A transcriptomic scan for potential candidate genes involved in osmoregulation in an obligate freshwater palaemonid prawn (Macrobrachium australiense)

BackgroundUnderstanding the genomic basis of osmoregulation (candidate genes and/or molecular mechanisms controlling the phenotype) addresses one of the fundamental questions in evolutionary ecology. Species distributions and adaptive radiations are thought to be controlled by environmental salinity levels, and efficient osmoregulatory (ionic balance) ability is the main mechanism to overcome the problems related to environmental salinity gradients.MethodsTo better understand how osmoregulatory performance in freshwater (FW) crustaceans allow individuals to acclimate and adapt to raised salinity conditions, here we (i), reviewed the literature on genes that have been identified to be associated with osmoregulation in FW crustaceans, and (ii), performed a transcriptomic analysis using cDNA libraries developed from mRNA isolated from three important osmoregulatory tissues (gill, antennal gland, hepatopancreas) and total mRNA from post larvae taken from the freshwater prawn,Macrobrachium australienseusing Illumina deep sequencing technology. This species was targeted because it can complete its life cycle totally in freshwater but, like manyMacrobrachiumsp., can also tolerate brackish water conditions and hence should have genes associated with tolerance of both FW and saline conditions.ResultsWe obtained between 55.4 and 65.2 million Illumina read pairs from four cDNA libraries. Overall, paired end sequences assembled into a total of 125,196 non-redundant contigs (≥200 bp) with an N50 length of 2,282 bp and an average contig length of 968 bp. Transcriptomic analysis ofM. australienseidentified 32 different gene families that were potentially involved with osmoregulatory capacity. A total of 32,597 transcripts were specified with gene ontology (GO) terms identified on the basis of GO categories. Abundance estimation of expressed genes based on TPM (transcript per million) ≥20 showed 1625 transcripts commonly expressed in all four libraries. Among the top 10 genes expressed in four tissue libraries associated with osmoregulation, arginine kinase and Na+/K+- ATPase showed the highest transcript copy number with 7098 and 660, respectively in gill which is considered to be the most important organ involved in osmoregulation.DiscussionThe current study provides the first broad transcriptome fromM. australienseusing next generation sequencing and identifies potential candidate genes involved in salinity tolerance and osmoregulation that can provide a foundation for investigating osmoregulatory capacity in a wide variety of freshwater crustaceans.

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Candidate genes that have facilitated freshwater adaptation by palaemonid prawns in the genusMacrobrachium: identification and expression validation in a model species (M. koombooloomba)

PeerJ ◽

10.7717/peerj.2977 ◽

2017 ◽

Vol 5 ◽

pp. e2977 ◽

Cited By ~ 17

Author(s):

Md Lifat Rahi ◽

Shorash Amin ◽

Peter B. Mather ◽

David A. Hurwood

Keyword(s):

Candidate Genes ◽

De Novo ◽

Water Channel ◽

Cell Volume Regulation ◽

Freshwater Prawn ◽

Cdna Libraries ◽

Potential Candidate ◽

Eukaryotic Genes ◽

Freshwater Adaptation ◽

Australian Freshwater

BackgroundThe endemic Australian freshwater prawn,Macrobrachium koombooloomba, provides a model for exploring genes involved with freshwater adaptation because it is one of the relatively fewMacrobrachiumspecies that can complete its entire life cycle in freshwater.MethodsThe present study was conducted to identify potential candidate genes that are likely to contribute to effective freshwater adaptation byM. koombooloombausing a transcriptomics approach.De novoassembly of 75 bp paired end 227,564,643 high quality Illumina raw reads from 6 different cDNA libraries revealed 125,917 contigs of variable lengths (200–18,050 bp) with an N50 value of 1597.ResultsIn total, 31,272 (24.83%) of the assembled contigs received significant blast hits, of which 27,686 and 22,560 contigs were mapped and functionally annotated, respectively. CEGMA (Core Eukaryotic Genes Mapping Approach) based transcriptome quality assessment revealed 96.37% completeness. We identified 43 different potential genes that are likely to be involved with freshwater adaptation inM. koombooloomba. Identified candidate genes included: 25 genes for osmoregulation, five for cell volume regulation, seven for stress tolerance, three for body fluid (haemolymph) maintenance, eight for epithelial permeability and water channel regulation, nine for egg size control and three for larval development. RSEM (RNA-Seq Expectation Maximization) based abundance estimation revealed that 6,253, 5,753 and 3,795 transcripts were expressed (at TPM value ≥10) in post larvae, juveniles and adults, respectively. Differential gene expression (DGE) analysis showed that 15 genes were expressed differentially in different individuals but these genes apparently were not involved with freshwater adaptation but rather were involved in growth, development and reproductive maturation.DiscussionThe genomic resources developed here will be useful for better understanding the molecular basis of freshwater adaptation inMacrobrachiumprawns and other crustaceans more broadly.

