scholarly journals Gene Duplication and Evolutionary Innovations in Hemoglobin-Oxygen Transport

Physiology ◽  
2016 ◽  
Vol 31 (3) ◽  
pp. 223-232 ◽  
Author(s):  
Jay F. Storz
Keyword(s):  
Gene Duplication ◽  
Functional Properties ◽  
Oxygen Transport ◽  
Developmental Stages ◽  
Functional Differentiation ◽  
Vertebrate Evolution ◽  
Developmental Timing

During vertebrate evolution, duplicated hemoglobin (Hb) genes diverged with respect to functional properties as well as the developmental timing of expression. For example, the subfamilies of genes that encode the different subunit chains of Hb are ontogenetically regulated such that functionally distinct Hb isoforms are expressed during different developmental stages. In some vertebrate taxa, functional differentiation between co-expressed Hb isoforms may also contribute to physiologically important divisions of labor.

Evolution of the archaeal rhodopsins: evolution rate changes by gene duplication and functional differentiation 1 1Edited by G. Von Heijnel

1999 ◽  
Vol 285 (1) ◽  
pp. 163-174 ◽  
Author(s):  
Kunio Ihara ◽  
Tohru Umemura ◽  
Izumi Katagiri ◽  
Tomomi Kitajima-Ihara ◽  
Yasuo Sugiyama ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Functional Differentiation ◽  
Evolution Rate

scholarly journals Recurrent Sequence Evolution After Independent Gene Duplication

2020 ◽  
Author(s):  
Samuel Hermann Alexander Von Der Dunk ◽  
Berend Snel
Keyword(s):  
Gene Duplication ◽  
Experimental Testing ◽  
Parallel Evolution ◽  
Gene Families ◽  
Functional Differentiation ◽  
Functional Change ◽  
Neutral Evolution ◽  
Sequence Evolution ◽  
Recurrent Sequence ◽  
Independent Gene

Abstract Background Convergent and parallel evolution provide unique insights into the mechanisms of natural selection. Some of the most striking convergent and parallel (collectively recurrent ) amino acid substitutions in proteins are adaptive, but there are also many that are selectively neutral. Accordingly, genome-wide assessment has shown that recurrent sequence evolution in orthologs is chiefly explained by nearly neutral evolution. For paralogs, more frequent functional change is expected because additional copies are generally not retained if they do not acquire their own niche. Yet, it is unknown to what extent recurrent sequence differentiation is discernible after independent gene duplications in different eukaryotic taxa. Results We develop a framework that detects patterns of recurrent sequence evolution in duplicated genes. This is used to analyze the genomes of 90 diverse eukaryotes. We find a remarkable number of families with a potentially predictable functional differentiation following gene duplication. In some protein families, more than ten independent duplications show a similar sequence-level differentiation between paralogs. Based on further analysis, the sequence divergence is found to be generally asymmetric. Moreover, about 6\% of the recurrent sequence evolution between paralog pairs can be attributed to recurrent differentiation of subcellular localization. Finally, we reveal the specific recurrent patterns for the gene families Hint1/Hint2, Sco1/Sco2 and vma11/vma3. Conclusions The presented methodology provides a means to study the biochemical underpinning of functional differentiation between paralogs. For instance, two abundantly repeated substitutions are identified between independently derived Sco1 and Sco2 paralogs. Such identified substitutions allow direct experimental testing of the biological role of these residues for the repeated functional differentiation. We also uncover a diverse set of families with recurrent sequence evolution and reveal trends in the functional and evolutionary trajectories of this hitherto understudied phenomenon.

scholarly journals A Transcriptomic Atlas of the Ectomycorrhizal Fungus Laccaria bicolor

