Comparative transcriptome analysis reveals the genetic basis of coat color variation in Pashmina goat.
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ABSTRACT:
SUBMITTER: Bhat B
PROVIDER: S-EPMC6478727 | biostudies-literature | 2019 Apr
REPOSITORIES: biostudies-literature
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Project description:BackgroundThe common carp is an important aquaculture species that is widely distributed across the world. During the long history of carp domestication, numerous carp strains with diverse skin colors have been established. Skin color is used as a visual criterion to determine the market value of carp. However, the genetic basis of common carp skin color has not been extensively studied.Methodology/principal findingsIn this study, we performed Illumina sequencing on two common carp strains: the reddish Xingguo red carp and the brownish-black Yellow River carp. A total of 435,348,868 reads were generated, resulting in 198,781 assembled contigs that were used as reference sequences. Comparisons of skin transcriptome files revealed 2,012 unigenes with significantly different expression in the two common carp strains, including 874 genes that were up-regulated in Xingguo red carp and 1,138 genes that were up-regulated in Yellow River carp. The expression patterns of 20 randomly selected differentially expressed genes were validated using quantitative RT-PCR. Gene pathway analysis of the differentially expressed genes indicated that melanin biosynthesis, along with the Wnt and MAPK signaling pathways, is highly likely to affect the skin pigmentation process. Several key genes involved in the skin pigmentation process, including TYRP1, SILV, ASIP and xCT, showed significant differences in their expression patterns between the two strains.ConclusionsIn this study, we conducted a comparative transcriptome analysis of Xingguo red carp and Yellow River carp skins, and we detected key genes involved in the common carp skin pigmentation process. We propose that common carp skin pigmentation depends upon at least three pathways. Understanding fish skin color genetics will facilitate future molecular selection of the fish skin colors with high market values.
| S-EPMC4177847 | biostudies-literature
Project description:Yellow seed coat in rapeseed (Brassica napus) is a desirable trait that can be targeted to improve the quality of this oilseed crop. To better understand the inheritance mechanism of the yellow-seeded trait, we performed transcriptome profiling of developing seeds in yellow- and black-seeded rapeseed with different backgrounds. The differentially expressed genes (DEGs) during seed development showed significant characteristics, these genes were mainly enriched for the Gene Ontology (GO) terms carbohydrate metabolic process, lipid metabolic process, photosynthesis, and embryo development. Moreover, 1206 and 276 DEGs, which represent candidates to be involved in seed coat color, were identified between yellow- and black-seeded rapeseed during the middle and late stages of seed development, respectively. Based on gene annotation, GO enrichment analysis, and protein-protein interaction network analysis, the downregulated DEGs were primarily enriched for the phenylpropanoid and flavonoid biosynthesis pathways. Notably, 25 transcription factors (TFs) involved in regulating flavonoid biosynthesis pathway, including known (e.g., KNAT7, NAC2, TTG2 and STK) and predicted TFs (e.g., C2H2-like, bZIP44, SHP1, and GBF6), were identified using integrated gene regulatory network (iGRN) and weight gene co-expression networks analysis (WGCNA). These candidate TF genes had differential expression profiles between yellow- and black-seeded rapeseed, suggesting they might function in seed color formation by regulating genes in the flavonoid biosynthesis pathway. Thus, our results provide in-depth insights that facilitate the exploration of candidate gene function in seed development. In addition, our data lay the foundation for revealing the roles of genes involved in the yellow-seeded trait in rapeseed.
| S-EPMC10042178 | biostudies-literature
Project description:BackgroundTo investigate the molecular mechanisms determining the coat color of native breed sheep in Xinjiang.MethodsBashibai sheep, Yemule white sheep and Tulufan black sheep were selected. Illumina HiSeq X Ten sequencing technology was used to detect the genes responsible for the white, light brown, black and cyan gray coat colors in sheep. Sequence analysis and functional gene annotation analysis were performed to analyze the results. The signal pathways and differentially expressed genes related to sheep hair color production regulation were screened and finally verified by real-time polymerase chain reaction.ResultsFunctional annotation by Kyoto Encyclopedia of Genes and Genomes analysis revealed significant differences in enrichment of immunity-related pathways as well as melanogenesis synthetic and tyrosine metabolism pathways. Our results showed that the DCT, TYR, TYRP1, PMEL, SLC45A2 and MLANA six genes may be associated with the regulation of coat color development and provide a theoretical basis for selecting natural coat colors of sheep.
