonic Liver ◽  
Selection Signature ◽  
Chicken Embryos ◽  
Hypoxia Adaptation

The Tibet chicken (Gallus gallus) lives on the Qinghai–Tibet Plateau and adapts to the hypoxic environment very well. The objectives of this study was to obtain candidate genes associated with hypoxia adaptation in the Tibet chicken embryos. In the present study, we used the fixation index (Fst) and cross population extended haplotype homozygosity (XPEHH) statistical methods to detect signatures of positive selection of the Tibet chicken, and analyzed the RNA sequencing data from the embryonic liver and heart with HISAT, StringTie and Ballgown for differentially expressed genes between the Tibet chicken and White leghorn (Gallus gallus, a kind of lowland chicken) embryos hatched under hypoxia condition. Genes which were screened out by both selection signature analysis and RNA sequencing analysis could be regarded as candidate genes for hypoxia adaptation of chicken embryos. We screened out 1772 genes by XPEHH and 601 genes by Fst, and obtained 384 and 353 differentially expressed genes in embryonic liver and heart, respectively. Among these genes, 89 genes were considered as candidate genes for hypoxia adaptation in chicken embryos. ARNT, AHR, GSTK1 and FGFR1 could be considered the most important candidate genes. Our findings provide references to elucidate the molecular mechanism of hypoxia adaptation in Tibet chicken embryos.

scholarly journals Genome-Wide Association Study and Transcriptome Differential Expression Analysis of the Feather Rate in Shouguang Chickens

2020 ◽  
Vol 11 ◽  
Author(s):  
Xiayi Liu ◽  
Zhou Wu ◽  
Junying Li ◽  
Haigang Bao ◽  
Changxin Wu
Keyword(s):  
Differential Expression ◽  
Candidate Genes ◽  
Rna Sequencing ◽  
Expression Analysis ◽  
Differential Expression Analysis ◽  
Serine Phosphorylation ◽  
Differentially Expressed ◽  
Genome Wide Association ◽  
Sequencing Analysis ◽  
Genome Wide

The feather rate phenotype in chicks, including early-feathering and late-feathering phenotypes, are widely used as a sexing system in the poultry industry. The objective of this study was to obtain candidate genes associated with the feather rate in Shouguang chickens. In the present study, we collected 56 blood samples and 12 hair follicle samples of flight feathers from female Shouguang chickens. Then we identified the chromosome region associated with the feather rate by genome-wide association analysis (GWAS). We also performed RNA sequencing and analyzed differentially expressed genes between the early-feathering and late-feathering phenotypes using HISAT2, StringTie, and DESeq2. We identified a genomic region of 10.0–13.0 Mb of chromosome Z, which is statistically associated with the feather rate of Shouguang chickens at one-day old. After RNA sequencing analysis, 342 differentially expressed known genes between the early-feathering (EF) and late-feathering (LF) phenotypes were screened out, which were involved in epithelial cell differentiation, intermediate filament organization, protein serine kinase activity, peptidyl-serine phosphorylation, retinoic acid binding, and so on. The sperm flagellar 2 gene (SPEF2) and prolactin receptor (PRLR) gene were the only two overlapping genes between the results of GWAS and differential expression analysis, which implies that SPEF2 and PRLR are possible candidate genes for the formation of the chicken feathering phenotype in the present study. Our findings help to elucidate the molecular mechanism of the feather rate in chicks.

scholarly journals Comparative transcriptome analysis of high-growth and wild-type strains of Pyropia yezoensis

2020 ◽  
Vol 79 (2) ◽  
pp. 148-156
Author(s):  
Kim Ngan Tran ◽  
Jong-il Choi
Keyword(s):  
Candidate Genes ◽  
De Novo ◽  
Transcriptome Assembly ◽  
High Growth ◽  
Pyropia Yezoensis ◽  
Differentially Expressed ◽  
Future Research ◽  
Wild Type ◽  
Intertidal Zones ◽  
Isolation And Characterization

