scholarly journals Evolution of Three Parent Genes and Their Retrogene Copies in Drosophila Species

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
Ryan S. O'Neill ◽  
Denise V. Clark
Keyword(s):  
Negative Selection ◽  
Expression Patterns ◽  
Single Copy ◽  
Regulatory Sequences ◽  
Sequence Evolution ◽  
Coding Sequences ◽  
Coding Regions ◽  
Gene Pairs ◽  
The Family ◽  
Gene Duplicate

Retrogenes form a class of gene duplicate lacking the regulatory sequences found outside of the mRNA-coding regions of the parent gene. It is not clear how a retrogene’s lack of parental regulatory sequences affects the evolution of the gene pair. To explore the evolution of parent genes and retrogenes, we investigated three such gene pairs in the family Drosophilidae; in Drosophila melanogaster, these gene pairs are CG8331 and CG4960, CG17734 and CG11825, and Sep2 and Sep5. We investigated the embryonic expression patterns of these gene pairs across multiple Drosophila species. Expression patterns of the parent genes and their single copy orthologs are relatively conserved across species, whether or not a species has a retrogene copy, although there is some variation in CG8331 and CG17734. In contrast, expression patterns of the retrogene orthologs have diversified. We used the genome sequences of 20 Drosophila species to investigate coding sequence evolution. The coding sequences of the three gene pairs appear to be evolving predominantly under negative selection; however, the parent genes and retrogenes show some distinct differences in amino acid sequence. Therefore, in general, retrogene expression patterns and coding sequences are distinct compared to their parents and, in some cases, retrogene expression patterns diversify.

Differential regulation of the two glyceraldehyde-3-phosphate dehydrogenase genes during Drosophila development

1988 ◽  
Vol 8 (12) ◽  
pp. 5200-5205
Author(s):  
X H Sun ◽  
J Y Tso ◽  
J Lis ◽  
R Wu
Keyword(s):  
Adult Stage ◽  
Expression Patterns ◽  
Differential Regulation ◽  
Regulatory Sequences ◽  
Coding Sequences ◽  
Translation Start ◽  
Genes Encoding ◽  
Flanking Sequences ◽  
Hybrid Genes ◽  
High Level

Drosophila melanogaster contains two genes encoding glyceraldehyde-3-phosphate dehydrogenase, Gapdh-1 and Gapdh-2. The two genes are highly conserved in their coding sequences but not in their noncoding and flanking sequences. We report that both genes are expressed at higher levels in larval, late pupal, and adult stages than in embryonic, early, and midpupal stages. However, a major difference in the expression of the two genes is observed in the adult stage, during which the level of the Gapdh-1 transcript decreases over fourfold, while that of the Gapdh-2 transcript remains at a constant high level. In addition, the Gapdh-1 transcript appears highly enriched in the thorax section compared with the head and abdomen sections, while the Gapdh-2 transcript is evenly distributed. Analyses of the expression patterns of the two Gapdh hybrid genes, GAP1/2 and GAP2/1, revealed that the two genes have a distinct organization of their regulatory sequences. The principle regulatory sequences of Gapdh-2 reside upstream of the translation start, while the principle sequences specifying the level and developmental pattern of Gapdh-1 expression reside downstream of the translation start.

scholarly journals Chloroplast Genome of Phyllanthus Emblica and Leptopus Cordifolius: Comparative Analysis and Phylogenetic within Family Phyllanthaceae

2021 ◽  
Author(s):  
Umar Rehman ◽  
Nighat Sultana ◽  
Abdullah . ◽  
Abbas Jamal ◽  
Maryam Muzaffar ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Related Species ◽  
Gc Content ◽  
Single Copy ◽  
Phyllanthus Emblica ◽  
Protein Coding ◽  
Coding Sequences ◽  
Tropical Regions ◽  
Chloroplast Genomes ◽  
The Family

