scholarly journals Contrasting patterns of coding and flanking region evolution in mammalian keratin associated protein-1 genes

2018 ◽  
Author(s):  
Huitong Zhou ◽  
Tina Visnovska ◽  
Hua Gong ◽  
Sebastian Schmeier ◽  
Jon Hickford ◽  
...  
Keyword(s):  
Concerted Evolution ◽  
Purifying Selection ◽  
Gene Families ◽  
Specific Protein ◽  
Common Mechanism ◽  
Dna Repeats ◽  
Coding Region ◽  
Evolutionary Patterns ◽  
Evolutionary Pattern ◽  
Species Specific

AbstractDNA repeats are common elements in eukaryotic genomes, and their multi-copy nature provides the opportunity for genetic exchange. This exchange can produce altered evolutionary patterns, including concerted evolution where within genome repeat copies are more similar to each other than to orthologous repeats in related species. Here we investigated the genetic architecture of the keratin-associated protein (KAP) gene family, KRTAP1. This family encodes proteins that are important components of hair and wool in mammals, and the genes are present in tandem copies. Comparison of KRTAP1 gene repeats from species across the mammalian phylogeny shows strongly contrasting evolutionary patterns between the coding regions, which have a concerted evolution pattern, and the flanking regions, which have a normal, radiating pattern of evolution. This dichotomy in evolutionary pattern transitions abruptly at the start and stop codons, and we show it is not the result of purifying selection acting to maintain species-specific protein sequences, nor of codon adaptation or reverse transcription of KRTAP1-n mRNA. Instead, the results are consistent with short-tract gene conversion events coupled with selection for these events in the coding region driving the contrasting evolutionary patterns found in the KRTAP1 repeats. Our work shows the power that repeat recombination has to complement selection and finely tune the sequences of repetitive genes. Interplay between selection and recombination may be a more common mechanism than currently appreciated for achieving specific adaptive outcomes in the many eukaryotic multi-gene families, and our work argues for greater emphasis on exploring the sequence structures of these families.

scholarly journals Analysis of substitution rates showed that TLR5 is evolving at different rates among mammalian groups

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Ana Pinheiro ◽  
Ana Águeda-Pinto ◽  
José Melo-Ferreira ◽  
Fabiana Neves ◽  
Joana Abrantes ◽  
...  
Keyword(s):  
Substitution Rate ◽  
Relative Rate ◽  
Purifying Selection ◽  
Genetic Distances ◽  
Major Protein ◽  
Substitution Rates ◽  
Evolutionary Pattern ◽  
Branch Model ◽  
Rate Test ◽  
Species Specific

Abstract Background Toll-like receptors (TLRs) are the most widely studied innate immunity receptors responsible for recognition of invading pathogens. Among the TLR family, TLR5 is the only that senses and recognizes flagellin, the major protein of bacterial flagella. TLR5 has been reported to be under overall purifying selection in mammals, with a small proportion of codons under positive selection. However, the variation of substitution rates among major mammalian groups has been neglected. Here, we studied the evolution of TLR5 in mammals, comparing the substitution rates among groups. Results In this study we analysed the TLR5 substitution rates in Euungulata, Carnivora, Chiroptera, Primata, Rodentia and Lagomorpha, groups. For that, Tajima’s relative rate test, Bayesian inference of evolutionary rates and genetic distances were estimated with CODEML’s branch model and RELAX. The combined results showed that in the Lagomorpha, Rodentia, Carnivora and Chiroptera lineages TLR5 is evolving at a higher substitution rate. The RELAX analysis further suggested a significant relaxation of selective pressures for the Lagomorpha (K = 0.22, p < 0.01), Rodentia (K = 0.58, p < 0.01) and Chiroptera (K = 0.65, p < 0.01) lineages and for the Carnivora ancestral branches (K = 0.13, p < 0.01). Conclusions Our results show that the TLR5 substitution rate is not uniform among mammals. In fact, among the different mammal groups studied, the Lagomorpha, Rodentia, Carnivora and Chiroptera are evolving faster. This evolutionary pattern could be explained by 1) the acquisition of new functions of TLR5 in the groups with higher substitution rate, i.e. TLR5 neofunctionalization, 2) by the beginning of a TLR5 pseudogenization in these groups due to some redundancy between the TLRs genes, or 3) an arms race between TLR5 and species-specific parasites.

scholarly journals Origins and Evolutionary Patterns of the 1.688 Satellite DNA Family in Drosophila Phylogeny