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PSVII-19 Transcriptomic analysis of the liver of laying hens fed diets containing supplemental fat at early laying stages

Journal of Animal Science ◽

10.1093/jas/skz258.703 ◽

2019 ◽

Vol 97 (Supplement_3) ◽

pp. 353-353

Author(s):

Gi Ppeum Han ◽

Geun Hyeon Park ◽

Jong Hyuk Kim ◽

Hyeon Seok Choi ◽

Hwan Ku Kang ◽

...

Keyword(s):

Fatty Acid ◽

Molecular Mechanisms ◽

Acid Metabolism ◽

Laying Hens ◽

Acid Synthesis ◽

Transcriptomic Analysis ◽

Cdna Libraries ◽

Feeding Diets ◽

Supplemental Fat ◽

Liver Tissues

Abstract Feeding diets containing supplemental fat to laying hens is reported to ameliorate pathogenesis of fatty liver hemorrhagic syndrome (FLHS). However, molecular mechanisms for this positive effect have not been investigated. Thus, we conducted a transcriptomic analysis of the liver of laying hens fed diets containing supplemental fat at early laying stages. Two dietary treatments included basal diets with no supplemental fat and basal diets supplemented with 3.0% tallow. A total of 256 18-week-old Hy-line Brown laying hens were allotted to 1 of 2 treatments. Diets were fed to hens for 12 weeks. At the end of the experiment (30 weeks of age), 5 hens with similar BW per treatment were euthanized to collect liver tissues. The cDNA libraries were constructed with extracted RNA from the liver tissues, and sequenced using the Illumina Nextseq 500 sequencer. Genes with False Discovery Rate (FDR) < 0.05 were defined as differentially expressed genes (DEGs). Results indicated that a total of 951 DEGs were identified, with 483 being up-regulated and 468 being down-regulated in the liver of hens fed diets containing 3.0% tallow. The KEGG analysis revealed that the DEGs belong to several biological pathways such as cellular signaling pathways, carbon metabolism, glycolysis, gluconeogenesis, TCA cycle, amino acid metabolism, drug metabolism, and glycerophospholipid metabolism. Especially for fatty acid metabolism, the DEGs associated with fatty acid degradation (ECI2, ACSL1, HADHA, EHHADH, ACOX1, CPT1) were up-regulated, whereas those related to fatty acid synthesis (ACACA, ACSL5, FASN) were down-regulated in the liver of hens fed diets containing 3.0% tallow, which indicates that supplemental fat in diets may increase fat oxidation but decrease fat synthesis in the liver. These results provide the molecular insights for hepatic lipid metabolisms by feeding diets containing supplemental fat to laying hens at early laying stages.

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Integrity transcriptome and proteome analyses provide new insights into the mechanisms regulating peel cracking in Akebia trifoliata fruit

10.21203/rs.2.19126/v1 ◽

2019 ◽

Author(s):

Juan Niu ◽

Yaliang Shi ◽

Kunyong Huang ◽

Yicheng Zhong ◽

Jing Chen ◽

...