Family Phyllanthaceae is one of the largest segregates of the eudicot order Malpighiales and its species are herb, shrub, and tree, which are mostly distributed in tropical regions. Certain taxonomic discrepancies exist at genus and family level. Here, we report chloroplast genomes of three Phyllanthaceae species—Phyllanthus emblica, Flueggea virosa, and Leptopus cordifolius— and compare them with six others previously reported Phyllanthaceae chloroplast genomes. The species of Phyllanthaceae displayed quadripartite structure, comprising inverted repeat regions (IRa and IRb) that separate large single copy (LSC) and small single copy (SSC) regions. The length of complete chloroplast genome ranged from 154,707 bp to 161,093 bp; LSC from 83,627 bp to 89,932 bp; IRs from 23,921 bp to 27,128 bp; and SSC from 17,424 bp to 19,441 bp. Chloroplast genomes contained 111 to 112 unique genes, including 77 to 78 protein-coding, 30 transfer RNA (tRNA), and 4 ribosomal RNA (rRNA) that showed similarities in arrangement. The number of protein-coding genes varied due to deletion/pseudogenization of rps16 genes in Baccaurea ramiflora and Leptopus cordifolius. High variability was seen in number of oligonucleotide repeats while analysis of guanine-cytosine (GC) content, codon usage, amino acid frequency, simple sequence repeats analysis, synonymous and non-synonymous substitutions, and transition and transversion substitutions showed similarities in all Phyllanthaceae species. We detected a higher number of transition substitutions in the coding sequences than non-coding sequences. Moreover, the high number of transition substitutions was determined among the distantly related species in comparison to closely related species. Phylogenetic analysis shows the polyphyletic nature of the genus Phyllanthus which requires further verification. We also determined suitable polymorphic coding genes, including rpl22, ycf1, matK, ndhF, and rps15 which may be helpful for the reconstruction of the high-resolution phylogenetic tree of the family Phyllanthaceae using a large number of species in the future. Overall, the current study provides insight into chloroplast genome evolution in Phyllanthaceae.

scholarly journals Distinct evolutionary trajectories of neuronal and hair cell nicotinic acetylcholine receptors

2019 ◽  
Author(s):  
Irina Marcovich ◽  
Marcelo J. Moglie ◽  
Agustín E. Carpaneto Freixas ◽  
Anabella P. Trigila ◽  
Lucia F. Franchini ◽  
...  
Keyword(s):  
Hair Cell ◽  
Functional Properties ◽  
Nicotinic Acetylcholine Receptors ◽  
Acetylcholine Receptors ◽  
Expression Patterns ◽  
Nicotinic Acetylcholine ◽  
Coding Sequences ◽  
The Family ◽  
Evolutionary Trajectories ◽  
Cell Expression

ABSTRACTThe expansion and pruning of ion channel families has played a crucial role in the evolution of nervous systems. Remarkably, with a highly conserved vertebrate complement, nicotinic acetylcholine receptors (nAChRs) are unique among ligand-gated ion channels in that members of the family have distinct roles in synaptic transmission in non-overlapping domains, either in the nervous system, the inner ear hair cells or the neuromuscular junction. Here, we performed a comprehensive analysis of vertebrate nAChRs sequences, single cell expression patterns and comparative functional properties of receptors from three representative tetrapod species. We show that hair cell nAChRs underwent a distinct evolutionary trajectory to that of neuronal receptors. These were most likely shaped by different co-expression patterns and co-assembly rules of component subunits. Thus, neuronal nAChRs showed high degree of coding sequence conservation, coupled to greater co-expression variance and conservation of functional properties across tetrapod clades. In contrast, hair cell α9α10 nAChRs exhibited greater sequence divergence, narrow co-expression pattern and great variability of functional properties across species. These results point to differential substrates for random change within the family of gene paralogs that relate to the segregated roles of nAChRs in synaptic transmission.Significance statementOur work exploits several peculiarities of the family of vertebrate nicotinic acetylcholine receptors (nAChRs) to explore the evolutionary trajectories of a ligand-gated ion channel family. By performing a comprehensive comparative analysis of nAChR subunits coding sequences, single cell expression patterns and functional properties we found a contrasting evolutionary history between nAChRs with widespread expression in the nervous system compared to those with isolated expression in the inner ear. Evolutionary changes were focused on differences in co-expression and co-assembly patterns for the former and coding sequences in the latter. This multidisciplinary approach provides further insight into the evolutionary processes that shaped the nervous and sensory systems of extant animals.

