scholarly journals Lineage-Specific Genes and Family Expansions in Dictyostelid Genomes Display Expression Bias and Evolutionary Diversification during Development

Genes ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1628
Author(s):  
Saara K. Luna ◽  
Frédéric J. J. Chain
Keyword(s):  
Gene Families ◽  
Developmental Time ◽  
Multicellular Development ◽  
Adaptive Diversification ◽  
Evolutionary Diversification ◽  
New Genes ◽  
Expression Bias ◽  
Species Specific ◽  
Molecular Signals ◽  
Lineage Specific Genes

Gene duplications generate new genes that can contribute to expression changes and the evolution of new functions. Genomes often consist of gene families that undergo expansions, some of which occur in specific lineages that reflect recent adaptive diversification. In this study, lineage-specific genes and gene family expansions were studied across five dictyostelid species to determine when and how they are expressed during multicellular development. Lineage-specific genes were found to be enriched among genes with biased expression (predominant expression in one developmental stage) in each species and at most developmental time points, suggesting independent functional innovations of new genes throughout the phylogeny. Biased duplicate genes had greater expression divergence than their orthologs and paralogs, consistent with subfunctionalization or neofunctionalization. Lineage-specific expansions in particular had biased genes with both molecular signals of positive selection and high expression, suggesting adaptive genetic and transcriptional diversification following duplication. Our results present insights into the potential contributions of lineage-specific genes and families in generating species-specific phenotypes during multicellular development in dictyostelids.

scholarly journals Pattern of New Gene Origination in a Special Fish Lineage, the Flatfishes

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1819
Author(s):  
Haorong Li ◽  
Chunyan Chen ◽  
Zhongkai Wang ◽  
Kun Wang ◽  
Yongxin Li ◽  
...  
Keyword(s):  
De Novo ◽  
General Pattern ◽  
Gene Identification ◽  
Whole Genome ◽  
Genome Data ◽  
New Genes ◽  
Emergence Rate ◽  
New Gene ◽  
Species Specific ◽  
Lineage Specific Genes

Origination of new genes are of inherent interest of evolutionary geneticists for decades, but few studies have addressed the general pattern in a fish lineage. Using our recent released whole genome data of flatfishes, which evolved one of the most specialized body plans in vertebrates, we identified 1541 (6.9% of the starry flounder genes) flatfish-lineage-specific genes. The origination pattern of these flatfish new genes is largely similar to those observed in other vertebrates, as shown by the proportion of DNA-mediated duplication (1317; 85.5%), RNA-mediated duplication (retrogenes; 96; 6.2%), and de novo–origination (128; 8.3%). The emergence rate of species-specific genes is 32.1 per Mya and the whole average level rate for the flatfish-lineage-specific genes is 20.9 per Mya. A large proportion (31.4%) of these new genes have been subjected to selection, in contrast to the 4.0% in primates, while the old genes remain quite similar (66.4% vs. 65.0%). In addition, most of these new genes (70.8%) are found to be expressed, indicating their functionality. This study not only presents one example of systematic new gene identification in a teleost taxon based on comprehensive phylogenomic data, but also shows that new genes may play roles in body planning.

scholarly journals The Tomato Interspecific NB-LRR Gene Arsenal and Its Impact on Breeding Strategies

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 184
Author(s):  
Giuseppe Andolfo ◽  
Nunzio D’Agostino ◽  
Luigi Frusciante ◽  
Maria Raffaella Ercolano
Keyword(s):  
Evolutionary Dynamics ◽  
Special Focus ◽  
Breeding Strategies ◽  
Adaptive Diversification ◽  
Solanum Lycopersicum L ◽  
Solanaceae Species ◽  
Specific Pathogen ◽  
Adaptive Processes ◽  
Species Specific ◽  
R Loci

Tomato (Solanum lycopersicum L.) is a model system for studying the molecular basis of resistance in plants. The investigation of evolutionary dynamics of tomato resistance (R)-loci provides unique opportunities for identifying factors that promote or constrain genome evolution. Nucleotide-binding domain and leucine-rich repeat (NB-LRR) receptors belong to one of the most plastic and diversified families. The vast amount of genomic data available for Solanaceae and wild tomato relatives provides unprecedented insights into the patterns and mechanisms of evolution of NB-LRR genes. Comparative analysis remarked a reshuffling of R-islands on chromosomes and a high degree of adaptive diversification in key R-loci induced by species-specific pathogen pressure. Unveiling NB-LRR natural variation in tomato and in other Solanaceae species offers the opportunity to effectively exploit genetic diversity in genomic-driven breeding programs with the aim of identifying and introducing new resistances in tomato cultivars. Within this motivating context, we reviewed the repertoire of NB-LRR genes available for tomato improvement with a special focus on signatures of adaptive processes. This issue is still relevant and not thoroughly investigated. We believe that the discovery of mechanisms involved in the generation of a gene with new resistance functions will bring great benefits to future breeding strategies.