Keyword(s):

Cell Wall ◽

Candidate Genes ◽

Fruit Ripening ◽

Structural Changes ◽

Molecular Mechanisms ◽

Sugar Metabolism ◽

Potential Candidate ◽

Proteomics Data ◽

Galactose Metabolism ◽

Fruit Cracking

Abstract Background Akebia trifoliata (Thunb.) Koidz, can be used as a new potential candidate biofuel and bioenergy crop due to its high productivity, adaptability and tolerance to cultivation conditions. However, the pericarp of A. trifoliata cracks open longitudinally and disperses its seeds along the ventral suture during fruit ripening, which is a serious problem that limits the usefulness of its biofuel feedstocks and causes significant losses of yield and commercial value. However, there have been no known previous investigations of the fruit cracking and its molecular mechanisms in A. trifoliata.Results The dynamic structural changes of the fruit peels were observed. In the non-cracking stage of growth, the exocarp was dense, had an orderly arrangement, and the cuticle was complete and distributed continuously. However, the cells became thinner, had reduced integrity, lost cell wall structures, and there was cell wall break down, in the fruit cracking stage. Moreover, analysis of the complementary RNA sequencing based transcriptomes and tandem mass tag based proteomes at different development stages of the fruit ripening, were performed to detect the genes and proteins related to the fruit cracking in A. trifoliata. A total of 20 differentially expressed genes and 17 differentially abundant proteins were identified from the transcriptomics and proteomics data that contribute to the fruit cracking, by participating in the biosynthesis of the phenylpropanoid pathway, galactose metabolism, pentose, and glucuronate interconversions, starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism. Several candidate genes and proteins related to pentose and glucuronate interconversions (pectate lyases and pectinesterase) and galactose metabolism (β-galactosidases 1 and β-galactosidases 2) may play key roles in A. trifoliata fruit cracking.Conclusions Complementary transcriptome and proteome level analyses indicated that a complex molecular network was controlling the fruit cracking process. This study provides new insights into the molecular basis of fruit cracking in A. trifoliata fruits. The candidate genes/proteins identified in this study may be useful for the genetic improvement of A. trifoliata and other crops.

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Discovery and validation of candidate genes for grain iron and zinc metabolism in pearl millet [Pennisetum glaucum (L.) R. Br.]

Scientific Reports ◽

10.1038/s41598-020-73241-7 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Mahesh D. Mahendrakar ◽

Maheshwari Parveda ◽

P. B. Kavi Kishor ◽

Rakesh K. Srivastava

Keyword(s):

Candidate Genes ◽

Pearl Millet ◽

Developmental Stages ◽

Pennisetum Glaucum ◽

Gene Families ◽

Zn Deficiency ◽

Zinc Metabolism ◽

Potential Candidate ◽

Crop Species ◽

Major Qtl

Abstract Pearl millet is an important crop for alleviating micronutrient malnutrition through genomics-assisted breeding for grain Fe (GFeC) and Zn (GZnC) content. In this study, we identified candidate genes related to iron (Fe) and zinc (Zn) metabolism through gene expression analysis and correlated it with known QTL regions for GFeC/GZnC. From a total of 114 Fe and Zn metabolism-related genes that were selected from the related crop species, we studied 29 genes. Different developmental stages exhibited tissue and stage-specific expressions for Fe and Zn metabolism genes in parents contrasting for GFeC and GZnC. Results revealed that PglZIP, PglNRAMP and PglFER gene families were candidates for GFeC and GZnC. Ferritin-like gene, PglFER1 may be the potential candidate gene for GFeC. Promoter analysis revealed Fe and Zn deficiency, hormone, metal-responsive, and salt-regulated elements. Genomic regions underlying GFeC and GZnC were validated by annotating major QTL regions for grain Fe and Zn. Interestingly, PglZIP and PglNRAMP gene families were found common with a previously reported linkage group 7 major QTL region for GFeC and GZnC. The study provides insights into the foundation for functional dissection of different Fe and Zn metabolism genes homologs and their subsequent use in pearl millet molecular breeding programs globally.