scholarly journals Comparative Chloroplast Genomics in Phyllanthaceae Species

Diversity ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 403
Author(s):  
Umar Rehman ◽  
Nighat Sultana ◽  
Abdullah ◽  
Abbas Jamal ◽  
Maryam Muzaffar ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
De Novo ◽  
Single Copy ◽  
Protein Coding ◽  
Coding Sequences ◽  
Tropical Regions ◽  
Chloroplast Genomes ◽  
The Family ◽  
Insight Into ◽  
Small Single Copy

Family Phyllanthaceae belongs to the eudicot order Malpighiales, and its species are herbs, shrubs, and trees that are mostly distributed in tropical regions. Here, we elucidate the molecular evolution of the chloroplast genome in Phyllanthaceae and identify the polymorphic loci for phylogenetic inference. We de novo assembled the chloroplast genomes of three Phyllanthaceae species, i.e., Phyllanthus emblica, Flueggea virosa, and Leptopus cordifolius, and compared them with six other previously reported genomes. All species comprised two inverted repeat regions (size range 23,921–27,128 bp) that separated large single-copy (83,627–89,932 bp) and small single-copy (17,424–19,441 bp) regions. Chloroplast genomes contained 111–112 unique genes, including 77–78 protein-coding, 30 tRNAs, and 4 rRNAs. The deletion/pseudogenization of rps16 genes was found in only two species. High variability was seen in the number of oligonucleotide repeats, while guanine-cytosine contents, codon usage, amino acid frequency, simple sequence repeats, synonymous and non-synonymous substitutions, and transition and transversion substitutions were similar. The transition substitutions were higher in coding sequences than in non-coding sequences. Phylogenetic analysis revealed the polyphyletic nature of the genus Phyllanthus. The polymorphic protein-coding genes, including rpl22, ycf1, matK, ndhF, and rps15, were also determined, which may be helpful for reconstructing the high-resolution phylogenetic tree of the family Phyllanthaceae. Overall, the study provides insight into the chloroplast genome evolution in Phyllanthaceae.

scholarly journals Structural variation of the complete chloroplast genome and plastid phylogenomics of the genus Asteropyrum (Ranunculaceae)

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Jian He ◽  
Min Yao ◽  
Ru-Dan Lyu ◽  
Le-Le Lin ◽  
Hui-Jie Liu ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Structural Variation ◽  
Single Copy ◽  
Systematic Position ◽  
Phylogenomic Analysis ◽  
Species Relationship ◽  
Complete Chloroplast Genome ◽  
Coding Regions ◽  
The Family ◽  
Cp Genome

Abstract Two complete chloroplast genome sequences of Asteropyrum, as well as those of 25 other species from Ranunculaceae, were assembled using both Illumina and Sanger sequencing methods to address the structural variation of the cp genome and the controversial systematic position of the genus. Synteny and plastome structure were compared across the family. The cp genomes of the only two subspecies of Asteropyrum were found to be differentiated with marked sequence variation and different inverted repeat-single copy (IR-SC) borders. The plastomes of both subspecies contains 112 genes. However, the IR region of subspecies peltatum carries 27 genes, whereas that of subspecies cavaleriei has only 25 genes. Gene inversions, transpositions, and IR expansion-contraction were very commonly detected in Ranunculaceae. The plastome of Asteropyrum has the longest IR regions in the family, but has no gene inversions or transpositions. Non-coding regions of the cp genome were not ideal markers for inferring the generic relationships of the family, but they may be applied to interpret species relationship within the genus. Plastid phylogenomic analysis using complete cp genome with Bayesian method and partitioned modeling obtained a fully resolved phylogenetic framework for Ranunculaceae. Asteropyrum was detected to be sister to Caltha, and diverged early from subfamily Ranunculoideae.

scholarly journals Differential regulation of the two glyceraldehyde-3-phosphate dehydrogenase genes during Drosophila development.

