scholarly journals The roles of LINEs, LTRs and SINEs in lineage-specific gene family expansions in the human and mouse genomes

2016 ◽  
Author(s):  
Václav Janoušek ◽  
Christina M Laukaitis ◽  
Alexey Yanchukov ◽  
Robert Karn
Keyword(s):  
Gene Family ◽  
Gene Families ◽  
Specific Gene ◽  
Second Phase ◽  
Open Chromatin ◽  
Gene Family Expansion ◽  
Family Expansion ◽  
Human And Mouse ◽  
Lineage Specific Gene ◽  
Runaway Process

We explored genome-wide patterns of RT content surrounding lineage-specific gene family expansions in the human and mouse genomes. Our results suggest that the size of a gene family is an important predictor of the RT distribution in close proximity to the family members. The distribution differs considerably between the three most common RT classes (LINEs, LTRs and SINEs). LINEs and LTRs tend to be more abundant around genes of multi-copy gene families, whereas SINEs tend to be depleted around such genes. Detailed analysis of the distribution and diversity of LINEs and LTRs with respect to gene family size suggests that each has a distinct involvement in gene family expansion. LTRs are associated with open chromatin sites surrounding the gene families, supporting their involvement in gene regulation, whereas LINEs may play a structural role, promoting gene duplication. This suggests that gene family expansions, especially in the mouse genome, might undergo two phases, the first is characterized by elevated deposition of LTRs and their utilization in reshaping gene regulatory networks. The second phase is characterized by rapid gene family expansion due to continuous accumulation of LINEs and it appears that, in some instances at least, this could become a runaway process. We provide an example in which this has happened and we present a simulation supporting the possibility of the runaway process. Our observations also suggest that specific differences exist in this gene family expansion process between human and mouse genomes.

scholarly journals Plant Receptor-Like Serine Threonine Kinases: Roles in Signaling and Plant Defense

2008 ◽  
Vol 21 (5) ◽  
pp. 507-517 ◽  
Author(s):  
Ahmed J. Afzal ◽  
Andrew J. Wood ◽  
David A. Lightfoot
Keyword(s):  
Plant Defense ◽  
Gene Family ◽  
Defense Mechanisms ◽  
Gene Families ◽  
Kinase Domain ◽  
Limited Information ◽  
Gene Family Expansion ◽  
Accelerated Evolution ◽  
Family Expansion ◽  
Pathogen Populations

Plants are hosts to a wide array of pathogens from all kingdoms of life. In the absence of an active immune system or combinatorial diversifications that lead to recombination-driven somatic gene flexibility, plants have evolved different strategies to combat both individual pathogen strains and changing pathogen populations. The receptor-like kinase (RLK) gene-family expansion in plants was hypothesized to have allowed accelerated evolution among domains implicated in signal reception, typically a leucine-rich repeat (LRR). Under that model, the gene-family expansion represents a plant-specific adaptation that leads to the production of numerous and variable cell surface and cytoplasmic receptors. More recently, it has emerged that the LRR domains of RLK interact with a diverse group of proteins leading to combinatorial variations in signal response specificity. Therefore, the RLK appear to play a central role in signaling during pathogen recognition, the subsequent activation of plant defense mechanisms, and developmental control. The future challenges will include determinations of RLK modes of action, the basis of recognition and specificity, which cellular responses each receptor mediates, and how both receptor and kinase domain interactions fit into the defense signaling cascades. These challenges will be complicated by the limited information that may be derived from the primary sequence of the LRR domain. The review focuses upon implications derived from recent studies of the secondary and tertiary structures of several plant RLK that change understanding of plant receptor function and signaling. In addition, the biological functions of plant and animal RLK-containing receptors were reviewed and commonalities among their signaling mechanisms identified. Further elucidated were the genomic and structural organizations of RLK gene families, with special emphasis on RLK implicated in resistance to disease and development.

The rat prolactin gene family locus: species-specific gene family expansion

2006 ◽  
Vol 17 (8) ◽  
pp. 858-877 ◽  
Author(s):  
S.M. Khorshed Alam ◽  
Rupasri Ain ◽  
Toshihiro Konno ◽  
Jennifer K. Ho-Chen ◽  
Michael J. Soares
Keyword(s):  
Gene Family ◽  
Specific Gene ◽  
Gene Family Expansion ◽  
Prolactin Gene ◽  
Family Expansion ◽  
Species Specific

scholarly journals Identification of lineage-specific gene family expansions in a database of gene families

2018 ◽  
Author(s):  
Avril Coghlan ◽  
Diogo Ribeiro ◽  
Avril Coghlan ◽  
Bhavana Harsha ◽  
Matthew Berriman
Keyword(s):  
Gene Family ◽  
Gene Families ◽  
Specific Gene ◽  
Lineage Specific Gene

scholarly journals Understanding the Early Evolutionary Stages of a Tandem Drosophilamelanogaster-Specific Gene Family: A Structural and Functional Population Study

2020 ◽  
Vol 37 (9) ◽  
pp. 2584-2600 ◽  
Author(s):  
Bryan D Clifton ◽  
Jamie Jimenez ◽  
Ashlyn Kimura ◽  
Zeinab Chahine ◽  
Pablo Librado ◽  
...  
Keyword(s):  
Gene Family ◽  
Sequence Similarity ◽  
Gene Families ◽  
Read Depth ◽  
Specific Gene ◽  
Protein Variant ◽  
Protein Coding ◽  
Expression Levels ◽  
Number Variation ◽  
Reference Quality

