scholarly journals Transcriptomes of plant gametophytes have a higher proportion of rapidly evolving and young genes than sporophytes

2015 ◽  
Author(s):  
Toni I Gossmann ◽  
Dounia Saleh ◽  
Marc W Schmid ◽  
Michael A Spence ◽  
Karl J Schmid
Keyword(s):  
Gene Expression ◽  
Genetic Diversity ◽  
Developmental Stages ◽  
Reproductive Traits ◽  
Pollen Competition ◽  
Significant Shift ◽  
Evolutionary Patterns ◽  
Protein Coding ◽  
Evolutionary Forces ◽  
Relationship Of

Reproductive traits in plants tend to evolve rapidly due to various causes that include plant-pollinator coevolution and pollen competition, but the genomic basis of reproductive trait evolution is still largely unknown. To characterise evolutionary patterns of genome wide gene expression in reproductive tissues in the gametophyte and to compare them to developmental stages of the sporophyte, we analysed evolutionary conservation and genetic diversity of protein-coding genes using microarray-based transcriptome data from three plant species,Arabidopsis thaliana, rice (Oryza sativa) and soybean (Glycine max). In all three species a significant shift in gene expression occurs during gametogenesis in which genes of younger evolutionary age and higher genetic diversity contribute significantly more to the transcriptome than in other stages. We refer to this phenomenon as ``evolutionary bulge'' during plant reproductive development because it differentiates the gametophyte from the sporophyte. We show that multiple, not mutually exclusive, causes may explain the bulge pattern, most prominently reduced tissue complexity of the gametophyte, a varying extent of selection on reproductive traits during gametogenesis as well as differences between male and female tissues. This highlights the importance of plant reproduction for understanding evolutionary forces determining the relationship of genomic and phenotypic variation in plants.

scholarly journals Evolutionary Patterns of Sex-Biased Genes in Three Species of Haplodiploid Insects

Insects ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 326
Author(s):  
Yu-Jun Wang ◽  
Hua-Ling Wang ◽  
Xiao-Wei Wang ◽  
Shu-Sheng Liu
Keyword(s):  
Gene Expression ◽  
Slow Rate ◽  
Species Complex ◽  
Evolutionary Patterns ◽  
Protein Coding ◽  
Coding Sequences ◽  
Species Comparisons ◽  
Differential Gene ◽  
Males And Females ◽  
And Behavior

Females and males often differ obviously in morphology and behavior, and the differences between sexes are the result of natural selection and/or sexual selection. To a great extent, the differences between the two sexes are the result of differential gene expression. In haplodiploid insects, this phenomenon is obvious, since males develop from unfertilized zygotes and females develop from fertilized zygotes. Whiteflies of the Bemisia tabaci species complex are typical haplodiploid insects, and some species of this complex are important pests of many crops worldwide. Here, we report the transcriptome profiles of males and females in three species of this whitefly complex. Between-species comparisons revealed that non-sex-biased genes display higher variation than male-biased or female-biased genes. Sex-biased genes evolve at a slow rate in protein coding sequences and gene expression and have a pattern of evolution that differs from those of social haplodiploid insects and diploid animals. Genes with high evolutionary rates are more related to non-sex-biased traits—such as nutrition, immune system, and detoxification—than to sex-biased traits, indicating that the evolution of protein coding sequences and gene expression has been mainly driven by non-sex-biased traits.

scholarly journals Long noncoding RNAs in hematopoiesis

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 1771 ◽  
Author(s):  
Xu Zhang ◽  
Wenqian Hu
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
Regulation Of Gene Expression ◽  
Noncoding Rnas ◽  
High Specificity ◽  
Long Noncoding Rnas ◽  
Mammalian Development ◽  
Functional Protein ◽  
Protein Coding ◽  
Functional Roles

Mammalian development is under tight control to ensure precise gene expression. Recent studies reveal a new layer of regulation of gene expression mediated by long noncoding RNAs. These transcripts are longer than 200nt that do not have functional protein coding capacity. Interestingly, many of these long noncoding RNAs are expressed with high specificity in different types of cells, tissues, and developmental stages in mammals, suggesting that they may have functional roles in diverse biological processes. Here, we summarize recent findings of long noncoding RNAs in hematopoiesis, which is one of the best-characterized mammalian cell differentiation processes. Then we provide our own perspectives on future studies of long noncoding RNAs in this field.