1988 ◽  
Vol 8 (12) ◽  
pp. 5200-5205 ◽  
Author(s):  
X H Sun ◽  
J Y Tso ◽  
J Lis ◽  
R Wu
Keyword(s):  
Adult Stage ◽  
Expression Patterns ◽  
Differential Regulation ◽  
Regulatory Sequences ◽  
Coding Sequences ◽  
Translation Start ◽  
Genes Encoding ◽  
Flanking Sequences ◽  
Hybrid Genes ◽  
High Level

Drosophila melanogaster contains two genes encoding glyceraldehyde-3-phosphate dehydrogenase, Gapdh-1 and Gapdh-2. The two genes are highly conserved in their coding sequences but not in their noncoding and flanking sequences. We report that both genes are expressed at higher levels in larval, late pupal, and adult stages than in embryonic, early, and midpupal stages. However, a major difference in the expression of the two genes is observed in the adult stage, during which the level of the Gapdh-1 transcript decreases over fourfold, while that of the Gapdh-2 transcript remains at a constant high level. In addition, the Gapdh-1 transcript appears highly enriched in the thorax section compared with the head and abdomen sections, while the Gapdh-2 transcript is evenly distributed. Analyses of the expression patterns of the two Gapdh hybrid genes, GAP1/2 and GAP2/1, revealed that the two genes have a distinct organization of their regulatory sequences. The principle regulatory sequences of Gapdh-2 reside upstream of the translation start, while the principle sequences specifying the level and developmental pattern of Gapdh-1 expression reside downstream of the translation start.

scholarly journals Phylogenetic comparison and splice site conservation of eukaryotic U1 snRNP-specific U1-70K gene family

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tao Fan ◽  
Yu-Zhen Zhao ◽  
Jing-Fang Yang ◽  
Qin-Lai Liu ◽  
Yuan Tian ◽  
...  
Keyword(s):  
Gene Family ◽  
Splice Site ◽  
Messenger Rna ◽  
Expression Patterns ◽  
Protein Structures ◽  
Single Copy ◽  
Central Component ◽  
Animal Kingdom ◽  
Functional Studies ◽  
U1 Snrnp

AbstractEukaryotic cells can expand their coding ability by using their splicing machinery, spliceosome, to process precursor mRNA (pre-mRNA) into mature messenger RNA. The mega-macromolecular spliceosome contains multiple subcomplexes, referred to as small nuclear ribonucleoproteins (snRNPs). Among these, U1 snRNP and its central component, U1-70K, are crucial for splice site recognition during early spliceosome assembly. The human U1-70K has been linked to several types of human autoimmune and neurodegenerative diseases. However, its phylogenetic relationship has been seldom reported. To this end, we carried out a systemic analysis of 95 animal U1-70K genes and compare these proteins to their yeast and plant counterparts. Analysis of their gene and protein structures, expression patterns and splicing conservation suggest that animal U1-70Ks are conserved in their molecular function, and may play essential role in cancers and juvenile development. In particular, animal U1-70Ks display unique characteristics of single copy number and a splicing isoform with truncated C-terminal, suggesting the specific role of these U1-70Ks in animal kingdom. In summary, our results provide phylogenetic overview of U1-70K gene family in vertebrates. In silico analyses conducted in this work will act as a reference for future functional studies of this crucial U1 splicing factor in animal kingdom.

scholarly journals Genome-wide identification and evolutionary analysis of RLKs involved in the response to aluminium stress in peanut

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xin Wang ◽  
Ming-Hua Wu ◽  
Dong Xiao ◽  
Ruo-Lan Huang ◽  
Jie Zhan ◽  
...  
Keyword(s):  
Stress Responses ◽  
Segmental Duplication ◽  
Tandem Duplication ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Segmental Duplications ◽  
Evolutionary Analysis ◽  
Gene Pairs ◽  
Al Stress ◽  
Peanut Genome