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Transcriptomic Analyses of the Hypothalamic-Pituitary-Gonadal Axis Identify Candidate Genes Related to Egg Production in Xinjiang Yili Geese

Animals ◽

10.3390/ani10010090 ◽

2020 ◽

Vol 10 (1) ◽

pp. 90

Author(s):

Yingping Wu ◽

Xiaoyu Zhao ◽

Li Chen ◽

Junhua Wang ◽

Yuqing Duan ◽

...

Keyword(s):

Candidate Genes ◽

Differentially Expressed Genes ◽

Egg Production ◽

Molecular Mechanisms ◽

Egg Laying ◽

Differentially Expressed ◽

Cdna Libraries ◽

Receptor Interaction ◽

Sequencing Data ◽

Pituitary Glands

The study was conducted to investigate the transcriptomic differences of the hypothalamic-pituitary-gonadal axis between Xinjiang Yili geese with high and low egg production and to find candidate genes regulating the egg production of Xinjiang Yili geese. The 8 selected Xinjiang Yili Geese with high or low egg production (4 for each group) were 3 years old, with good health, and under the same feeding condition. High-throughput sequencing technology was used to sequence cDNA libraries of the hypothalami, pituitary glands, and ovaries. The sequencing data were compared and analyzed, and the transcripts with significant differences were identified and analyzed with bioinformatics. The study showed that the transcriptome sequencing data of the 24 samples contained a total of 1,176,496,146 valid reads and 176.47 gigabase data. Differential expression analyses identified 135, 56, and 331 genes in the hypothalami, pituitary glands, and ovaries of Xinjiang Yili geese with high and low egg production. Further annotation of these differentially expressed genes in the non-redundant protein sequence database (Nr) revealed that 98, 52, and 309 genes were annotated, respectively. Through the annotations of GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases, 30 candidate genes related to the egg production of Xinjiang Yili geese were preliminarily selected. The gap junction, focal adhesion, and ECM-receptor interaction signaling pathways were enriched with the hypothalamic, pituitary, and ovarian differentially expressed genes, and the calcium signaling pathway was enriched with the pituitary and ovarian differentially expressed genes. Thus, these pathways in the hypothalamic-pituitary-gonadal axis may play an important role in regulating egg production of Xinjiang Yili geese. The results provided the transcriptomic information of the hypothalamic-pituitary-gonadal axis of Xinjiang Yili geese and laid the theoretical basis for revealing the molecular mechanisms regulating the egg-laying traits of Xinjiang Yili geese.

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Analysis of Differentially Expressed Genes and Signaling Pathways Related to Intramuscular Fat Deposition in Skeletal Muscle of Sex-Linked Dwarf Chickens

BioMed Research International ◽

10.1155/2014/724274 ◽

2014 ◽

Vol 2014 ◽

pp. 1-7 ◽

Cited By ~ 3

Author(s):

Yaqiong Ye ◽

Shumao Lin ◽

Heping Mu ◽

Xiaohong Tang ◽

Yangdan Ou ◽

...

Keyword(s):

Gene Expression ◽

Skeletal Muscle ◽

Signaling Pathways ◽

Candidate Genes ◽

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Muscle Development ◽

Intramuscular Fat ◽

Differentially Expressed ◽

Potential Candidate

Intramuscular fat (IMF) plays an important role in meat quality. However, the molecular mechanisms underlying IMF deposition in skeletal muscle have not been addressed for the sex-linked dwarf (SLD) chicken. In this study, potential candidate genes and signaling pathways related to IMF deposition in chicken leg muscle tissue were characterized using gene expression profiling of both 7-week-old SLD and normal chickens. A total of 173 differentially expressed genes (DEGs) were identified between the two breeds. Subsequently, 6 DEGs related to lipid metabolism or muscle development were verified in each breed based on gene ontology (GO) analysis. In addition, KEGG pathway analysis of DEGs indicated that some of them (GHR, SOCS3, and IGF2BP3) participate in adipocytokine and insulin signaling pathways. To investigate the role of the above signaling pathways in IMF deposition, the gene expression of pathway factors and other downstream genes were measured by using qRT-PCR and Western blot analyses. Collectively, the results identified potential candidate genes related to IMF deposition and suggested that IMF deposition in skeletal muscle of SLD chicken is regulated partially by pathways of adipocytokine and insulin and other downstream signaling pathways (TGF-β/SMAD3 and Wnt/catenin-βpathway).

