scholarly journals Parallel molecular mechanisms underlie convergent evolution of the exaggerated snout phenotype in East African cichlids

2022 ◽  
Author(s):  
Anna Duenser ◽  
Pooja Singh ◽  
Laurene Alicia Lecaudey ◽  
Christian Sturmbauer ◽  
Craig Albertson ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Soft Tissue ◽  
Convergent Evolution ◽  
Molecular Mechanisms ◽  
Lake Tanganyika ◽  
Expression Patterns ◽  
Lake Malawi ◽  
Differentially Expressed ◽  
Prime Model ◽  
East African

Studying instances of convergent evolution of novel phenotypes can shed light on the evolutionary constraints that shape morphological diversity. Cichlid fishes from the East African Great Lakes are a prime model to investigate convergent adaptations. However, most studies on cichlid craniofacial morphologies have primarily considered bony structures, while soft tissue adaptations have been less intensely scrutinised. A rare example of an exaggerated soft tissue phenotype is the formation of a snout flap. This tissue flap develops from the upper lip and has evolved in only one cichlid genus from Lake Malawi and one genus from Lake Tanganyika. To investigate the molecular basis of snout flap convergence, we used mRNA sequencing to compare two species with snout flap (Labeotropheus trewavasae and Ophthalmotilapia nasuta) to their close relatives without snout flaps (Tropheops tropheops and Ophthalmotilapia ventralis) from Lake Tanganyika and Malawi. Our analysis revealed a greater complexity of differential gene expression patterns underlying the snout flap in the younger adaptive radiation of Lake Malawi than in the older Lake Tanganyika radiation. We identified 201 genes that were repeatedly differentially expressed between species with and without the snout flap in both lakes, suggesting that the pathway that gives rise to snout flaps is evolutionarily constrained, even though the flaps play very different functions in each species. The convergently expressed genes are involved in proline and hydroxyproline metabolism, which have been linked to human skin and facial deformities. Additionally, we also found enrichment for transcription factor binding sites upstream of differentially expressed genes such as members of the FOX transcription factor family, especially foxf1 and foxa2, which also showed an increased expression in the flapped snout and are linked to nose morphogenesis in mammals, as well as ap4 (tfap4), a transcription factor showing reduced expression in the flapped snout with an unknown role in the development of craniofacial soft tissues. As genes involved in cichlids snout flap development are associated with many human mid-line facial dysmorphologies, our findings imply a conservation of genes involved in mid-line patterning across vastly distant evolutionary lineages of vertebrates.

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 Integration of mRNA and miRNA Analysis Reveals the Molecular Mechanism Underlying Salt and Alkali Stress Tolerance in Tobacco

2019 ◽  
Vol 20 (10) ◽  
pp. 2391 ◽  
Author(s):  
Jiayang Xu ◽  
Qiansi Chen ◽  
Pingping Liu ◽  
Wei Jia ◽  
Zheng Chen ◽  
...  
Keyword(s):  
Salinity Stress ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Crop Yields ◽  
Antioxidant Activities ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Alkali Stress ◽  
Rna Seq ◽  
Alkali Tolerance

Salinity is one of the most severe forms of abiotic stress and affects crop yields worldwide. Plants respond to salinity stress via a sophisticated mechanism at the physiological, transcriptional and metabolic levels. However, the molecular regulatory networks involved in salt and alkali tolerance have not yet been elucidated. We developed an RNA-seq technique to perform mRNA and small RNA (sRNA) sequencing of plants under salt (NaCl) and alkali (NaHCO3) stress in tobacco. Overall, 8064 differentially expressed genes (DEGs) and 33 differentially expressed microRNAs (DE miRNAs) were identified in response to salt and alkali stress. A total of 1578 overlapping DEGs, which exhibit the same expression patterns and are involved in ion channel, aquaporin (AQP) and antioxidant activities, were identified. Furthermore, genes involved in several biological processes, such as “photosynthesis” and “starch and sucrose metabolism,” were specifically enriched under NaHCO3 treatment. We also identified 15 and 22 miRNAs that were differentially expressed in response to NaCl and NaHCO3, respectively. Analysis of inverse correlations between miRNAs and target mRNAs revealed 26 mRNA-miRNA interactions under NaCl treatment and 139 mRNA-miRNA interactions under NaHCO3 treatment. This study provides new insights into the molecular mechanisms underlying the response of tobacco to salinity stress.