2021 ◽  
Vol 9 (12) ◽  
pp. 2612
Author(s):  
Joske Ruytinx ◽  
Shingo Miyauchi ◽  
Sebastian Hartmann-Wittulsky ◽  
Maíra de Freitas Pereira ◽  
Frédéric Guinet ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Morphological Differentiation ◽  
Functional Differentiation ◽  
Ectomycorrhizal Fungus ◽  
Fine Tuning ◽  
Laccaria Bicolor ◽  
Transcriptional Responses ◽  
Wide Range ◽  
Transcriptional Changes ◽  
Ecm Fungi

Trees are able to colonize, establish and survive in a wide range of soils through associations with ectomycorrhizal (EcM) fungi. Proper functioning of EcM fungi implies the differentiation of structures within the fungal colony. A symbiotic structure is dedicated to nutrient exchange and the extramatricular mycelium explores soil for nutrients. Eventually, basidiocarps develop to assure last stages of sexual reproduction. The aim of this study is to understand how an EcM fungus uses its gene set to support functional differentiation and development of specialized morphological structures. We examined the transcriptomes of Laccaria bicolor under a series of experimental setups, including the growth with Populus tremula x alba at different developmental stages, basidiocarps and free-living mycelium, under various conditions of N, P and C supply. In particular, N supply induced global transcriptional changes, whereas responses to P supply seemed to be independent from it. Symbiosis development with poplar is characterized by transcriptional waves. Basidiocarp development shares transcriptional signatures with other basidiomycetes. Overlaps in transcriptional responses of L. bicolor hyphae to a host plant and N/C supply next to co-regulation of genes in basidiocarps and mature mycorrhiza were detected. Few genes are induced in a single condition only, but functional and morphological differentiation rather involves fine tuning of larger gene sets. Overall, this transcriptomic atlas builds a reference to study the function and stability of EcM symbiosis in distinct conditions using L. bicolor as a model and indicates both similarities and differences with other ectomycorrhizal fungi, allowing researchers to distinguish conserved processes such as basidiocarp development from nutrient homeostasis.

Gene duplication and hemoglobin isoform differentiation

Hemoglobin ◽  
2018 ◽  
pp. 124-151
Author(s):  
Jay F. Storz
Keyword(s):  
Gene Duplication ◽  
Division Of Labor ◽  
Functional Differentiation ◽  
Prenatal Development ◽  
Adaptive Significance ◽  
Postnatal Life ◽  
Tissue Oxygen ◽  
Developmentally Regulated ◽  
Adaptive Enhancement ◽  
Tissue Oxygen Delivery

Chapter 6 explores the physiological significance of gene duplication and hemoglobin isoform differentiation. Repeated rounds of gene duplication and divergence during the evolution of jawed vertebrates promoted the diversification of the subfamilies of genes that encode the different subunit chains of tetrameric hemoglobin, leading to functional differentiation between hemoglobin isoforms that are expressed during different stages of prenatal development and postnatal life. The differentiation in oxygenation properties among developmentally regulated hemoglobin isoforms has clear adaptive significance in viviparous and oviviparous vertebrates alike. In some cases, a physiological division of labor between coexpressed isoforms may also contribute to the adaptive enhancement of tissue oxygen delivery.

scholarly journals Recurrent Sequence Evolution After Independent Gene Duplication

2020 ◽  
Author(s):  
Samuel Hermann Alexander Von Der Dunk ◽  
Berend Snel
Keyword(s):  
Gene Duplication ◽  
Experimental Testing ◽  
Parallel Evolution ◽  
Gene Families ◽  
Functional Differentiation ◽  
Functional Change ◽  
Neutral Evolution ◽  
Sequence Evolution ◽  
Recurrent Sequence ◽  
Independent Gene