2020 ◽  
Vol 10 (11) ◽  
pp. 4129-4146
Author(s):  
Leonardo G. de Lima ◽  
Stacey L. Hanlon ◽  
Jennifer L. Gerton
Keyword(s):  
Repetitive Sequences ◽  
Specific Pattern ◽  
Evolutionary Patterns ◽  
Satellite Dnas ◽  
Evolutionary Pattern ◽  
Functional Roles ◽  
Drosophila Phylogeny ◽  
Species Specific ◽  
Future Work ◽  
Eukaryotic Genomes

Satellite DNAs (satDNAs) are a ubiquitous feature of eukaryotic genomes and are usually the major components of constitutive heterochromatin. The 1.688 satDNA, also known as the 359 bp satellite, is one of the most abundant repetitive sequences in Drosophila melanogaster and has been linked to several different biological functions. We investigated the presence and evolution of the 1.688 satDNA in 16 Drosophila genomes. We find that the 1.688 satDNA family is much more ancient than previously appreciated, being shared among part of the melanogaster group that diverged from a common ancestor ∼27 Mya. We found that the 1.688 satDNA family has two major subfamilies spread throughout Drosophila phylogeny (∼360 bp and ∼190 bp). Phylogenetic analysis of ∼10,000 repeats extracted from 14 of the species revealed that the 1.688 satDNA family is present within heterochromatin and euchromatin. A high number of euchromatic repeats are gene proximal, suggesting the potential for local gene regulation. Notably, heterochromatic copies display concerted evolution and a species-specific pattern, whereas euchromatic repeats display a more typical evolutionary pattern, suggesting that chromatin domains may influence the evolution of these sequences. Overall, our data indicate the 1.688 satDNA as the most perduring satDNA family described in Drosophila phylogeny to date. Our study provides a strong foundation for future work on the functional roles of 1.688 satDNA across many Drosophila species.

scholarly journals Molecular cloning and evolutionary analysis of the GJA1 (connexin43) gene from bats (Chiroptera)

2009 ◽  
Vol 91 (2) ◽  
pp. 101-109 ◽  
Author(s):  
LI WANG ◽  
GANG LI ◽  
JINHONG WANG ◽  
SHAOHUI YE ◽  
GARETH JONES ◽  
...  
Keyword(s):  
Amino Acid ◽  
Phylogenetic Reconstruction ◽  
Purifying Selection ◽  
Likelihood Method ◽  
Evolutionary Analysis ◽  
Coding Region ◽  
Specific Amino Acid ◽  
Junction Protein ◽  
Gap Junction Protein ◽  
Species Specific

SummaryGap junction protein connexin43 (Cx43), encoded by the GJA1 gene, is the most abundant connexin in the cardiovascular system and was reported as a crucial factor maintaining cardiac electrical conduction, as well as having a very important function in facilitating the recycling of potassium ions from hair cells in the cochlea back into the cochlear endolymph during auditory transduction processes. In mammals, bats are the only taxon possessing powered flight, placing exceptional demand on many organismal processes. To meet the demands of flying, the hearts of bats show many specialties. Moreover, ultrasonic echolocation allows bat species to orientate and often detect and locate food in darkness. In this study, we cloned the full-length coding region of GJA1 gene from 12 different species of bats and obtained orthologous sequences from other mammals. We used the maximum likelihood method to analyse the evolution of GJA1 gene in mammals and the lineage of bats. Our results showed this gene is much conserved in mammals, as well as in bats' lineage. Compared with other mammals, we found one private amino acid substitution shared by bats, which is located on the inner loop domain, as well as some species-specific amino acid substitutions. The evolution rate analyses showed the signature of purifying selection on not only different classification level lineages but also the different domains and amino acid residue sites of this gene. Also, we suggested that GJA1 gene could be used as a good molecular marker to do the phylogenetic reconstruction.

scholarly journals Different scales of gene duplications occurring at different times have jointly shaped the NBS-LRR genes in Prunus species

2022 ◽  
Author(s):  
Yan Zhong ◽  
Zhao Chen ◽  
Zong-Ming Cheng
Keyword(s):  
Plant Disease Resistance ◽  
Resistance Breeding ◽  
Gene Families ◽  
Gene Duplications ◽  
Evolutionary Patterns ◽  
Genome Wide ◽  
Prunus Yedoensis ◽  
Species Specific ◽  
Plant Disease Resistance Genes ◽  
Duplication Time