scholarly journals A comparative study of endoderm differentiation in humans and chimpanzees

2017 ◽  
Author(s):  
Lauren E. Blake ◽  
Samantha M. Thomas ◽  
John D. Blischak ◽  
Chiaowen Joyce Hsiao ◽  
Claudia Chavarria ◽  
...  
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
Primitive Streak ◽  
Species Variation ◽  
Expression Levels ◽  
Evolutionary Forces ◽  
Differentiation Stage ◽  
Early Human ◽  
Gene Expression Levels

AbstractThere is substantial interest in the evolutionary forces that shaped the regulatory framework that is established in early human development. Progress in this area has been slow because it is difficult to obtain relevant biological samples. Inducible pluripotent stem cells (iPSCs) provide the ability to establish in vitro models of early human and non-human primate developmental stages. Using matched iPSC panels from humans and chimpanzees, we comparatively characterized gene regulatory changes through a four-day timecourse differentiation of iPSCs (day 0) into primary streak (day 1), endoderm progenitors (day 2), and definitive endoderm (day 3). As might be expected, we found that differentiation stage is the major driver of variation in gene expression levels, followed by species. We identified thousands of differentially expressed genes between humans and chimpanzees in each differentiation stage. Yet, when we considered gene-specific dynamic regulatory trajectories throughout the timecourse, we found that 75‥ of genes, including nearly all known endoderm developmental markers, have similar trajectories in the two species. Interestingly, we observed a marked reduction of both intra-and inter-species variation in gene expression levels in primitive streak samples compared to the iPSCs, with a recovery of regulatory variation in endoderm progenitors. The reduction of variation in gene expression levels at a specific developmental stage, paired with overall high degree of conservation of temporal gene regulation, is consistent with the dynamics of developmental canalization. Overall, we conclude that endoderm development in iPSC-based models are highly conserved and canalized between humans and our closest evolutionary relative.

scholarly journals A switch in the development: microRNA arm usage screening in zebrafish suggests an important role of arm switching events in ontogenesis

2021 ◽  
Author(s):  
Arthur C. Oliveira ◽  
Luiz A. Bovolenta ◽  
Lucas Figueiredo ◽  
James G. Patton ◽  
Danillo Pinhal
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
Gene Expression Regulation ◽  
In Silico Analysis ◽  
Mirna Biogenesis ◽  
Rna Seq ◽  
Protein Coding ◽  
Coordinate Gene Expression ◽  
Silico Analysis

In metazoan, regulatory molecules tightly control gene expression. Among them, microRNAs (miRNAs) are key regulators of several important features, like cell proliferation, differentiation, and homeostasis. During miRNA biogenesis, the canonical strand that loads onto RISC may be switched, in a process called "arm switching". Due to the miRNA-to-target pairing peculiarities, switching events may lead to changes on the gene-targeted repertoire, promoting the modulation of a distinct set of biological routes. To understand how these events affect cell regulation, we carried out an extensive and detailed in silico analysis of RNA-seq datasets from several tissues and key developmental stages of zebrafish. We identified interesting patterns of miRNA arm switching occurrence, mainly associated with the control of protein coding genes during embryonic development. Additionally, our data shows that miRNA isoforms (isomiRs) seem to play an important role to differential arm usage. Our findings provide new insights on how such events emerge and coordinate gene expression regulation, opening perspectives for novel investigations in the area.

scholarly journals A high resolution atlas of gene expression in the domestic sheep (Ovis aries)

2017 ◽  
Author(s):  
EL Clark ◽  
SJ Bush ◽  
MEB McCulloch ◽  
IL Farquhar ◽  
R Young ◽  
...  
Keyword(s):  
Gene Expression ◽  
Reference Genome ◽  
Developmental Stages ◽  
Ovis Aries ◽  
Informative Gene ◽  
Protein Coding ◽  
Gene Expression Atlas ◽  
Organ Systems ◽  
Expression Atlas ◽  
Insight Into