scholarly journals Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Hong-Lei Li ◽  
Lin Wu ◽  
Zhaoming Dong ◽  
Yusong Jiang ◽  
Sanjie Jiang ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
Southwest China ◽  
Reference Genome ◽  
Zingiber Officinale ◽  
Gene Families ◽  
Chromosome Conformation ◽  
Long Reads ◽  
Transcription Factor Networks ◽  
Species Specific ◽  
Haplotype 1

AbstractGinger (Zingiber officinale), the type species of Zingiberaceae, is one of the most widespread medicinal plants and spices. Here, we report a high-quality, chromosome-scale reference genome of ginger ‘Zhugen’, a traditionally cultivated ginger in Southwest China used as a fresh vegetable, assembled from PacBio long reads, Illumina short reads, and high-throughput chromosome conformation capture (Hi-C) reads. The ginger genome was phased into two haplotypes, haplotype 1 (1.53 Gb with a contig N50 of 4.68 M) and haplotype 0 (1.51 Gb with a contig N50 of 5.28 M). Homologous ginger chromosomes maintained excellent gene pair collinearity. In 17,226 pairs of allelic genes, 11.9% exhibited differential expression between alleles. Based on the results of ginger genome sequencing, transcriptome analysis, and metabolomic analysis, we proposed a backbone biosynthetic pathway of gingerol analogs, which consists of 12 enzymatic gene families, PAL, C4H, 4CL, CST, C3’H, C3OMT, CCOMT, CSE, PKS, AOR, DHN, and DHT. These analyses also identified the likely transcription factor networks that regulate the synthesis of gingerol analogs. Overall, this study serves as an excellent resource for further research on ginger biology and breeding, lays a foundation for a better understanding of ginger evolution, and presents an intact biosynthetic pathway for species-specific gingerol biosynthesis.

scholarly journals Base editing in bovine embryos reveals a species-specific role of SOX2 in regulation of pluripotency

2021 ◽  
Author(s):  
Lei Luo ◽  
Yan Shi ◽  
Huanan Wang ◽  
Zizengchen Wang ◽  
Yanna Dang ◽  
...  
Keyword(s):  
Inner Cell Mass ◽  
Cell Mass ◽  
Rna Seq ◽  
Bovine Embryos ◽  
Base Editing ◽  
Sox2 Expression ◽  
Nanog Expression ◽  
Species Specific ◽  
Lineage Specific Genes

The emergence of the first three lineages during development are orchestrated by a network of transcription factors, which are best characterized in mice. However, the role and regulation of these factors are not completely conserved in other mammals, including human and cattle. Here, we establish a gene inactivation system by introducing premature codon with cytosine base editor in bovine embryos with a robust efficiency. Of interest, SOX2 is universally localized in early blastocysts but gradually restricted into the inner cell mass in cattle. SOX2 knockout results in a failure of the establishment of pluripotency. Indeed, OCT4 level is significantly reduced and NANOG was barely detectable. Furthermore, the formation of primitive endoderm is compromised with few SOX17 positive cells. Single embryo RNA-seq reveals a dysregulation of 2074 genes, among which 90% are up-regulated in SOX2-null blastocysts. Intriguingly, more than a dozen lineage-specific genes, including OCT4 and NANOG, are down-regulated. Moreover, SOX2 expression is sustained in the trophectoderm in absence of CDX2 in bovine late blastocysts. Overall, we propose that SOX2 is dispensable for OCT4 and NANOG expression and disappearance of SOX2 in the trophectoderm depends on CDX2 in cattle, which are all in sharp contrast with results in mice.

scholarly journals A Screen for Gene Paralogies Delineating Evolutionary Branching Order of Early Metazoa

2019 ◽  
Vol 10 (2) ◽  
pp. 811-826 ◽  
Author(s):  
Albert Erives ◽  
Bernd Fritzsch
Keyword(s):  
Phylogenetic Analyses ◽  
Gene Families ◽  
Single Copy ◽  
Gene Duplications ◽  
Nervous Systems ◽  
Evolutionary Diversification ◽  
Transmembrane Channel ◽  
Sensory Epithelia ◽  
Protein X ◽  
Ancient Gene