scholarly journals Transcription Factor Erg Variants and Functional Diversification of Chondrocytes during Limb Long Bone Development

2000 ◽  
Vol 150 (1) ◽  
pp. 27-40 ◽  
Author(s):  
Masahiro Iwamoto ◽  
Yoshinobu Higuchi ◽  
Eiki Koyama ◽  
Motomi Enomoto-Iwamoto ◽  
Kojiro Kurisu ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Limb Development ◽  
Matrix Protein ◽  
Molecular Mechanisms ◽  
Articular Chondrocytes ◽  
Bone Cells ◽  
Expression Patterns ◽  
Extracellular Matrix Protein ◽  
Long Bone ◽  
Chondrocyte Maturation

During limb development, chondrocytes located at the epiphyseal tip of long bone models give rise to articular tissue, whereas the more numerous chondrocytes in the shaft undergo maturation, hypertrophy, and mineralization and are replaced by bone cells. It is not understood how chondrocytes follow these alternative pathways to distinct fates and functions. In this study we describe the cloning of C-1-1, a novel variant of the ets transcription factor ch-ERG. C-1-1 lacks a short 27–amino acid segment located ∼80 amino acids upstream of the ets DNA binding domain. We found that in chick embryo long bone anlagen, C-1-1 expression characterizes developing articular chondrocytes, whereas ch-ERG expression is particularly prominent in prehypertrophic chondrocytes in the growth plate. To analyze the function of C-1-1 and ch-ERG, viral vectors were used to constitutively express each factor in developing chick leg buds and cultured chondrocytes. We found that virally driven expression of C-1-1 maintained chondrocytes in a stable and immature phenotype, blocked their maturation into hypertrophic cells, and prevented the replacement of cartilage with bone. It also induced synthesis of tenascin-C, an extracellular matrix protein that is a unique product of developing articular chondrocytes. In contrast, virally driven expression of ch-ERG significantly stimulated chondrocyte maturation in culture, as indicated by increases in alkaline phosphatase activity and deposition of a mineralized matrix; however, it had modest effects in vivo. The data show that C-1-1 and ch-ERG have diverse biological properties and distinct expression patterns during skeletogenesis, and are part of molecular mechanisms by which limb chondrocytes follow alternative developmental pathways. C-1-1 is the first transcription factor identified to date that appears to be instrumental in the genesis and function of epiphyseal articular chondrocytes.

scholarly journals Lacustrine mollusc radiations in the Malawi Basin: experiments in a natural laboratory for evolution

2012 ◽  
Vol 9 (12) ◽  
pp. 18519-18544 ◽  
Author(s):  
D. Van Damme ◽  
A. Gautier
Keyword(s):  
Lake Tanganyika ◽  
Environmental Changes ◽  
Lake Malawi ◽  
Early Pleistocene ◽  
Divergent Evolution ◽  
Freshwater Ecosystem ◽  
East African ◽  
African Lakes ◽  
East African Lakes ◽  
Natural Laboratory

Abstract. In Terminal Pliocene-Early Pleistocene times, part of the Malawi Basin was occupied by palaeo-lake Chiwondo. Molluscan biostratigraphy situates this freshwater lake either in the East African wet phase between 2.7–2.4 Ma or that of 2.0–1.8 Ma. In-lake divergent evolution remained restricted to a few molluscan taxa and was very modest. The lacustrine Chiwondo fauna went extinct at the beginning of the Pleistocene. The Modern Lake Malawi malacofauna is poor and descends from ubiquistic South-East African taxa and some Malawi Basin endemics that invaded the present lake after the Late Pleistocene mega-droughts. The Pleistocene aridity crises caused dramatic changes, affecting the malacofauna of all East African lakes. All lacustrine endemic faunas that had evolved in the Pliocene rift lakes, such as palaeo-lake Chiwondo, became extinct. In Lake Tanganyika, the freshwater ecosystem did not crash as in other lakes, but the environmental changes were sufficiently important to trigger a vast radiation. All African endemic lacustrine molluscan clades that are the result of in-lake divergence are hence geologically young, including the vast Lavigeria clade in Lake Tanganyika (ca. 43 species).

scholarly journals Transcriptome analysis identifies genes involved in the somatic embryogenesis of Eucalyptus

