scholarly journals Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3′-end of genes

2008 ◽  
Vol 36 (17) ◽  
pp. 5581-5590 ◽  
Author(s):  
Ju Youn Lee ◽  
Zhe Ji ◽  
Bin Tian
Keyword(s):  
Phylogenetic Analysis ◽  
Transposable Elements ◽  
Polyadenylation Sites ◽  
Mrna Polyadenylation

scholarly journals In silico Phylogenetic Analysis of hAT Transposable Elements in Plants

Genes ◽  
2018 ◽  
Vol 9 (6) ◽  
pp. 284 ◽  
Author(s):  
Gökhan Karakülah ◽  
Athanasia Pavlopoulou
Keyword(s):  
Phylogenetic Analysis ◽  
Transposable Elements ◽  
In Silico

Phylogenetic Analysis of Mos1-Like Transposable Elements in the Drosophilidae

1999 ◽  
Vol 49 (6) ◽  
pp. 760-768 ◽  
Author(s):  
Frédéric Brunet ◽  
Fabienne Godin ◽  
Claude Bazin ◽  
Pierre Capy
Keyword(s):  
Phylogenetic Analysis ◽  
Transposable Elements

scholarly journals The evolution of the metazoan Toll receptor family and its expression during protostome development

2021 ◽  
Author(s):  
Andrea Orús-Alcalde ◽  
Tsai-Ming Lu ◽  
Andreas Hejnol
Keyword(s):  
Phylogenetic Analysis ◽  
Transmembrane Domain ◽  
Leucine Rich Repeat ◽  
Animal Development ◽  
Phylogenetic Studies ◽  
Repeat Domain ◽  
Toll Receptor ◽  
P Type

Abstract Background: Toll-like receptors (TLRs) play a crucial role in immunity and development. They contain leucine-rich repeat domains, one transmembrane domain, and one Toll/IL-1 receptor domain. TLRs have been classified into V-type/scc and P-type/mcc TLRs, based on differences in the leucine-rich repeat domain region. Although TLRs are widespread in animals, detailed phylogenetic studies of this gene family are lacking. Here we aim to uncover TLR evolution by conducting a survey and a phylogenetic analysis in species across Bilateria. To discriminate between their role in development and immunity we furthermore analyzed stage-specific transcriptomes of the ecdysozoans Priapulus caudatus and Hypsibius exemplaris, and the spiralians Crassostrea gigas and Terebratalia transversa.Results: We detected a low number of TLRs in ecdysozoan species, and multiple independent radiations within the Spiralia. V-type/scc and P-type/mcc type-receptors are present in cnidarians, protostomes and deuterostomes, and therefore they emerged early in TLR evolution, followed by a loss in xenacoelomorphs. Our phylogenetic analysis shows that TLRs cluster into three major clades: clade α is present in cnidarians, ecdysozoans, and spiralians; clade β in deuterostomes, ecdysozoans, and spiralians; and clade γ is only found in spiralians. Our stage-specific transcriptome and in situ hybridization analyses show that TLRs are expressed during development in all species analyzed, which indicates a broad role of TLRs during animal development.Conclusions: Our findings suggest that the bilaterian TLRs likely emerged by duplication from a single TLR encoding gene (proto-TLR) present in the last common cnidarian-bilaterian ancestor. This proto-TLR gene duplicated before the split of protostomes and deuterostomes; a second duplication occurred in the lineage to the Trochozoa. While all three clades further radiated in several spiralian lineages, specific TLRs clades have been presumably lost in others. Furthermore, the expression of the majority of these genes during protostome ontogeny suggests their involvement in immunity and development.

scholarly journals Diversity of Ascomycetes Mushroom in Para Rubber Plantation, Thailand

2021 ◽  
Author(s):  
Saowapha Surawut ◽  
Sorasak Nak-aim ◽  
Chutapa Kunsook ◽  
Laddawan Kamhaengkul ◽  
Pornpimon Kanjanavas ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Internal Transcribed Spacer ◽  
Genetic Relatedness ◽  
Sequence Similarity ◽  
Its Region ◽  
Bioactive Compound ◽  
Rubber Plantation ◽  
Mushroom Species ◽  
Reference Strains

