Intron Positions Research Articles

From benign to pathogenic variants and vice versa: pyrimidine transitions at position -3 of TAG and CAG 3' splice sites.

In the human genome, CAG 3' splice sites (3'ss) are more than twice as frequent as TAG 3'ss. The greater abundance of the former has been attributed to a higher probability of exon skipping upon cytosine-to-thymine transitions at intron position -3 (-3C > T) than thymine-to-cytosine variants (-3T > C). However, molecular mechanisms underlying this bias and its clinical impact are poorly understood. In this study, base-pairing probabilities (BPPs) and RNA secondary structures were compared between CAG 3'ss that produced more skipping of downstream exons than their mutated UAG versions (termed "laggard" CAG 3'ss) and UAG 3'ss that resulted in more skipping than their mutated CAG counterparts (canonical 3'ss). The laggard CAG 3'ss showed significantly higher BPPs across intron-exon boundaries than canonical 3'ss. The difference was centered on positions -5 to -1 relative to the intron-exon junction, the region previously shown to exhibit the strongest high-resolution ultraviolet crosslinking to the small subunit of auxiliary factor of U2 snRNP (U2AF1). RNA secondary structure predictions suggested that laggard CAG 3'ss were more often sequestered in paired conformations and in longer stem structures while canonical 3'ss were more frequently unpaired. Taken together, the excess of base-pairing at 3'ss has a potential to alter the hierarchy in intrinsic splicing efficiency of human YAG 3'ss from canonical CAG > UAG to non-canonical UAG > CAG, to modify the clinical impact of transitions at this position and to change their classification from pathogenic to benign or vice versa.

D299T Mutation in CYP76F14 Led to a Decrease in Wine Bouquet Precursor Production in Wine Grape.

Bouquet is a crucial characteristic indicative of wine quality that develops during the aging stage. The cytochrome P450 VvCYP76F14 multi-functionally catalyzes linalool into (E)-8-hydroxylinalool, (E)-8-oxolinalool, and (E)-8-carboxylinalool, which are direct precursors for wine bouquet. Wine bouquet was closely related to VvCYP76F14 activities. The VvCYP76F14 genes were cloned from five wine grape varieties using a homologous cloning method. The variation in residues of VvCYP76F14s were assessed by multiple alignment of amino acid sequences. Functional studies were implemented by in vitro enzyme activity and transient over-expression systems. D299T variation was observed in VvCYP76F14s of 'Yantai 2-2-08', 'Yantai 2-2-19', and 'Yantai 2-3-37' offspring lines, which was correlated with the decreased content of wine bouquet precursors of (E)-8-hydroxylinalool, (E)-8-oxolinalool, and (E)-8-carboxylinalool, respectively. Notably, the key amino acid residue D299 was located at the phase 0 intron positions of VvCYP76F14 genes isolated from distinct wine grape varieties or offspring lines, respectively. Notably, VvCYP76F14s of the 'Yantai2-2-08', 'Yantai 2-2-19', and 'Yantai 2-3-37' mutant lines exhibited lower in vitro enzymatic activities than those of 'L35' and 'Merlot'. In addition, the transient expression of VvCYP76F14 cloned from 'L35' and 'Merlot' restored the levels of wine bouquet precursors in berries of three D299T mutant lines, respectively, whereas VvCYP76F14 cloned from D299T mutant lines failed. D299T variation was observed in three offspring lines and D299T mutation in VvCYP76F14 led to the decrease in wine bouquet precursor contents. VvCYP76F14 was implicated in the regulation of wine bouquet precursors in wine grapes.