2020 ◽  
Author(s):  
Yufei Xiao ◽  
Junji Li ◽  
Ye Zhang ◽  
Xiaoning Zhang ◽  
Hailong Liu ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Somatic Embryogenesis ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Zinc Finger Protein ◽  
Expression Patterns ◽  
Late Embryogenesis Abundant ◽  
Arabinogalactan Protein ◽  
Late Embryogenesis Abundant Protein ◽  
Eucalyptus Species

Abstract Background: Eucalyptus, a highly diverse genus of the Myrtaceae family, is the most widely planted hardwood in the world due to its increasing importance for fiber and energy. Somatic embryogenesis (SE) is one large-scale method to provide commercial use of the vegetative propagation of Eucalyptus and dedifferentiation is a key step for plant cells to become meristematic. However, little is known about the molecular changes during the Eucalyptus SE.Results: We compared the transcriptome profiles of the differentiated and dedifferentiated tissues of two Eucalyptus species – E. camaldulensis (high embryogenetic potential) and E. grandis x urophylla (low embryogenetic potential). Initially, we identified 18,777 to 20,240 genes in all samples. Compared to the differentiated tissues, we identified 9,229 and 8,989 differentially expressed genes (DEGs) in the dedifferentiated tissues of E. camaldulensis and E. grandis x urophylla, respectively, and 2,687 up-regulated and 2,581 down-regulated genes shared. Next, we identified 2,003 up-regulated and 1,958 down-regulated genes only in E. camaldulensis, including 6 somatic embryogenesis receptor kinase, 17 ethylene, 12 auxin, 83 ribosomal protein, 28 zinc finger protein, 10 heat shock protein, 9 histone, 122 cell wall related and 98 transcription factor genes. Genes from other families like ABA, arabinogalactan protein and late embryogenesis abundant protein were also found to be specifically dysregulated in the dedifferentiation process of E. camaldulensis. Further, we identified 48,447 variants (SNPs and small indels) specific to E. camaldulensis, including 13,434 exonic variants from 4,723 genes (e.g., annexin, GN, ARF and AP2-like ethylene-responsive transcription factor). qRT-PCR was used to confirm the gene expression patterns in both E. camaldulensis and E. grandis x urophylla. Conclusions: This is the first time to study the somatic embryogenesis of Eucalyptus using transcriptome sequencing. It will improve our understanding of the molecular mechanisms of somatic embryogenesis and dedifferentiation in Eucalyptus. Our results provide a valuable resource for future studies in the field of Eucalyptus and will benefit the Eucalyptus breeding program.

scholarly journals Comparative Transcriptome Analysis of a Fan-shaped Inflorescence in Pineapple Using RNA-seq

2020 ◽  
Author(s):  
Tao Xie ◽  
Zhiquan Cai ◽  
Aiping Luan ◽  
Wei Zhang ◽  
Jing Wu ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Soluble Sugar ◽  
Differentially Expressed ◽  
Soluble Solids ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Stem Apex ◽  
Inflorescence Axis ◽  
Flower Stem

Abstract Background: Pineapple plant usually has a capitulum. However, a fan-shaped inflorescence was evolved in an exceptional material, having multiple crown buds. In order to reveal the molecular mechanisms of the formation of the fan-shaped inflorescence, fruit traits and the transcriptional differences between a fan-shaped inflorescence (FI) and a capitulum inflorescence (CI) pineapples were analyzed in the three tissues, i.e., the flower stem apex (FIs and CIs), the base of the inflorescence (FIb and CIb), and the inflorescence axis (FIa and CIa).Results: Except for a clear differentiation of inflorescence morphology, no significant differences in the structure of inflorescence organs and the main nutritional components (soluble solids, soluble sugar, titratable acid, and VC) in fruits were found between the two pineapples. Between the fan- and capitulum-shaped inflorescences, a total of 5370 differentially expressed genes (DEGs) were identified across the three tissues; and 3142, 2526 and 2255 DEGs were found in the flower stem apex, the base of the inflorescence, and the inflorescence axis, respectively. Of these genes, there were 489 overlapping DEGs in all three tissue comparisons. In addition, 5769 DEGs were identified between different tissues within each pineapple. Functional analysis indicated between the two pineapples that 444 transcription factors (TFs) and 206 inflorescence development related genes (IDGs) were differentially expressed in at least one tissue comparison, while 45 TFs and 21 IDGs were overlapped across the 3 tissues. Among the 489 overlapping DEGs in the 3 tissue comparisons between the two pineapples, excluding the IDGs and TFs, 80 of them revealed a higher percentage of involvement in the biological processes relating to response to auxin, and reproductive processes. RNA-seq value and real-time quantitative PCR analysis exhibited the same gene expression patterns in the three tissues. Conclusions: Our result provided novel cues for understanding the molecular mechanisms of the formation of fan-shaped inflorescence in pineapple, making a valuable resource for the study of plant breeding and the speciation of the pineapples.