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Genetic mapping and transcriptomic characterization of a new fuzzless-tufted cottonseed mutant

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkaa042 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Qian-Hao Zhu ◽

Warwick Stiller ◽

Philippe Moncuquet ◽

Stuart Gordon ◽

Yuman Yuan ◽

...

Keyword(s):

Molecular Mechanisms ◽

Agronomic Traits ◽

Gene Families ◽

Mutant Phenotype ◽

Wild Type ◽

Calcium Dependent ◽

Dependent Protein ◽

Flanking Region ◽

Comparative Transcriptomic Analysis

Abstract Fiber mutants are unique and valuable resources for understanding the genetic and molecular mechanisms controlling initiation and development of cotton fibers that are extremely elongated single epidermal cells protruding from the seed coat of cottonseeds. In this study, we reported a new fuzzless-tufted cotton mutant (Gossypium hirsutum) and showed that fuzzless-tufted near-isogenic lines (NILs) had similar agronomic traits and a higher ginning efficiency compared to their recurrent parents with normal fuzzy seeds. Genetic analysis revealed that the mutant phenotype is determined by a single incomplete dominant locus, designated N5. The mutation was fine mapped to an approximately 250-kb interval containing 33 annotated genes using a combination of bulked segregant sequencing, SNP chip genotyping, and fine mapping. Comparative transcriptomic analysis using 0–6 days post-anthesis (dpa) ovules from NILs segregating for the phenotypes of fuzzless-tufted (mutant) and normal fuzzy cottonseeds (wild-type) uncovered candidate genes responsible for the mutant phenotype. It also revealed that the flanking region of the N5 locus is enriched with differentially expressed genes (DEGs) between the mutant and wild-type. Several of those DEGs are members of the gene families with demonstrated roles in cell initiation and elongation, such as calcium-dependent protein kinase and expansin. The transcriptome landscape of the mutant was significantly reprogrammed in the 6 dpa ovules and, to a less extent, in the 0 dpa ovules, but not in the 2 and 4 dpa ovules. At both 0 and 6 dpa, the reprogrammed mutant transcriptome was mainly associated with cell wall modifications and transmembrane transportation, while transcription factor activity was significantly altered in the 6 dpa mutant ovules. These results imply a similar molecular basis for initiation of lint and fuzz fibers despite certain differences.

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Genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice

Scientific Reports ◽

10.1038/s41598-021-85921-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Raju Bheemanahalli ◽

Montana Knight ◽

Cherryl Quinones ◽

Colleen J. Doherty ◽

S. V. Krishna Jagadish

Keyword(s):

Grain Size ◽

Candidate Genes ◽

Gene Network ◽

Genome Wide Association ◽

Potential Candidate ◽

Genetic Loci ◽

Stay Green ◽

Yield And Quality ◽

Genome Wide ◽

Wide Range

AbstractHigh night temperatures (HNT) are shown to significantly reduce rice (Oryza sativa L.) yield and quality. A better understanding of the genetic architecture of HNT tolerance will help rice breeders to develop varieties adapted to future warmer climates. In this study, a diverse indica rice panel displayed a wide range of phenotypic variability in yield and quality traits under control night (24 °C) and higher night (29 °C) temperatures. Genome-wide association analysis revealed 38 genetic loci associated across treatments (18 for control and 20 for HNT). Nineteen loci were detected with the relative changes in the traits between control and HNT. Positive phenotypic correlations and co-located genetic loci with previously cloned grain size genes revealed common genetic regulation between control and HNT, particularly grain size. Network-based predictive models prioritized 20 causal genes at the genetic loci based on known gene/s expression under HNT in rice. Our study provides important insights for future candidate gene validation and molecular marker development to enhance HNT tolerance in rice. Integrated physiological, genomic, and gene network-informed approaches indicate that the candidate genes for stay-green trait may be relevant to minimizing HNT-induced yield and quality losses during grain filling in rice by optimizing source-sink relationships.