Abstract Background Convergent and parallel evolution provide unique insights into the mechanisms of natural selection. Some of the most striking convergent and parallel (collectively recurrent ) amino acid substitutions in proteins are adaptive, but there are also many that are selectively neutral. Accordingly, genome-wide assessment has shown that recurrent sequence evolution in orthologs is chiefly explained by nearly neutral evolution. For paralogs, more frequent functional change is expected because additional copies are generally not retained if they do not acquire their own niche. Yet, it is unknown to what extent recurrent sequence differentiation is discernible after independent gene duplications in different eukaryotic taxa. Results We develop a framework that detects patterns of recurrent sequence evolution in duplicated genes. This is used to analyze the genomes of 90 diverse eukaryotes. We find a remarkable number of families with a potentially predictable functional differentiation following gene duplication. In some protein families, more than ten independent duplications show a similar sequence-level differentiation between paralogs. Based on further analysis, the sequence divergence is found to be generally asymmetric. Moreover, about 6\% of the recurrent sequence evolution between paralog pairs can be attributed to recurrent differentiation of subcellular localization. Finally, we reveal the specific recurrent patterns for the gene families Hint1/Hint2, Sco1/Sco2 and vma11/vma3. Conclusions The presented methodology provides a means to study the biochemical underpinning of functional differentiation between paralogs. For instance, two abundantly repeated substitutions are identified between independently derived Sco1 and Sco2 paralogs. Such identified substitutions allow direct experimental testing of the biological role of these residues for the repeated functional differentiation. We also uncover a diverse set of families with recurrent sequence evolution and reveal trends in the functional and evolutionary trajectories of this hitherto understudied phenomenon.

scholarly journals Genome-wide comparative analysis of the BAHD superfamily in seven Rosaceae species and expression analysis in pear (Pyrus☓ bretschneideri)

2019 ◽  
Author(s):  
Chunxin Liu ◽  
Xin Qiao ◽  
Qionghou Li ◽  
Weiwei Zeng ◽  
Shuwei Wei ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Gene Duplication ◽  
Candidate Genes ◽  
Fruit Quality ◽  
Prunus Persica ◽  
Prunus Avium ◽  
Developmental Stages ◽  
Pear Fruit ◽  
Gene Pairs ◽  
Rosaceae Species

Abstract Background: The BAHD acyltransferase superfamily exhibits various biological roles in plants, including regulating fruit quality, catalytic synthesizing of terpene, phenolics and esters, and improving stress resistance. However, the copy numbers, expression characteristics and associations with fruit aroma formation of the BAHD genes remain unclear. Results: In total, 717 BAHD genes were obtained from the genomes of seven Rosaceae, ( Pyrus bretschneideri , Malus domestica , Prunus avium , Prunus persica , Fragaria vesca , Pyrus communis and Rubus occidentalis ). Based on the classifications in model plants, we divided the BAHD family genes into seven groups, I-a, I-b, II-a, II-b, III-a, IV and V. An intra-species synteny analysis detected 78 syntenic gene pairs among the seven Rosaceae species. Dispersed gene duplication occurred frequently in all the investigated species. Different modes of duplicated gene pairs identified in each investigated species revealed that the Ka/Ks ratios were less than one, indicating that they evolved through purifying selection. Based on the correlation analysis between the ester content and expression levels of BAHD genes at different developmental stages, we selected five genes for verification as assessed by qRT-PCR. Pbr020016.1 , Pbr019034.1 , Pbr014028.1 and Pbr029551.1 are important candidate genes involved in aroma formation during pear fruit development. Conclusion: We have thoroughly annotated the BAHD superfamily genes and performed a comprehensive comparative analysis of their colinearity, phylogenetic relationships and gene duplication patterns in seven Rosaceae species, and we also obtained four candidate genes involved in aroma synthesis in pear fruit. These results provide a theoretical basis for future studies of the specific biological functions of BAHD superfamily members and the improvement of pear fruit quality. Keywords : BAHD, pear, evolution, Rosaceae, transcriptome, volatile esters

scholarly journals Genome-wide identification and expression pattern analysis of the ribonuclease T2 family in Eucommia ulmoides