scholarly journals Transcriptome analysis identifies genes involved in the somatic embryogenesis of Eucalyptus

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Yufei Xiao ◽  
Junji Li ◽  
Ye Zhang ◽  
Xiaoning Zhang ◽  
Hailong Liu ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Somatic Embryogenesis ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Zinc Finger Protein ◽  
Expression Patterns ◽  
Late Embryogenesis Abundant ◽  
Arabinogalactan Protein ◽  
Late Embryogenesis Abundant Protein ◽  
Eucalyptus Species

Abstract Background Eucalyptus, a highly diverse genus of the Myrtaceae family, is the most widely planted hardwood in the world due to its increasing importance for fiber and energy. Somatic embryogenesis (SE) is one large-scale method to provide commercial use of the vegetative propagation of Eucalyptus and dedifferentiation is a key step for plant cells to become meristematic. However, little is known about the molecular changes during the Eucalyptus SE. Results We compared the transcriptome profiles of the differentiated and dedifferentiated tissues of two Eucalyptus species – E. camaldulensis (high embryogenetic potential) and E. grandis x urophylla (low embryogenetic potential). Initially, we identified 18,777 to 20,240 genes in all samples. Compared to the differentiated tissues, we identified 9229 and 8989 differentially expressed genes (DEGs) in the dedifferentiated tissues of E. camaldulensis and E. grandis x urophylla, respectively, and 2687 up-regulated and 2581 down-regulated genes shared. Next, we identified 2003 up-regulated and 1958 down-regulated genes only in E. camaldulensis, including 6 somatic embryogenesis receptor kinase, 17 ethylene, 12 auxin, 83 ribosomal protein, 28 zinc finger protein, 10 heat shock protein, 9 histone, 122 cell wall related and 98 transcription factor genes. Genes from other families like ABA, arabinogalactan protein and late embryogenesis abundant protein were also found to be specifically dysregulated in the dedifferentiation process of E. camaldulensis. Further, we identified 48,447 variants (SNPs and small indels) specific to E. camaldulensis, including 13,434 exonic variants from 4723 genes (e.g., annexin, GN, ARF and AP2-like ethylene-responsive transcription factor). qRT-PCR was used to confirm the gene expression patterns in both E. camaldulensis and E. grandis x urophylla. Conclusions This is the first time to study the somatic embryogenesis of Eucalyptus using transcriptome sequencing. It will improve our understanding of the molecular mechanisms of somatic embryogenesis and dedifferentiation in Eucalyptus. Our results provide a valuable resource for future studies in the field of Eucalyptus and will benefit the Eucalyptus breeding program.

scholarly journals Expression Analysis of the NAC Transcription Factor Family of Populus in Response to Salt Stress

Forests ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 688 ◽  
Author(s):  
Wang ◽  
Huang ◽  
Wang ◽  
Dang ◽  
Jiang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Salt Stress ◽  
Expression Pattern ◽  
Gene Structure ◽  
Expression Patterns ◽  
Nac Transcription Factor ◽  
Differentially Expressed ◽  
Genome Organisation ◽  
Cis Element ◽  
Wide Range