Pyropia yezoensis (Ueda) M.S.Hwang et H.G.Choi is a popular edible macro-alga that is found mostly in intertidal zones. It is one of the most economically important seaweed species and has been cultivated extensively in the cold waters of East Asia. Various reports have been published on the isolation and characterization of improved strains of Pyropia. However, there are few studies focusing on the molecular basis underlying these mutant strains. In this study, we performed a comparative analysis of whole transcriptomes of wild-type (PyWT) and high-growth (Py500G) strains of P. yezoensis using next generation RNA sequencing (RNA-seq). After sequencing, a total of 167,110,896 paired-end reads with a length of 151 nucleotides, were obtained. De novo transcriptome assembly and redundancy removal generated 19,441 transcripts. The assembly was annotated in NCBI nr, Swiss-Prot, Pfam, KEGG, GO and KOG databases. To unravel the differences in Py500G and PyWT, we mapped Py500G and PyWT reads to the assembly and calculated the expression levels. In total, there were 454 transcripts that were differentially expressed. Among the differentially expressed transcripts, candidate genes were identified with well-known growth and development functions. This study not only identifies candidate genes responsible for the high-growth phenotype of Py500G, but it also provides more comprehensive genomic data for future research on P. yezoensis.

Circular RNA Sequencing of Maternal Platelets: A Novel Tool for the Identification of Pregnancy-Specific Biomarkers

2020 ◽  
Author(s):  
Cees Oudejans ◽  
Vera Manders ◽  
Allerdien Visser ◽  
Remco Keijser ◽  
Naomi Min ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Test Performance ◽  
De Novo ◽  
Well Being ◽  
First Trimester ◽  
Circular Rna ◽  
Positive Control ◽  
Differentially Expressed ◽  
Extravillous Trophoblast ◽  
Trophoblast Invasion

Abstract Background In the first trimester of pregnancy, the maternal platelet is directly involved in a positive feedback mechanism that facilitates invasion of the extravillous trophoblast into the maternal spiral arteries. Dysfunctional trophoblast invasion with defective deep placentation is primordial in the etiology of the “great obstetrical syndromes.” Methods In this proof-of-concept study, using transcriptome analysis of circular RNA (circRNA) following RNA sequencing of maternal platelets, we tested whether pregnancy-specific circRNA markers could be identified in the first trimester of normal pregnancies. Differential transcript expression analysis of circRNAs, as predicted by Accurate CircRNA Finder Suite, CircRNA Identifier (version 2), and Known and Novel Isoform Explorer, was done using thromboSeq.R with variation of multiple settings. Test performance was checked for (a) de novo circRNA identification using the novel platelet-specific Plt-circR4 as a positive control, (b) complete segregation of groups (pregnant vs nonpregnant) after heat map–dendrogram clustering, (c) identification of pregnancy-specific circRNA markers at a false discovery rate (FDR) <0.05, and (d) confirmation of differentially expressed circRNA markers with an FDR <0.05 by an independent method, reverse transcription–quantitative PCR. Results Of the differentially expressed circRNAs with P values <0.05, 41 circRNAs were upregulated (logFC >2), and 52 circRNAs were downregulated (logFC less than −2) in first-trimester platelet RNA. Of these, nuclear receptor-interacting protein 1 circRNA covering exons 2 and 3 of the 5′-untranslated region was pregnancy specific with upregulation in first-trimester maternal platelets compared to nonpregnant controls. Conclusion CircRNA sequencing of first-trimester maternal platelets permits the identification of novel pregnancy-specific RNA biomarkers. Future use could include the assessment of maternal and fetal well-being.

scholarly journals Rapid identification of a candidate gene related to fiber strength using a superior chromosome segment substitution line from Gossypium hirsutum ×Gossypium barbadense via bulked segregant RNA-sequencing

2019 ◽  
Author(s):  
Qi Zhang ◽  
Pengtao Li ◽  
Aiying Liu ◽  
Quanwei Lu ◽  
Juwu Gong ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Rna Sequencing ◽  
Fiber Strength ◽  
Rapid Identification ◽  
Differentially Expressed ◽  
Chromosome Segment ◽  
Strength Development ◽  
Recurrent Parent ◽  
Allelic Polymorphism ◽  
Segment Substitution