AbstractIn this study, genome-wide identification, phylogenetic relationships, duplication time and selective pressure of the NBS-LRR genes, an important group of plant disease-resistance genes (R genes), were performed to uncover their genetic evolutionary patterns in the six Prunus species. A total of 1946 NBS-LRR genes were identified; specifically, 589, 361, 284, 281, 318, and 113 were identified in Prunus yedoensis, P. domestica, P. avium, P. dulcis, P. persica and P. yedoensis var. nudiflora, respectively. Two NBS-LRR gene subclasses, TIR-NBS-LRR (TNL) and non-TIR-NBS-LRR (non-TNL), were also discovered. In total, 435 TNL and 1511 non-TNL genes were identified and could be classified into 30/55/75 and 103/158/191 multi-gene families, respectively, according to three different criteria. Higher Ks and Ka/Ks values were detected in TNL gene families than in non-TNL gene families. These results indicated that the TNL genes had more members involved in relatively ancient duplications and were affected by stronger selection pressure than the non-TNL genes. In general, the NBS-LRR genes were shaped by species-specific duplications, and lineage-specific duplications occurred at recent and relatively ancient periods among the six Prunus species. Therefore, different duplicated copies of NBS-LRRs can resist specific pathogens and will provide an R-gene library for resistance breeding in Prunus species.

scholarly journals The Evolutionary Pattern and the Regulation of Stearoyl-CoA Desaturase Genes

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
Xiaoyun Wu ◽  
Xiaoju Zou ◽  
Qing Chang ◽  
Yuru Zhang ◽  
Yunhai Li ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Relative Rate ◽  
Saturated Fatty Acids ◽  
Purifying Selection ◽  
Similar Rate ◽  
Ratio Test ◽  
Evolutionary Patterns ◽  
Variable Binding ◽  
Evolutionary Pattern ◽  
Stearoyl Coa Desaturase

Stearoyl-CoA desaturase (SCD) is a key enzyme that converts saturated fatty acids (SFAs) to monounsaturated fatty acids (MUFAs) in the biosynthesis of fat. To date, two isoforms ofscdgene (scd1andscd5) have been found widely existent in most of the vertebrate animals. However, the evolutionary patterns of both isofoms and the function ofscd5are poorly understandable. Herein, we aim to characterize the evolutionary pattern ofscdgenes and further predict the function differentiation ofscdgenes. The sequences ofscdgenes were highly conserved among eukaryote. Phylogenetic analysis identified two duplications ofscdgene early in vertebrate evolution. The relative rate ratio test, branch-specificdN/dSratio tests, and branch-sitedN/dSratio tests all suggested that thescdgenes were evolved at a similar rate. The evolution ofscdgenes among eukaryote was under strictly purifying selection though several sites inscd1andscd5were undergone a relaxed selection pressure. The variable binding sites by transcriptional factors at the 5′-UTR and by miRNAs at 3′-UTR ofscdgenes suggested that the regulators ofscd5may be different from that ofscd1. This study promotes our understanding of the evolutionary patterns and function of SCD genes in eukaryote.

scholarly journals Genome-Wide Identification, Molecular Evolution, and Expression Divergence of Aluminum-Activated Malate Transporters in Apples

2018 ◽  
Vol 19 (9) ◽  
pp. 2807 ◽  
Author(s):  
Baiquan Ma ◽  
Yangyang Yuan ◽  
Meng Gao ◽  
Tonghui Qi ◽  
Mingjun Li ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Gene Duplication ◽  
Gene Family ◽  
Functional Divergence ◽  
Aluminum Tolerance ◽  
Evolutionary Process ◽  
Purifying Selection ◽  
Gene Families ◽  
Biochemical Properties ◽  
Evolutionary Pattern

Aluminum-activated malate transporters (ALMTs) play an important role in aluminum tolerance, stomatal opening, and fruit acidity in plants. However, the evolutionary pattern of the ALMT gene family in apples remains relatively unknown. In this study, a total of 25 MdALMT genes were identified from the apple reference genome of the “Golden Delicious” doubled-haploid tree (GDDH13). The physiological and biochemical properties, gene structure, and conserved motifs of MdALMT genes were examined. Chromosome location and gene-duplication analysis indicated that whole-genome duplication/segmental duplication played an important role in the expansion of the MdALMT gene family. The Ka/Ks ratio of duplicated MdALMT genes showed that members of this family have undergone strong purifying selection. Through exploration of the phylogenetic relationships, seven subgroups were classified, and higher old gene duplication frequency and significantly different evolutionary rates of the ALMT gene families were detected. In addition, the functional divergence of ALMT genes occurred during the evolutionary process of Rosaceae species. Furthermore, the functional divergence of MdALMT genes was confirmed by expression discrepancy and different subcellular localizations. This study provides the foundation to better understand the molecular evolution of MdALMT genes and further facilitate functional analysis to unravel their exact role in apples.

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.