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jun Qing ◽  
Qingxin Du ◽  
Yide Meng ◽  
Panfeng Liu ◽  
Hongyan Du ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Phylogenetic Tree ◽  
Gene Family ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Eucommia Ulmoides ◽  
Class Iii ◽  
Specific Expression ◽  
Eukaryotic Organisms ◽  
Rnase T2

AbstractThe 2′,3′-cycling ribonuclease (RNase) genes are catalysts of RNA cleavage and include the RNase T2 gene family. RNase T2 genes perform important roles in plants and have been conserved in the genome of eukaryotic organisms. In this study we identified 21 EURNS genes in Eucommia ulmoides Oliver (E. ulmoides) and analyzed their structure, chromosomal location, phylogenetic tree, gene duplication, stress-related cis-elements, and expression patterns in different tissues. The length of 21 predicted EURNS proteins ranged from 143 to 374 amino acids (aa), their molecular weight (MW) ranged from 16.21 to 42.38 kDa, and their isoelectric point (PI) value ranged from 5.08 to 9.09. Two classifications (class I and class III) were obtained from the conserved domains analysis and phylogenetic tree. EURNS proteins contained a total of 15 motifs. Motif 1, motif 2, motif 3, and motif 7 were distributed in multiple sequences and were similar to the conserved domain of RNase T2. EURNS genes with similar structure and the predicted EURNS proteins with conserved motif compositions are in the same group in the phylogenetic tree. The results of RT-PCR and transcription data showed that EURNS genes have tissue-specific expression and exhibited obvious trends in different developmental stages. Gene duplication analysis results indicated that segment duplication may be the dominant duplication mode in this gene family. This study provides a theoretical basis for research on the RNase T2 gene family and lays a foundation for the further study of EURNS genes.

Developmental, Molecular, and Genetic Dissection of INa In Vivo in Embryonic Zebrafish Sensory Neurons

2005 ◽  
Vol 93 (6) ◽  
pp. 3582-3593 ◽  
Author(s):  
Ricardo H. Pineda ◽  
Ryan A. Heiser ◽  
Angeles B. Ribera
Keyword(s):  
Functional Properties ◽  
Developmental Stages ◽  
Sodium Current ◽  
Molecular Genetic ◽  
Genetic Dissection ◽  
Developmentally Regulated ◽  
Cell Stage ◽  
Voltage Dependent ◽  
Developing Neurons

The presence of multiple Nav1 isotypes within a neuron and the lack of specific blockers hamper identification of the in vivo roles of sodium current ( INa) components, especially during embryonic stages. To identify the functional properties of INa components in vivo in developing neurons, we took a molecular genetic approach. Embryonic zebrafish Rohon–Beard (RB) mechanosensory neurons express two different sodium channel isotypes: Nav1.1 and Nav1.6. To examine the properties of Nav1.1- and Nav1.6-encoded currents in RB cells at different developmental stages, we eliminated the contribution of Nav1.6 and Nav1.1 channels, respectively, using an antisense morpholino (MO) approach. MOs were injected into one-cell stage embryos, and RB sodium currents were recorded using patch-clamp techniques in both conventional whole cell mode as well from nucleated patches. Only a subset of RB cells appeared to be affected by the Nav1.1MO. Overall, the effect of the Nav1.1MO was a small 25% average reduction in current amplitude. Further, Nav1.1MO effects were most pronounced in RB cells of younger embryos. In contrast, the effects of the Nav1.6 MO were observed in all cells and increased as development proceeded. These results indicated that developmental upregulation of RB INa entailed an increase in the number of functional Nav1.6 channels. In addition, analysis of voltage-dependent steady-state activation and inactivation parameters revealed that specific functional properties of channels were also developmentally regulated. Finally, analysis of macho mutants indicated that developmental upregulation of INa was absent in RB cells. These results indicate that MOs are a useful tool for the molecular dissection and analysis of ion channel function in vivo.