Abstract Gossypium is the most widely cultivated commercial crop producing natural fiber around the world, and fiber strength principally determined during the secondary wall thickening period is a critical trait for fiber quality. Based on the developed BC 5 F 3:5 CSSLs (chromosome segment substitution lines) from G. hisutum CCRI36 × G. barbadense Hai1, the superior MBI9915 was chosen to construct the secondary segregated population BC 7 F 2 with its recurrent parent CCRI36, which was subjected to Bulk segregant RNA-sequencing (BSR-seq) for rapid identification of candidate genes related to fiber strength. Four fiber-transcriptome libraries were separately constructed and sequenced, including two parents (CCRI36 and MBI9915) and two extreme pools at 20 DPA (days post anathesis). Through multiple comparisons, 3742 DEGs (differentially expressed genes) and 3252 DEGs were separately identified between two parents and between two extreme pools, while 536 DEGs were overlapped between parent and extreme pool groups. A total of 831high-probability SNPs (single nucleotide polymorphism) were identified relevant to fiber strength between two extreme pools through allelic-polymorphism comparison in mRNA sequences, and 18 correlated regions with 1981 annotation genes were finally screened by linkage analysis with SNP-index method, of which including only 12 common genes differentially expressed both between two parents and two pools. Interesting, there was one correlated region consistent with the previous study with the same parents on chromosome A07 with 13-14 Mb, and one common DEG ( Gh_A07G0837 ) in the candidate region was identified in both parents and extreme pools, which has been reported to be involved in fiber strength development through regulating reactive oxygen species (ROS) activity. The reliability of BSR-seq results was validated by the quantitative real-time PCR (qRT-PCR) experiments on 5 DEGs at 20 DPA. This study focuses on bulked segregant analysis of the extreme pools from segregation population developed by superior CSSL and its recurrent parent, indicating that BSR-seq can be efficiently applied on rapid identification for candidate genes related to the significant quantitative traits, which provides valuable contributions for comprehension of fiber strength formation in cotton.

scholarly journals The ‘Tommy Atkins’ mango genome reveals candidate genes for fruit quality

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ian S. E. Bally ◽  
◽  
Aureliano Bombarely ◽  
Alan H. Chambers ◽  
Yuval Cohen ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Fruit Quality ◽  
De Novo ◽  
Mapping Population ◽  
Mangifera Indica ◽  
Consensus Sequence ◽  
Fruit Size ◽  
Hybrid Population ◽  
High Molecular Weight Dna ◽  
Tropical Fruit

Abstract Background Mango, Mangifera indica L., an important tropical fruit crop, is grown for its sweet and aromatic fruits. Past improvement of this species has predominantly relied on chance seedlings derived from over 1000 cultivars in the Indian sub-continent with a large variation for fruit size, yield, biotic and abiotic stress resistance, and fruit quality among other traits. Historically, mango has been an orphan crop with very limited molecular information. Only recently have molecular and genomics-based analyses enabled the creation of linkage maps, transcriptomes, and diversity analysis of large collections. Additionally, the combined analysis of genomic and phenotypic information is poised to improve mango breeding efficiency. Results This study sequenced, de novo assembled, analyzed, and annotated the genome of the monoembryonic mango cultivar ‘Tommy Atkins’. The draft genome sequence was generated using NRGene de-novo Magic on high molecular weight DNA of ‘Tommy Atkins’, supplemented by 10X Genomics long read sequencing to improve the initial assembly. A hybrid population between ‘Tommy Atkins’ x ‘Kensington Pride’ was used to generate phased haplotype chromosomes and a highly resolved phased SNP map. The final ‘Tommy Atkins’ genome assembly was a consensus sequence that included 20 pseudomolecules representing the 20 chromosomes of mango and included ~ 86% of the ~ 439 Mb haploid mango genome. Skim sequencing identified ~ 3.3 M SNPs using the ‘Tommy Atkins’ x ‘Kensington Pride’ mapping population. Repeat masking identified 26,616 genes with a median length of 3348 bp. A whole genome duplication analysis revealed an ancestral 65 MYA polyploidization event shared with Anacardium occidentale. Two regions, one on LG4 and one on LG7 containing 28 candidate genes, were associated with the commercially important fruit size characteristic in the mapping population. Conclusions The availability of the complete ‘Tommy Atkins’ mango genome will aid global initiatives to study mango genetics.

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