Genes divided according to the relative position of the longest intron show increased representation in different KEGG pathways

Despite the fact that introns mean an energy and time burden for eukaryotic cells, they play an irreplaceable role in the diversification and regulation of protein production. As a common feature of eukaryotic genomes, it has been reported that in protein-coding genes, the longest intron is usually one of the first introns. The goal of our work was to find a possible difference in the biological function of genes that fulfill this common feature compared to genes that do not. Data on the lengths of all introns in genes were extracted from the genomes of six vertebrates (human, mouse, koala, chicken, zebrafish and fugu) and two other model organisms (nematode worm and arabidopsis). We showed that more than 40% of protein-coding genes have the relative position of the longest intron located in the second or third tertile of all introns. Genes divided according to the relative position of the longest intron were found to be significantly increased in different KEGG pathways. Genes with the longest intron in the first tertile predominate in a range of pathways for amino acid and lipid metabolism, various signaling, cell junctions or ABC transporters. Genes with the longest intron in the second or third tertile show increased representation in pathways associated with the formation and function of the spliceosome and ribosomes. In the two groups of genes defined in this way, we further demonstrated the difference in the length of the longest introns and the distribution of their absolute positions. We also pointed out other characteristics, namely the positive correlation between the length of the longest intron and the sum of the lengths of all other introns in the gene and the preservation of the exact same absolute and relative position of the longest intron between orthologous genes.

Molecular taxonomic characterization and infra-specific diversity of entomopathogenic Beauveria bassiana fungi from Argentina

It has been the aim of this study to molecular-taxonomically identify 15 Beauveria isolates collected from different geographical regions and insect hosts in Argentina and to investigate the levels of inter- and intra-specific diversity across this set of isolates. Based on phylogenetic analyses of EF1A-RPB1-RPB2 concatenated genes and BLOC markers, all Beauveria strains were identify as Beauveria bassiana. Within the B. bassiana clades of both phylogenies, isolates from Argentina were not clustered according to geographic origin or host. The 15 fungal isolates were further analyzed by PCR amplification of the intron insertion hot spot region of the nuclear 28S rRNA encoding sequence. By intron sequence and position, seven different group-I intron combinations termed variants A, B1, B2, C, D, E and F were found in the 15 isolates under study. Variants B1/B2 consisting of a single 28Si2 intron were found in ten isolates, whereas variant A occurred twice and variants C through F were unique across the set of isolates under study. The determination of the different introns and intron combinations in the 28S rRNA gene is a powerful tool for achieving infraspecific differentiation of B. bassiana isolates from Argentina.

Selection on synonymous sites: the unwanted transcript hypothesis.

Although translational selection to favour codons that match the most abundant tRNAs is not readily observed in humans, there is nonetheless selection in humans on synonymous mutations. We hypothesize that much of this synonymous site selection can be explained in terms of protection against unwanted RNAs - spurious transcripts, mis-spliced forms or RNAs derived from transposable elements or viruses. We propose not only that selection on synonymous sites functions to reduce the rate of creation of unwanted transcripts (for example, through selection on exonic splice enhancers and cryptic splice sites) but also that high-GC content (but low-CpG content), together with intron presence and position, is both particular to functional native mRNAs and used to recognize transcripts as native. In support of this hypothesis, transcription, nuclear export, liquid phase condensation and RNA degradation have all recently been shown to promote GC-rich transcripts and suppress AU/CpG-rich ones. With such 'traps' being set against AU/CpG-rich transcripts, the codon usage of native genes has, in turn, evolved to avoid such suppression. That parallel filters against AU/CpG-rich transcripts also affect the endosomal import of RNAs further supports the unwanted transcript hypothesis of synonymous site selection and explains the similar design rules that have enabled the successful use of transgenes and RNA vaccines.

Nematode histone H2A variant evolution reveals diverse histories of retention and loss and evidence for conserved core-like variant histone genes.