scholarly journals Absence of mDazl produces a final block on germ cell development at meiosis

Reproduction ◽  
2003 ◽  
pp. 589-597 ◽  
Author(s):  
PT Saunders ◽  
JM Turner ◽  
M Ruggiu ◽  
M Taggart ◽  
PS Burgoyne ◽  
...  
Keyword(s):  
Germ Cell ◽  
Germ Cells ◽  
Meiotic Prophase ◽  
Rna Binding ◽  
Developmental Stages ◽  
Cell Loss ◽  
Functional Differentiation ◽  
Autosomal Gene ◽  
Fetal Life ◽  
Male And Female

The autosomal gene DAZL is a member of a family of genes (DAZL, DAZ, BOULE), all of which contain a consensus RNA binding domain and are expressed in germ cells. Adult male and female mice null for Dazl lack gametes. In order to define more precisely the developmental stages in germ cells that require Dazl expression, the patterns of germ cell loss in immature male and female wild-type (+/+, WT) and Dazl -/- (DazlKO) mice were analysed. In females, loss of germ cells occurred during fetal life and was coincident with progression of cells through meiotic prophase. In males, testes were recovered from WT and DazlKO males obtained before and during the first wave of spermatogenesis (days 2-19). Mitotically active germ cells were present up to and including day 19. Functional differentiation of spermatogonia associated with detection of c-kit positive cells did not depend upon expression of Dazl. RBMY-positive cells (A, intermediate, B spermatogonia, zygotene and preleptotene spermatocytes) were reduced in DazlKO compared with WT testes. Staining of cell squashes from day 19 testes with anti-gamma-H2AX and anti-SCP3 antibodies showed that germ cells from DazlKO males were unable to progress beyond the leptotene stage of meiotic prophase I. It was concluded that in the absence of Dazl, germ cells can complete mitosis, and embark on functional differentiation but that, in both sexes, progression through meiotic prophase requires this RNA binding protein.

scholarly journals Global Investigation of TBL Gene Family in Rose (Rosa chinensis) Unveils RcTBL16 Is a Susceptibility Gene in Gray Mold Resistance

2021 ◽  
Vol 12 ◽  
Author(s):  
Yu Tian ◽  
Shiya Zhang ◽  
Xintong Liu ◽  
Zhao Zhang
Keyword(s):  
Gene Duplication ◽  
Gene Family ◽  
Susceptibility Gene ◽  
Purifying Selection ◽  
Functional Differentiation ◽  
Gray Mold ◽  
Virus Induced Gene Silencing ◽  
Cell Wall Polysaccharides ◽  
A Genome ◽  
Mold Resistance

The TRICHOME BIREFRINGENCE-LIKE (TBL) family is an important gene family engaged in the O-acetylation of cell wall polysaccharides. There have been a few reports showing that TBL participated in the resistance against phytopathogens in Arabidopsis and rice. However, no relevant studies in rose (Rosa sp.) have been published. In this study, a genome-wide analysis of the TBL gene family in rose was presented, including their phylogenetic relationships, gene structure, chromosomal positioning, and collinearity analysis. The phylogenetic analysis revealed a total of 50 RcTBL genes in the rose genome, and they are unevenly distributed across all seven chromosomes. The occurrence of gene duplication events suggests that both the whole genome duplication and partial duplication may play a role in gene duplication of RcTBLs. The analysis of Ka/Ks showed that the replicated RcTBL genes underwent mainly purifying selection with limited functional differentiation. Gene expression analysis indicated that 12 RcTBLs were down-regulated upon the infection of Botrytis cinerea, the causal agent of the gray mold disease of rose. These RcTBLs may be a sort of candidate genes for regulating the response of rose to B. cinerea. Through virus-induced gene silencing, RcTBL16 was shown to be associated with susceptibility to gray mold in rose. Through this study, meaningful information for further studies on the function of the TBL protein family in rose is provided.

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