Abstract Background As an important cash crop, the yield of peanut is influenced by soil acidification and pathogen infection. Receptor-like protein kinases play important roles in plant growth, development and stress responses. However, little is known about the number, location, structure, molecular phylogeny, and expression of RLKs in peanut, and no comprehensive analysis of RLKs in the Al stress response in peanuts have been reported. Results A total of 1311 AhRLKs were identified from the peanut genome. The AhLRR-RLKs and AhLecRLKs were further divided into 24 and 35 subfamilies, respectively. The AhRLKs were randomly distributed across all 20 chromosomes in the peanut. Among these AhRLKs, 9.53% and 61.78% originated from tandem duplications and segmental duplications, respectively. The ka/ks ratios of 96.97% (96/99) of tandem duplication gene pairs and 98.78% (646/654) of segmental duplication gene pairs were less than 1. Among the tested tandem duplication clusters, there were 28 gene conversion events. Moreover, all total of 90 Al-responsive AhRLKs were identified by mining transcriptome data, and they were divided into 7 groups. Most of the Al-responsive AhRLKs that clustered together had similar motifs and evolutionarily conserved structures. The gene expression patterns of these genes in different tissues were further analysed, and tissue-specifically expressed genes, including 14 root-specific Al-responsive AhRLKs were found. In addition, all 90 Al-responsive AhRLKs which were distributed unevenly in the subfamilies of AhRLKs, showed different expression patterns between the two peanut varieties (Al-sensitive and Al-tolerant) under Al stress. Conclusions In this study, we analysed the RLK gene family in the peanut genome. Segmental duplication events were the main driving force for AhRLK evolution, and most AhRLKs subject to purifying selection. A total of 90 genes were identified as Al-responsive AhRLKs, and the classification, conserved motifs, structures, tissue expression patterns and predicted functions of Al-responsive AhRLKs were further analysed and discussed, revealing their putative roles. This study provides a better understanding of the structures and functions of AhRLKs and Al-responsive AhRLKs.

scholarly journals Unravelling the hidden inter and intra-varietal diversity of durum wheat commercial varieties used in Portugal

2019 ◽  
Vol 17 (04) ◽  
pp. 386-389
Author(s):  
Miguel Bento ◽  
Sónia Gomes Pereira ◽  
Wanda Viegas ◽  
Manuela Silva
Keyword(s):  
Durum Wheat ◽  
Repetitive Sequences ◽  
Inter Simple Sequence Repeat ◽  
Wheat Breeding ◽  
Genomic Diversity ◽  
Varietal Diversity ◽  
Wheat Varieties ◽  
Coding Sequences ◽  
Coding Regions ◽  
High Level

AbstractAssessing durum wheat genomic diversity is crucial in a changing environmental particularly in the Mediterranean region where it is largely used to produce pasta. Durum wheat varieties cultivated in Portugal and previously assessed regarding thermotolerance ability were screened for the variability of coding sequences associated with technological traits and repetitive sequences. As expected, reduced variability was observed regarding low molecular weight glutenin subunits (LMW-GS) but a specific LMW-GS allelic form associated with improved pasta-making characteristics was absent in one variety. Contrastingly, molecular markers targeting repetitive elements like microsatellites and retrotransposons – Inter Simple Sequence Repeat (ISSR) and Inter Retrotransposons Amplified Polymorphism (IRAP) – disclosed significant inter and intra-varietal diversity. This high level of polymorphism was revealed by the 20 distinct ISSR/IRAP concatenated profiles observed among the 23 individuals analysed. Interestingly, median joining networks and PCoA analysis grouped individuals of the same variety and clustered varieties accordingly with geographical origin. Globally, this work demonstrates that durum wheat breeding strategies induced selection pressure for some relevant coding sequences while maintaining high levels of genomic variability in non-coding regions enriched in repetitive sequences.

scholarly journals A Comprehensive, Flexible Collection of SARS-CoV-2 Coding Regions

2020 ◽  
Vol 10 (9) ◽  
pp. 3399-3402 ◽  
Author(s):  
Dae-Kyum Kim ◽  
Jennifer J Knapp ◽  
Da Kuang ◽  
Aditya Chawla ◽  
Patricia Cassonnet ◽  
...  
Keyword(s):  
Life Cycle ◽  
Viral Life Cycle ◽  
Coding Sequences ◽  
Coding Regions ◽  
Global Pandemic ◽  
The World ◽  
Molecular Studies ◽  
Widespread Availability ◽  
Rapid Transfer

Abstract The world is facing a global pandemic of COVID-19 caused by the SARS-CoV-2 coronavirus. Here we describe a collection of codon-optimized coding sequences for SARS-CoV-2 cloned into Gateway-compatible entry vectors, which enable rapid transfer into a variety of expression and tagging vectors. The collection is freely available. We hope that widespread availability of this SARS-CoV-2 resource will enable many subsequent molecular studies to better understand the viral life cycle and how to block it.

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