| S-EPMC6875393 | biostudies-literature
Project description:BackgroundHericium erinaceus, also known as lion's mane mushroom, is a widely distributed edible and medicinal fungus in Asian countries. H. erinaceus harbors diverse bioactive metabolites with anticancer, immunomodulating, anti-inflammatory, antimicrobial, antihypertensive, antidiabetic and neuroprotective properties. Although the chemical synthesis processes of these bioactive metabolites are known, the biosynthetic processes remain unknown.ResultsIn this study, we obtained the transcriptomes of six H. erinaceus strains using next-generation RNA sequencing and investigated the characteristics of the transcriptomes and biosynthesis of bioactive compounds, especially polysaccharides. The transcriptomes ranged in size from 46.58 to 58.14 Mb, with the number of unigenes ranging from 20,902 to 37,259 across the six H. erinaceus strains. Approximately 60% of the unigenes were successfully annotated by comparing sequences against different databases, including the nonredundant (NR), Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), clusters of orthologous groups for eukaryotic complete genomes (KOG) and Swiss-Prot databases. Most of the transcripts were putatively involved in signal transduction, carbohydrate metabolism, translation, transport and catabolism, and amino acid metabolism. Genes involved in polysaccharide biosynthesis were identified, and these genes encoded phosphoglucomutase (PGM), glucose phosphate isomerase (PGI), UDP-glucose pyrophosphorylase (UGP), glycoside hydrolase family proteins, glycosyltransferase family proteins and other proteins. Moreover, the putative pathway for the intracellular polysaccharide biosynthesis of H. erinaceus was analyzed. Additionally, the open reading frames (ORFs) and simple sequence repeats (SSRs) were predicted from the transcriptome data of the six strains.ConclusionsOverall, the present study may facilitate the discovery of polysaccharide biosynthesis processes in H. erinaceus and provide useful information for exploring the secondary metabolites in other members of the Basidiomycetes genus.
| S-EPMC6667577 | biostudies-literature
Project description:The seed coat takes an important function in the life cycle of plants, especially seed growth and development. It promotes the accumulation of nutrients inside the seed and protects the seed embryo from mechanical damage. Seed coat permeability is an important characteristic of seeds, which not only affects seed germination, but also hinders the detection of seed vigor by electrical conductivity (EC) method. This research aimed to elucidate the mechanism of seed coat permeability formation through metabolome and transcriptome analysis of Elymus nutans. We collected the samples at 8, 18, and 28 days post-anthesis (dpa), and conducted a seed inclusion exosmosis experiment and observed the seed coat permeability. Moreover, we analyzed the changes in the metabolome and transcriptome during different development stages. Here, taking 8 dpa as control, 252 upregulated and 157 downregulated differentially expressed metabolites (DEMs) were observed and 886 upregulated unigenes and 1170 downregulated unigenes were identified at 18 dpa, while 4907 upregulated unigenes and 8561 downregulated unigenes were identified at 28 dpa. Meanwhile, we observed the components of ABC transporters, the biosynthesis of unsaturated fatty acids, and phenylalanine metabolism pathways. The key metabolites and genes affecting seed coat permeability were thiamine and salicylic acid. Furthermore, there were 13 and 14 genes with correlation coefficients greater than 0.8 with two key metabolites, respectively, and the -log2Fold Change- of these genes were greater than 1 at different development stages. Meanwhile, pathogenesis-related protein 1 and phenylalanine ammonia-lyase play an important role in regulating the formation of compounds. Our results outline a framework for understanding the development changes during seed growth of E. nutans and provide insights into the traits of seed coat permeability and supply a great significance value to seed production and quality evaluation.
| S-EPMC9437961 | biostudies-literature
Project description:Fish skin color is often strongly affected by background color. We hypothesized that the regulatory mechanism of variations in skin color in P. leopardus is linked to the background color. In this study, we conducted transcriptome analysis of Plectropomus leopardus cultured under different background colors to compare gene expression levels and the important signaling pathways. The RNA-seq analysis yielded 26,675 known mRNAs, 3278 novel mRNAs, and 3179 differentially expressed genes (DEGs). The DEGs related to melanin synthesis were screened out. Some key melanin-related genes were identified, specifically tyr, slc7a11, mc1r, ednrb, dct, tat, and wnt1. These DEGs were mainly involved in melanogenesis, including tyrosine metabolism, the Wnt signaling pathway, and the cAMP signaling pathway. The expression levels of some key genes were upregulated when background color deepened, such as α-msh, wnt, and gf. The α-MSH/cAMP-dependent, Wnt/β-catenin, and PI3K/Akt signaling pathways were activated, resulting in the accumulation of intracellular mitf. mitf promoted melanin production by binding to the tyr/tyrp1/dct promoter region. In the present study, we explored the molecular mechanism underlying the darkened skin color pattern of P. leopardus, providing a theoretical basis for the molecular mechanism underlying pigmentation in P. leopardus.