Abstract Gene families underlie genetic innovation and phenotypic diversification. However, our understanding of the early genomic and functional evolution of tandemly arranged gene families remains incomplete as paralog sequence similarity hinders their accurate characterization. The Drosophila melanogaster-specific gene family Sdic is tandemly repeated and impacts sperm competition. We scrutinized Sdic in 20 geographically diverse populations using reference-quality genome assemblies, read-depth methodologies, and qPCR, finding that ∼90% of the individuals harbor 3–7 copies as well as evidence of population differentiation. In strains with reliable gene annotations, copy number variation (CNV) and differential transposable element insertions distinguish one structurally distinct version of the Sdic region per strain. All 31 annotated copies featured protein-coding potential and, based on the protein variant encoded, were categorized into 13 paratypes differing in their 3′ ends, with 3–5 paratypes coexisting in any strain examined. Despite widespread gene conversion, the only copy present in all strains has functionally diverged at both coding and regulatory levels under positive selection. Contrary to artificial tandem duplications of the Sdic region that resulted in increased male expression, CNV in cosmopolitan strains did not correlate with expression levels, likely as a result of differential genome modifier composition. Duplicating the region did not enhance sperm competitiveness, suggesting a fitness cost at high expression levels or a plateau effect. Beyond facilitating a minimally optimal expression level, Sdic CNV acts as a catalyst of protein and regulatory diversity, showcasing a possible evolutionary path recently formed tandem multigene families can follow toward long-term consolidation in eukaryotic genomes.

scholarly journals Network-based microsynteny analysis identifies major differences and genomic outliers in mammalian and angiosperm genomes

2019 ◽  
Vol 116 (6) ◽  
pp. 2165-2174 ◽  
Author(s):  
Tao Zhao ◽  
M. Eric Schranz
Keyword(s):  
Gene Families ◽  
Single Copy ◽  
Specific Gene ◽  
Phylogenetic Groups ◽  
History Of ◽  
Mammalian Genomes ◽  
Syntenic Conservation ◽  
Genome Assemblies ◽  
Lineage Specific Gene ◽  
Relative Gene

A comprehensive analysis of relative gene order, or microsynteny, can provide valuable information for understanding the evolutionary history of genes and genomes, and ultimately traits and species, across broad phylogenetic groups and divergence times. We have used our network-based phylogenomic synteny analysis pipeline to first analyze the overall patterns and major differences between 87 mammalian and 107 angiosperm genomes. These two important groups have both evolved and radiated over the last ∼170 MYR. Secondly, we identified the genomic outliers or “rebel genes” within each clade. We theorize that rebel genes potentially have influenced trait and lineage evolution. Microsynteny networks use genes as nodes and syntenic relationships between genes as edges. Networks were decomposed into clusters using the Infomap algorithm, followed by phylogenomic copy-number profiling of each cluster. The differences in syntenic properties of all annotated gene families, including BUSCO genes, between the two clades are striking: most genes are single copy and syntenic across mammalian genomes, whereas most genes are multicopy and/or have lineage-specific distributions for angiosperms. We propose microsynteny scores as an alternative and complementary metric to BUSCO for assessing genome assemblies. We further found that the rebel genes are different between the two groups: lineage-specific gene transpositions are unusual in mammals, whereas single-copy highly syntenic genes are rare for flowering plants. We illustrate several examples of mammalian transpositions, such as brain-development genes in primates, and syntenic conservation across angiosperms, such as single-copy genes related to photosynthesis. Future experimental work can test if these are indeed rebels with a cause.

scholarly journals The Evolution, Gene Expression Profile, and Secretion of Digestive Peptidases in Lepidoptera Species

Catalysts ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 217
Author(s):  
Lucas R. Lima ◽  
Renata O. Dias ◽  
Felipe Jun Fuzita ◽  
Clélia Ferreira ◽  
Walter R. Terra ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profile ◽  
Catalytic Triad ◽  
Rna Seq ◽  
Anterior Portion ◽  
Gene Family Expansion ◽  
Genes Encoding ◽  
Peptidase Inhibitor ◽  
Family Expansion ◽  
Midgut Lumen

Serine peptidases (SPs) are responsible for most primary protein digestion in Lepidoptera species. An expansion of the number of genes encoding trypsin and chymotrypsin enzymes and the ability to upregulate the expression of some of these genes in response to peptidase inhibitor (PI) ingestion have been associated with the adaptation of Noctuidae moths to herbivory. To investigate whether these gene family expansion events are common to other Lepidoptera groups, we searched for all genes encoding putative trypsin and chymotrypsin enzymes in 23 publicly available genomes from this taxon. Phylogenetic analysis showed that several gene family expansion events may have occurred in the taxon’s evolutionary history and that these events gave rise to a very diverse group of enzymes, including proteins lacking the canonical SP catalytic triad. The expression profile of these enzymes along the midgut and the secretion mechanisms by which these enzymes enter the luminal content were also analyzed in Spodoptera frugiperda larvae using RNA-seq and proteomics. These results support the proposal of a midgut countercurrent flux responsible for the direction of these proteins to the anterior portion of the midgut and show that these enzymes reach the midgut lumen via both exocytosis and microapocrine secretion mechanisms.

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