The evolutionary diversification of animals is one of Earth’s greatest marvels, yet its earliest steps are shrouded in mystery. Animals, the monophyletic clade known as Metazoa, evolved wildly divergent multicellular life strategies featuring ciliated sensory epithelia. In many lineages epithelial sensoria became coupled to increasingly complex nervous systems. Currently, different phylogenetic analyses of single-copy genes support mutually-exclusive possibilities that either Porifera or Ctenophora is sister to all other animals. Resolving this dilemma would advance the ecological and evolutionary understanding of the first animals and the evolution of nervous systems. Here we describe a comparative phylogenetic approach based on gene duplications. We computationally identify and analyze gene families with early metazoan duplications using an approach that mitigates apparent gene loss resulting from the miscalling of paralogs. In the transmembrane channel-like (TMC) family of mechano-transducing channels, we find ancient duplications that define separate clades for Eumetazoa (Placozoa + Cnidaria + Bilateria) vs. Ctenophora, and one duplication that is shared only by Eumetazoa and Porifera. In the Max-like protein X (MLX and MLXIP) family of bHLH-ZIP regulators of metabolism, we find that all major lineages from Eumetazoa and Porifera (sponges) share a duplicated gene pair that is sister to the single-copy gene maintained in Ctenophora. These results suggest a new avenue for deducing deep phylogeny by choosing rather than avoiding ancient gene paralogies.

scholarly journals The chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Lisong Hu ◽  
Zhongping Xu ◽  
Maojun Wang ◽  
Rui Fan ◽  
Daojun Yuan ◽  
...  
Keyword(s):  
Reference Genome ◽  
Gene Families ◽  
Black Pepper ◽  
Piper Nigrum ◽  
Comparative Genomic ◽  
Specific Gene ◽  
Phylogenomic Analysis ◽  
Genomic Analyses ◽  
Species Specific ◽  
Insight Into

Abstract Black pepper (Piper nigrum), dubbed the ‘King of Spices’ and ‘Black Gold’, is one of the most widely used spices. Here, we present its reference genome assembly by integrating PacBio, 10x Chromium, BioNano DLS optical mapping, and Hi-C mapping technologies. The 761.2 Mb sequences (45 scaffolds with an N50 of 29.8 Mb) are assembled into 26 pseudochromosomes. A phylogenomic analysis of representative plant genomes places magnoliids as sister to the monocots-eudicots clade and indicates that black pepper has diverged from the shared Laurales-Magnoliales lineage approximately 180 million years ago. Comparative genomic analyses reveal specific gene expansions in the glycosyltransferase, cytochrome P450, shikimate hydroxycinnamoyl transferase, lysine decarboxylase, and acyltransferase gene families. Comparative transcriptomic analyses disclose berry-specific upregulated expression in representative genes in each of these gene families. These data provide an evolutionary perspective and shed light on the metabolic processes relevant to the molecular basis of species-specific piperine biosynthesis.

scholarly journals A high-resolution mRNA expression time course of embryonic development in zebrafish

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Richard J White ◽  
John E Collins ◽  
Ian M Sealy ◽  
Neha Wali ◽  
Christopher M Dooley ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Time Course ◽  
Expression Profiles ◽  
Developmental Time ◽  
Rna Seq ◽  
Time Points ◽  
New Genes ◽  
Expression Atlas ◽  
Genome Activation ◽  
Expression Time

We have produced an mRNA expression time course of zebrafish development across 18 time points from 1 cell to 5 days post-fertilisation sampling individual and pools of embryos. Using poly(A) pulldown stranded RNA-seq and a 3′ end transcript counting method we characterise temporal expression profiles of 23,642 genes. We identify temporal and functional transcript co-variance that associates 5024 unnamed genes with distinct developmental time points. Specifically, a class of over 100 previously uncharacterised zinc finger domain containing genes, located on the long arm of chromosome 4, is expressed in a sharp peak during zygotic genome activation. In addition, the data reveal new genes and transcripts, differential use of exons and previously unidentified 3′ ends across development, new primary microRNAs and temporal divergence of gene paralogues generated in the teleost genome duplication. To make this dataset a useful baseline reference, the data can be browsed and downloaded at Expression Atlas and Ensembl.

scholarly journals Evo-devo and accounting for Darwin's endless forms

2011 ◽  
Vol 366 (1574) ◽  
pp. 2069-2075 ◽  
Author(s):  
Paul M. Brakefield
Keyword(s):  
Natural Selection ◽  
Common Ancestry ◽  
Developmental Constraints ◽  
Evolutionary Diversification ◽  
New Genes ◽  
The Earth ◽  
Regulatory Machinery ◽  
Evo Devo ◽  
Opening Up ◽  
Trait Space