Abstract Ascomycetes mushrooms are fungi that produce ascospores in asci and some with perithecia. Not only they have a role of decomposer in ecology but also produced some bioactive compound, anti-microbial activity, and cytotoxicity. This study aims to explore the diversity of ascomycetes mushroom species in para rubber plantations and to identify them by morphological and sequence analysis of the internal transcribed spacer (ITS) region. The results found ascomycetes mushroom consist of Trichoderma pezizoides (RP1, % identity 98.79, DQ835513.1), Daldinia eschscholtzii (RP2, % identity 100, MN310384.1), Cookeina sulcipes (RP3, % identity 98.44, KY094620.1), Cookeina garethjonesii (RP4, % identity 99.06, KY094622.1), Cookeina tricholoma (RP5, % identity 100, KY094619.1) and Xylaria terricola (RP6, % identity 88.42, MF577038.1). Most of the ascomycetes in this study have previously been described in Thailand except Xylaria terricola. Additionally, phylogenetic analysis of ascomycetes mushroom showed high genetic relatedness with reference strains. Therefore, the sequence similarity and phylogenetic analysis confirmed the identity of six ascomycetes mushroom species, and further study of bioactive compound from these mushrooms may be investigated for other applications.

scholarly journals The Genomic Ecosystem of Transposable Elements in Maize

2019 ◽  
Author(s):  
Michelle C. Stitzer ◽  
Sarah N. Anderson ◽  
Nathan M. Springer ◽  
Jeffrey Ross-Ibarra
Keyword(s):  
Transposable Elements ◽  
Evolutionary Dynamics ◽  
Phenotypic Diversity ◽  
Flowering Plant ◽  
Genome Wide ◽  
Family Level ◽  
Genomic Environment ◽  
Single Category ◽  
The Impact

Transposable elements (TEs) constitute the majority of flowering plant DNA, reflecting their tremendous success in subverting, avoiding, and surviving the defenses of their host genomes to ensure their selfish replication. More than 85% of the sequence of the maize genome can be ascribed to past transposition, providing a major contribution to the structure of the genome. Evidence from individual loci has informed our understanding of how transposition has shaped the genome, and a number of individual TE insertions have been causally linked to dramatic phenotypic changes. But genome-wide analyses in maize and other taxa have frequently represented TEs as a relatively homogeneous class of fragmentary relics of past transposition, obscuring their evolutionary history and interaction with their host genome. Using an updated annotation of structurally intact TEs in the maize reference genome, we investigate the family-level ecological and evolutionary dynamics of TEs in maize. Integrating a variety of data, from descriptors of individual TEs like coding capacity, expression, and methylation, as well as similar features of the sequence they inserted into, we model the relationship between these attributes of the genomic environment and the survival of TE copies and families. Our analyses reveal a diversity of ecological strategies of TE families, each representing the evolution of a distinct ecological niche allowing survival of the TE family. In contrast to the wholesale relegation of all TEs to a single category of junk DNA, these differences generate a rich ecology of the genome, suggesting families of TEs that coexist in time and space compete and cooperate with each other. We conclude that while the impact of transposition is highly family- and context-dependent, a family-level understanding of the ecology of TEs in the genome can refine our ability to predict the role of TEs in generating genetic and phenotypic diversity.‘Lumping our beautiful collection of transposons into a single category is a crime’-Michael R. Freeling, Mar. 10, 2017

scholarly journals Transposable elements contribute to dynamic genome content in maize

2019 ◽  
Author(s):  
Sarah N Anderson ◽  
Michelle C Stitzer ◽  
Alex B. Brohammer ◽  
Peng Zhou ◽  
Jaclyn M Noshay ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Genomic Variation ◽  
Gene Content ◽  
Maize Genome ◽  
Large Scope ◽  
Shared Ancestry ◽  
Dynamic Genome ◽  
Genomic Studies ◽  
Genome Assemblies

AbstractTransposable elements (TEs) are ubiquitous components of eukaryotic genomes and can create variation in genomic organization. The majority of maize genomes are composed of TEs. We developed an approach to define shared and variable TE insertions across genome assemblies and applied this method to four maize genomes (B73, W22, Mo17, and PH207). Among these genomes we identified 1.6 Gb of variable TE sequence representing a combination of recent TE movement and deletion of previously existing TEs. Although recent TE movement only accounted for a portion of the TE variability, we identified 4,737 TEs unique to one genome with defined insertion sites in all other genomes. Variable TEs are found for all superfamilies and are distributed across the genome, including in regions of recent shared ancestry among individuals. There are 2,380 genes annotated in the B73 genome located within variable TEs, providing evidence for the role of TEs in contributing to the substantial differences in gene content among these genotypes. The large scope of TE variation present in this limited sample of temperate maize genomes highlights the major contribution of TEs in driving variation in genome organization and gene content.Significance StatementThe majority of the maize genome is comprised of transposable elements (TEs) that have the potential to create genomic variation within species. We developed a method to identify shared and non-shared TEs using whole genome assemblies of four maize inbred lines. Variable TEs are found throughout the maize genome and in comparisons of any two genomes we find ~20% of the genome is due to non-shared TEs. Several thousand maize genes are found within TEs that are variable across lines, highlighting the contribution of TEs to gene content variation. This study creates a comprehensive resource for genomic studies of TE variability among four maize genomes, which will enable studies on the consequences of variable TEs on genome function.

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