| S-EPMC9569894 | biostudies-literature
Project description:The follicle development (FD) is an important factor determining litter size in animals. Recent studies have found that noncoding RNAs (ncRNAs) play an important role in FD. In particular, the role of the regulatory mechanism of competing endogenous RNAs (ceRNAs) that drive FD has attracted increasing attention. Therefore, this study explored the genetic basis of goat FD by obtaining the complete follicular transcriptome of Dazu black goats at different developmental stages. Results revealed that 128 messenger RNAs (mRNAs), 4 long noncoding RNAs (lncRNAs), 49 microRNAs (miRNAs), and 290 circular RNAs (circRNAs) were significantly differentially expressed (DE) between large and small follicles. Moreover, DEmRNAs were enriched in many signaling pathways related to FD, as well as GO terms related to molecular binding and enzyme activity. Based on the analysis of the ceRNA network (CRN), 34 nodes (1 DElncRNAs, 10 DEcircRNAs, 14 DEmiRNAs, and 9 DEmRNAs) and 35 interactions (17 DEcircRNAs-DEmRNAs, 2 DElncRNAs-DEmiRNAs, and 16 DEmRNA-DEmiRNAs) implied that the CRN could be involved in the FD of goats. In conclusion, we described gene regulation by DERNAs and lncRNA/circRNA-miRNA-mRNA CRNs in the FD of goats. This study provided insights into the genetic basis of FD in precise transcriptional regulation.
| S-EPMC8697922 | biostudies-literature
Project description:BackgroundPrevious molecular genetic studies of physiology and pigmentation of sheep skin have focused primarily on a limited number of genes and proteins. To identify additional genes that may play important roles in coat color regulation, Illumina sequencing technology was used to catalog global gene expression profiles in skin of sheep with white versus black coat color.ResultsThere were 90,006 and 74,533 unigenes assembled from the reads obtained from white and black sheep skin, respectively. Genes encoding for the ribosomal proteins and keratin associated proteins were most highly expressed. A total of 2,235 known genes were differentially expressed in black versus white sheep skin, with 479 genes up-regulated and 1,756 genes down-regulated. A total of 845 novel genes were differentially expressed in black versus white sheep skin, consisting of 107 genes which were up-regulated (including 2 highly expressed genes exclusively expressed in black sheep skin) and 738 genes that were down-regulated. There was also a total of 49 known coat color genes expressed in sheep skin, from which 13 genes showed higher expression in black sheep skin. Many of these up-regulated genes, such as DCT, MATP, TYR and TYRP1, are members of the components of melanosomes and their precursor ontology category.ConclusionThe white and black sheep skin transcriptome profiles obtained provide a valuable resource for future research to understand the network of gene expression controlling skin physiology and melanogenesis in sheep.
| S-EPMC3689618 | biostudies-literature
Project description:The transformation of wild animals into domestic ones available for human nutrition was a key prerequisite for modern human societies. However, no other domestic species has had such a substantial impact on the warfare, transportation, and communication capabilities of human societies as the horse. Here, we show that the analysis of ancient DNA targeting nuclear genes responsible for coat coloration allows us to shed light on the timing and place of horse domestication. We conclude that it is unlikely that horse domestication substantially predates the occurrence of coat color variation, which was found to begin around the third millennium before the common era.
| S-EPMC5102060 | biostudies-literature
Project description:The allotetraploid species Brassica juncea (mustard) is grown worldwide as oilseed and vegetable crops; the yellow seed-color trait is particularly important for oilseed crops. Here, to examine the factors affecting seed coat color, we performed a metabolic and transcriptomic analysis of yellow- and dark-seeded B. juncea seeds. In this study, we identified 236 compounds, including 31 phenolic acids, 47 flavonoids, 17 glucosinolates, 38 lipids, 69 other hydroxycinnamic acid compounds, and 34 novel unknown compounds. Of these, 36 compounds (especially epicatechin and its derivatives) accumulated significantly different levels during the development of yellow- and dark-seeded B. juncea. In addition, the transcript levels of BjuDFR, BjuANS,BjuBAN, BjuTT8, and BjuTT19 were closely associated with changes to epicatechin and its derivatives during seed development, implicating this pathway in the seed coat color determinant in B. juncea. Furthermore, we found numerous variations of sequences in the TT8A genes that may be associated with the stability of seed coat color in B. rapa, B. napus, and B. juncea, which might have undergone functional differentiation during polyploidization in the Brassica species. The results provide valuable information for understanding the accumulation of metabolites in the seed coat color of B. juncea and lay a foundation for exploring the underlying mechanism.
| S-EPMC8268557 | biostudies-literature