Evo-devo has led to dramatic advances in our understanding of how the processes of development can contribute to explaining patterns of evolutionary diversification that underlie the endless forms of animal life on the Earth. This is increasingly the case not only for the origins of evolutionary novelties that permit new functions and open up new adaptive zones, but also for the processes of evolutionary tinkering that occur within the subsequent radiations of related species. Evo-devo has time and again yielded spectacular examples of Darwin's notions of common ancestry and of descent with modification. It has also shown that the evolution of endless forms is more about the evolution of the regulatory machinery of ancient genes than the origin and elaboration of new genes. Evolvability, especially with respect to the capacity of a developmental system to evolve and to generate the variation in form for natural selection to screen, has become a pivotal focus of evo-devo. As a consequence, a balancing of the concept of endless forms in morphospace with a greater awareness of the potential for developmental constraints and bias is becoming more general. The prospect of parallel horizons opening up for the evolution of behaviour is exciting; in particular, does Sean Carroll's phrase referring to old genes learning new tricks in the evolution of endless forms apply equally as well to patterns of diversity and disparity in behavioural trait-space?

Some like it hot? Developmental differences in Yellow-bellied Toad (Bombina variegata) tadpoles from geographically close but different habitats

2016 ◽  
Vol 94 (2) ◽  
pp. 69-77 ◽  
Author(s):  
C. Dittrich ◽  
S. Drakulić ◽  
M. Schellenberg ◽  
J. Thein ◽  
M.-O. Rödel
Keyword(s):  
Body Condition ◽  
Common Garden ◽  
Developmental Time ◽  
Climatic Conditions ◽  
Developmental Differences ◽  
Future Climate Change ◽  
Term Survival ◽  
Species Population ◽  
Bombina Variegata ◽  
Species Specific

The key for the long-term survival of species is their potential to respond to changing conditions. These reactions are usually species-specific and may vary between populations. The Yellow-bellied Toad (Bombina variegata (L., 1758)) occurs in forested and open areas. We wanted to know whether tadpoles react plastically to different environmental conditions, and if so, whether reaction norms are species, population, or season specific. In a common garden experiment, we compared developmental traits (developmental time, size, body condition) of metamorphs from different habitats (forest vs. quarry) in close geographic proximity. Tadpoles from both habitats grew up under shaded and sunny conditions. The experiments were run during early and late breeding season. We detected different developmental strategies between populations, concerning treatments and season on a microgeographic scale. Tadpoles with quarry origin developed faster and reached larger body sizes, at the expense of lower body condition. Major risks affecting tadpole’s survival in the open habitat are high temperatures and high desiccation. Forest tadpoles were comparatively smaller in size, but showed higher plasticity and higher body condition. Under changing climatic conditions, quarry population may reach temperatures above their thermal limits. In contrast, forest conditions may mitigate increasing temperatures. Forest populations could be better adapted to future climate change.

scholarly journals Adaptation of Fig Wasps (Agaodinae) to Their Host Revealed by Large-Scale Transcriptomic Data

Insects ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 815
Author(s):  
Lianfu Chen ◽  
Simon T. Segar ◽  
Bhanumas Chantarasuwan ◽  
Da-Mien Wong ◽  
Rong Wang ◽  
...  
Keyword(s):  
Host Specificity ◽  
Large Scale ◽  
Sequence Data ◽  
Fig Wasp ◽  
Fig Wasps ◽  
Wasp Species ◽  
Functional Changes ◽  
Evolutionary Diversification ◽  
Species Specific ◽  
Close Relatives

Figs and fig wasps are highly species-specific and comprise a model system for studying co-evolution and co-speciation. The evolutionary relationships and molecular adaptations of fig wasps to their fig hosts are poorly understood, and this is in part due to limited sequence data. Here, we present large-scale transcriptomic datasets of 25 fig wasp species with the aim of uncovering the genetic basis for host specificity. Our phylogenetic results support the monophyly of all genera associated with dioecious figs, and two genera associated with monoecious figs, Eupristina and Platyscapa, were revealed to be close relatives. We identified gene loss and gain, potentially rapidly evolving genes, and genes under positive selection. Potentially functional changes were documented and we hypothesize as to how these may determine host specificity. Overall, our study provides new insights into the evolutionary diversification of fig wasps and contributes to our understanding of adaptation in this group.

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