Cross-species Transcriptomes Reveal Species-specific and Shared Molecular Adaptations for Plants Development on Iron-rich Rocky Outcrops Soils

2021 ◽  
Author(s):  
Mariana Costa Dias ◽  
Cecílio Caldeira ◽  
Markus Gastauer ◽  
Silvio Ramos ◽  
Guilherme Oliveira
Keyword(s):  
Circadian Rhythm ◽  
Differential Expression ◽  
Native Species ◽  
Molecular Mechanisms ◽  
Light Stimulus ◽  
Differential Expression Analysis ◽  
Common Mechanism ◽  
Dependent Manner ◽  
Rocky Outcrops ◽  
Species Specific

Abstract BackgroundCanga is the Brazilian term for the savanna-like vegetation harboring several endemic species on iron-rich rocky outcrops, usually considered for mining activities. Parkia platycephala Benth. and Stryphnodendron pulcherrimum (Willd.) Hochr. naturally occur in the cangas of Serra dos Carajás (eastern Amazonia, Brazil) and the surrounding forest, indicating high phenotypic plasticity. The morphological and physiological mechanisms of the plants’ establishment in the canga environment are well studied, but the molecular adaptative responses are still unknown. We aimed to identify molecular mechanisms that allow the establishment of these plants in the canga environment.ResultsPlants were grown in canga and forest substrates collected in the Carajás Mineral Province. RNA was extracted from pooled leaf tissue, and RNA-seq paired-end reads were assembled into representative transcriptomes for P. platycephala and S. pulcherrimum containing 31,728 and 31,311 primary transcripts, respectively. We identified both species-specific and core molecular responses in plants grown in the canga substrate using differential expression analyses. In the species-specific analysis, we identified 1,112 and 838 differentially expressed genes for P. platycephala and S. pulcherrimum, respectively. Enrichment analyses showed unique biological processes and metabolic pathways affected for each species. Comparative differential expression analysis was based on shared single-copy orthologs. The overall pattern of ortholog expression was species-specific. Even so, almost 300 altered genes were identified between plants in canga and forest substrates, responding the same way in both species. The genes were functionally associated with the response to light stimulus and the circadian rhythm pathway.ConclusionsPlants possess species-specific adaptative responses to cope with the substrates. Our results also suggest that plants adapted to both canga and forest environments can adjust the circadian rhythm in a substrate-dependent manner. The circadian clock gene modulation might be a central mechanism regulating the plants’ development in the canga substrate in the studied legume species. The mechanism may be shared as a common mechanism to abiotic stress compensation in other native species.

scholarly journals Restricting nonclassical MHC genes coevolve with TRAV genes used by innate-like T cells in mammals

2016 ◽  
Vol 113 (21) ◽  
pp. E2983-E2992 ◽  
Author(s):  
Pierre Boudinot ◽  
Stanislas Mondot ◽  
Luc Jouneau ◽  
Luc Teyton ◽  
Marie-Paule Lefranc ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Purifying Selection ◽  
Cell Receptor ◽  
Nkt Cells ◽  
Evolutionary Patterns ◽  
Mait Cells ◽  
Mhc Genes ◽  
Class 1 ◽  
Complementarity Determining Regions

Whereas major histocompatibility class-1 (MH1) proteins present peptides to T cells displaying a large T-cell receptor (TR) repertoire, MH1Like proteins, such as CD1D and MR1, present glycolipids and microbial riboflavin precursor derivatives, respectively, to T cells expressing invariant TR-α (iTRA) chains. The groove of such MH1Like, as well as iTRA chains used by mucosal-associated invariant T (MAIT) and natural killer T (NKT) cells, respectively, may result from a coevolution under particular selection pressures. Herein, we investigated the evolutionary patterns of the iTRA of MAIT and NKT cells and restricting MH1Like proteins: MR1 appeared 170 Mya and is highly conserved across mammals, evolving more slowly than other MH1Like. It has been pseudogenized or independently lost three times in carnivores, the armadillo, and lagomorphs. The corresponding TRAV1 gene also evolved slowly and harbors highly conserved complementarity determining regions 1 and 2. TRAV1 is absent exclusively from species in which MR1 is lacking, suggesting that its loss released the purifying selection on MR1. In the rabbit, which has very few NKT and no MAIT cells, a previously unrecognized iTRA was identified by sequencing leukocyte RNA. This iTRA uses TRAV41, which is highly conserved across several groups of mammals. A rabbit MH1Like gene was found that appeared with mammals and is highly conserved. It was independently lost in a few groups in which MR1 is present, like primates and Muridae, illustrating compensatory emergences of new MH1Like/Invariant T-cell combinations during evolution. Deciphering their role is warranted to search similar effector functions in humans.

Sign in / Sign up

Export Citation Format

Share Document