AbstractSheep are a key source of meat, milk and fibre for the global livestock sector, and an important biomedical model. Global analysis of gene expression across multiple tissues has aided genome annotation and supported functional annotation of mammalian genes. We present a large-scale RNA-Seq dataset representing all the major organ systems from adult sheep and from several juvenile, neonatal and prenatal developmental time points. The Ovis aries reference genome (Oar v3.1) includes 27,504 genes (20,921 protein coding), of which 25,350 (19,921 protein coding) had detectable expression in at least one tissue in the sheep gene expression atlas dataset. Network-based cluster analysis of this dataset grouped genes according to their expression pattern. The principle of ‘guilt by association’ was used to infer the function of uncharacterised genes from their co-expression with genes of known function. We describe the overall transcriptional signatures present in the sheep gene expression atlas and assign those signatures, where possible, to specific cell populations or pathways. The findings are related to innate immunity by focusing on clusters with an immune signature, and to the advantages of cross-breeding by examining the patterns of genes exhibiting the greatest expression differences between purebred and crossbred animals. This high-resolution gene expression atlas for sheep is, to our knowledge, the largest transcriptomic dataset from any livestock species to date. It provides a resource to improve the annotation of the current reference genome for sheep, presenting a model transcriptome for ruminants and insight into gene, cell and tissue function at multiple developmental stages.Author SummarySheep are ruminant mammals kept as livestock for the production of meat, milk and wool in agricultural industries across the globe. Genetic and genomic information can be used to improve production traits such as disease resiliance. The sheep genome is however missing important information relating to gene function and many genes, which may be important for productivity, have no informative gene name. This can be remedied using RNA-Sequencing to generate a global expression profile of all protein-coding genes, across multiple organ systems and developmental stages. Clustering genes based on their expression profile across tissues and cells allows us to assign function to those genes. If for example a gene with no informative gene name is expressed in macrophages and is found within a cluster of known macrophage related genes it is likely to be involved in macrophage function and play a role in innate immunity. This information improves the quality of the reference genome and provides insight into biological processes underlying the complex traits that influence the productivity of sheep and other livestock species.

Genetic Diversity and Relationship of Tea Germplasm in Yunnan Revealed by ISSR Analysis

2010 ◽  
Vol 36 (3) ◽  
pp. 391-400 ◽  
Author(s):  
Ben-Ying LIU ◽  
You-Yong LI ◽  
Yi-Chun TANG ◽  
Li-Yuan WANG ◽  
Hao CHENG ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Issr Analysis ◽  
Relationship Of

scholarly journals The Complete Mitochondrial Genome of endemic giant tarantula, Lyrognathus crotalus (Araneae: Theraphosidae) and comparative analysis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Vikas Kumar ◽  
Kaomud Tyagi ◽  
Rajasree Chakraborty ◽  
Priya Prasad ◽  
Shantanu Kundu ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Start Codon ◽  
Gene Arrangement ◽  
Sister Relationship ◽  
Protein Coding ◽  
Relationship Of ◽  
Rna Genes ◽  
Boundary Mapping ◽  
Cloverleaf Structure

AbstractThe complete mitochondrial genome of Lyrognathus crotalus is sequenced, annotated and compared with other spider mitogenomes. It is 13,865 bp long and featured by 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and a control region (CR). Most of the PCGs used ATN start codon except cox3, and nad4 with TTG. Comparative studies indicated the use of TTG, TTA, TTT, GTG, CTG, CTA as start codons by few PCGs. Most of the tRNAs were truncated and do not fold into the typical cloverleaf structure. Further, the motif (CATATA) was detected in CR of nine species including L. crotalus. The gene arrangement of L. crotalus compared with ancestral arthropod showed the transposition of five tRNAs and one tandem duplication random loss (TDRL) event. Five plesiomophic gene blocks (A-E) were identified, of which, four (A, B, D, E) retained in all taxa except family Salticidae. However, block C was retained in Mygalomorphae and two families of Araneomorphae (Hypochilidae and Pholcidae). Out of 146 derived gene boundaries in all taxa, 15 synapomorphic gene boundaries were identified. TreeREx analysis also revealed the transposition of trnI, which makes three derived boundaries and congruent with the result of the gene boundary mapping. Maximum likelihood and Bayesian inference showed similar topologies and congruent with morphology, and previously reported multi-gene phylogeny. However, the Gene-Order based phylogeny showed sister relationship of L. crotalus with two Araneomorphae family members (Hypochilidae and Pholcidae) and other Mygalomorphae species.

Sign in / Sign up

Export Citation Format

Share Document