Research Highlights: Sequence phylogeny, genome organisation, gene structure, conserved motifs, promoter cis-element and expression profiling of poplar NACs related to salt stress were detected. In addition, expression of two salt-induced NACs was analysed. Background and Objectives: NAC transcription factor (TF) proteins are involved in a wide range of functions during plant development and stress-related endurance processes. To understand the function of Populus NAC TFs in salt stress tolerance, we characterised the structure and expression profile of a total of 289 NAC members. Materials and Methods: Sequence phylogeny, genome organisation, gene structure, motif composition and promoter cis-element were detected using bioinformatics. The expression pattern of Populus NAC TFs under salt stress was also detected using RNA-Seq and RT-qPCR. Results: Synteny analysis showed that 46 and 37 Populus NAC genes were involved in whole-genome duplication and tandem duplication events, respectively. The expression pattern of Populus NAC TFs under salt stress showed the expression of the 289 PtNACs of 84K poplar was induced. Similar expression trends of NACs were found in Populus simonii × P. nigra T. S. Hwang et Liang and Arabidopsis thaliana (L.) Heynh. Conclusions: The correlation analysis showed that the expression of two differentially expressed NAC genes PtNAC024 and PtNAC182 was significantly associated with most of the 63 differentially expressed genes tested. The expression of PtNAC024 and PtNAC182 in different tissues was also analysed in silico and different expression patterns were found. Together, this study provides a solid basis to explore stress-related NAC TF functions in Populus salt tolerance and development.

scholarly journals Transcriptome Analysis of Long Noncoding RNAs in Toll-Like Receptor 3-Activated Mesenchymal Stem Cells

2016 ◽  
Vol 2016 ◽  
pp. 1-11 ◽  
Author(s):  
Shihua Wang ◽  
Xiaoxia Li ◽  
Robert Chunhua Zhao
Keyword(s):  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Length Distribution ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Differentially Expressed ◽  
Therapeutic Effects ◽  
Wide Range

Mesenchymal stem cells (MSCs) possess great immunomodulatory capacity which lays the foundation for their therapeutic effects in a variety of diseases. Recently, toll-like receptors (TLR) have been shown to modulate MSC functions; however, the underlying molecular mechanisms are poorly understood. Emerging evidence suggests that long noncoding RNAs (lncRNAs) are an important class of regulators involved in a wide range of biological processes. To explore the potential involvement of lncRNAs in TLR stimulated MSCs, we performed a comprehensive lncRNA and mRNA profiling through microarray. 10.2% of lncRNAs (1733 out of 16967) and 15.1% of mRNA transcripts (1760 out of 11632) were significantly differentially expressed (absolute fold-change≥5 ,Pvalue≤0.05) in TLR3 stimulated MSCs. Furthermore, we characterized the differentially expressed lncRNAs through their classes and length distribution and correlated them with differentially expressed mRNA. Here, we are the first to determine genome-wide lncRNAs expression patterns in TLR3 stimulated MSCs by microarray and this work could provide a comprehensive framework of the transcriptome landscapes of TLR3 stimulated MSCs.

scholarly journals Autopolyploidization affects transcript patterns and gene targeting frequencies in Physcomitrella

2021 ◽  
Author(s):  
Christine Rempfer ◽  
Gertrud Wiedemann ◽  
Gabriele Schween ◽  
Klaus L. Kerres ◽  
Jan M. Lucht ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Targeting ◽  
Molecular Mechanisms ◽  
Single Cells ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Whole Genome ◽  
Dsb Repair ◽  
Genome Duplication Event ◽  
Precise Integration

Qualitative changes in gene expression after an autopolyploidization event, a pure duplication of the whole genome, might be relevant for a different regulation of molecular mechanisms between angiosperms growing in a life cycle with a dominant diploid sporophytic stage and the haploid-dominant bryophytes. Whereas angiosperms repair DNA double strand breaks (DSB) preferentially via non-homologous end joining (NHEJ), in bryophytes homologous recombination (HR) is the main DNA-DSB repair pathway facilitating the precise integration of foreign DNA into the genome via gene targeting (GT). Here, we studied the influence of ploidy on gene expression patterns and GT efficiency in the moss Physcomitrella using haploid plants and autodiploid plants, generated via an artificial duplication of the whole genome. Single cells (protoplasts) were transfected with a GT construct and material from different time-points after transfection was analysed by microarrays and SuperSAGE sequencing. In the SuperSAGE data, we detected 3.7% of the Physcomitrella genes as differentially expressed in response to the whole genome duplication event. Among the differentially expressed genes involved in DNA-DSB repair was an upregulated gene encoding the X-ray repair cross-complementing protein 4 (XRCC4), a key player in NHEJ. Analysing the GT efficiency, we observed that autodiploid plants were significantly GT suppressed (p<0.001) attaining only one third of the expected GT rates. Hence, an alteration of global transcript patterns, including genes related to DNA repair, in autodiploid Physcomitrella plants correlated with a drastic suppression of HR.

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