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Transcriptome profiling analysis of muscle tissue reveals potential candidate genes affecting water holding capacity in Chinese Simmental beef cattle

Scientific Reports ◽

10.1038/s41598-021-91373-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Lili Du ◽

Tianpeng Chang ◽

Bingxing An ◽

Mang Liang ◽

Xinghai Duan ◽

...

Keyword(s):

Beef Cattle ◽

Candidate Genes ◽

Molecular Mechanism ◽

Meat Quality ◽

Relevant Literature ◽

Transcriptome Profiling ◽

Water Holding Capacity ◽

Potential Candidate ◽

Protein Protein Interaction ◽

Water Holding

AbstractWater holding capacity (WHC) is an important sensory attribute that greatly influences meat quality. However, the molecular mechanism that regulates the beef WHC remains to be elucidated. In this study, the longissimus dorsi (LD) muscles of 49 Chinese Simmental beef cattle were measured for meat quality traits and subjected to RNA sequencing. WHC had significant correlation with 35 kg water loss (r = − 0.99, p < 0.01) and IMF content (r = 0.31, p < 0.05), but not with SF (r = − 0.20, p = 0.18) and pH (r = 0.11, p = 0.44). Eight individuals with the highest WHC (H-WHC) and the lowest WHC (L-WHC) were selected for transcriptome analysis. A total of 865 genes were identified as differentially expressed genes (DEGs) between two groups, of which 633 genes were up-regulated and 232 genes were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment revealed that DEGs were significantly enriched in 15 GO terms and 96 pathways. Additionally, based on protein–protein interaction (PPI) network, animal QTL database (QTLdb), and relevant literature, the study not only confirmed seven genes (HSPA12A, HSPA13, PPARγ, MYL2, MYPN, TPI, and ATP2A1) influenced WHC in accordance with previous studies, but also identified ATP2B4, ACTN1, ITGAV, TGFBR1, THBS1, and TEK as the most promising novel candidate genes affecting the WHC. These findings could offer important insight for exploring the molecular mechanism underlying the WHC trait and facilitate the improvement of beef quality.

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Amynthas corticis genome reveals molecular mechanisms behind global distribution

Communications Biology ◽

10.1038/s42003-021-01659-4 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Xing Wang ◽

Yi Zhang ◽

Yufeng Zhang ◽

Mingming Kang ◽

Yuanbo Li ◽

...

Keyword(s):

Genome Assembly ◽

Molecular Mechanisms ◽

Gene Families ◽

The Body ◽

Gene Family Evolution ◽

Complex Environments ◽

Protein Coding ◽

Itraq Analysis ◽

Rdna Sequencing ◽

Long Read

AbstractEarthworms (Annelida: Crassiclitellata) are widely distributed around the world due to their ancient origination as well as adaptation and invasion after introduction into new habitats over the past few centuries. Herein, we report a 1.2 Gb complete genome assembly of the earthworm Amynthas corticis based on a strategy combining third-generation long-read sequencing and Hi-C mapping. A total of 29,256 protein-coding genes are annotated in this genome. Analysis of resequencing data indicates that this earthworm is a triploid species. Furthermore, gene family evolution analysis shows that comprehensive expansion of gene families in the Amynthas corticis genome has produced more defensive functions compared with other species in Annelida. Quantitative proteomic iTRAQ analysis shows that expression of 147 proteins changed in the body of Amynthas corticis and 16 S rDNA sequencing shows that abundance of 28 microorganisms changed in the gut of Amynthas corticis when the earthworm was incubated with pathogenic Escherichia coli O157:H7. Our genome assembly provides abundant and valuable resources for the earthworm research community, serving as a first step toward uncovering the mysteries of this species, and may provide molecular level indicators of its powerful defensive functions, adaptation to complex environments and invasion ability.

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