Histone variants are paralogs that replace canonical histones in nucleosomes, often imparting novel functions. However, how histone variants arise and evolve is poorly understood. Reconstruction of histone protein evolution is challenging due to large differences in evolutionary rates across gene lineages and sites. Here we used intron position data from 108 nematode genomes in combination with amino acid sequence data to find disparate evolutionary histories of the three H2A variants found in Caenorhabditis elegans: the ancient H2A.ZHTZ-1, the sperm-specific HTAS-1, and HIS-35, which differs from the canonical S-phase H2A by a single glycine-to-alanine C-terminal change. Although the H2A.ZHTZ-1 protein sequence is highly conserved, its gene exhibits recurrent intron gain and loss. This pattern suggests that specific intron sequences or positions may not be important to H2A.Z functionality. For HTAS-1 and HIS-35, we find variant-specific intron positions that are conserved across species. Patterns of intron position conservation indicate that the sperm-specific variant HTAS-1 arose more recently in the ancestor of a subset of Caenorhabditis species, while HIS-35 arose in the ancestor of Caenorhabditis and its sister group, including the genus Diploscapter. HIS-35 exhibits gene retention in some descendent lineages but gene loss in others, suggesting that histone variant use or functionality can be highly flexible. Surprisingly, we find the single amino acid differentiating HIS-35 from core H2A is ancestral and common across canonical Caenorhabditis H2A sequences. Thus, we speculate that the role of HIS-35 lies not in encoding a functionally distinct protein, but instead in enabling H2A expression across the cell cycle or in distinct tissues. This work illustrates how genes encoding such partially-redundant functions may be advantageous yet relatively replaceable over evolutionary timescales, consistent with the patchwork pattern of retention and loss of both genes. Our study shows the utility of intron positions for reconstructing evolutionary histories of gene families, particularly those undergoing idiosyncratic sequence evolution.

BIOINFORMATICS-BASED CHARACTERIZATION OF THE CHALCONE SYNTHASE (CHS) FAMILY GENES IN FLOWERING PLANTS

Chalcone synthase (CHS) is an essential rate-limiting enzyme in the biosynthesis of anthocyanin pigments found in plant organs, such as, flowers and fruits. The CHS gene family appears in all flowering plants. Here, we searched and characterized the CHS genes from different flowering plants. Database search resulted in identifying Chalcone synthase genes from 29 diverse plant species. Phylogenetic analysis indicated significantly higher similarity between the various CHS genes, divided into at least six closely related rooted clades. Gene structure analysis identified the relative sizes and positions of UTRs, introns, and exons. Protein sequence alignment specified more than 95% similarity between the CHS genes, with eight highly conserved domains of different lengths. Likewise, in-depth analysis showed the presence of three highly conserved motifs in the protein sequence of all the 29 chalcone synthase genes. Physicochemical properties, such as, molecular weight, instability index, aliphatic index, hydropathicity (GRAVY), length, and isoelectric point (pI) of the CHS genes were significantly similar. Furthermore, the predicted 3D structures of CHS genes from different plant species highly remained and are homologous to each other, indicating that the CHS family genes have significantly conserved sequences and functionality across the plant kingdom.

The novel candidate genes related to live weight trait in southern meat sheep breed revealed by genome-wide genotyping

The study of the local sheep breeds’ genetic architecture is an important step on the way to preserve their gene pool. The aim of our work was to identify candidate genes associated with the live weight trait in adult southern meat breed sheep. This breed has high productivity, but is under threat of a critical decrease in genetic diversity due to a small number. The live weight of farm animals is one of the key breeding indicators. This quantitative trait is polygenic and breed specific as it has been shown by a number of authors. Animals were genotyped on the Illumina Ovine SNP50 Genotyping Bead Chip assay using standard procedures. Results in quality control, statistics and visualization were carried out in Rstudio 2023.03.0 and plink1.9. Genotyped animals were divided into two groups according to the case/control principle with differences in live weight between representatives of groups of 25–30 kg. Significant genetic variants were determined by the fixation indices method. Further analysis of significant variants (in intron positions) was performed in Ensembl genomic browser and revealed candidate genes localized in chromosomes 5, 6, 12, 20. The statistical analysis of live mass showed significant differences of the studied trait in different genotypes on four genes. The candidate genes identified can be recommended for using as genetic markers, their study could improve the productivity of southern meat sheep breed and help to preserve its gene pool.

Intronic position +9 and −9 are potentially splicing sites boundary from intronic variants analysis of whole exome sequencing data

Whole exome sequencing (WES) can also detect some intronic variants, which may affect splicing and gene expression, but how to use these intronic variants, and the characteristics about them has not been reported. This study aims to reveal the characteristics of intronic variant in WES data, to further improve the clinical diagnostic value of WES. A total of 269 WES data was analyzed, 688,778 raw variants were called, among these 367,469 intronic variants were in intronic regions flanking exons which was upstream/downstream region of the exon (default is 200 bps). Contrary to expectation, the number of intronic variants with quality control (QC) passed was the lowest at the +2 and −2 positions but not at the +1 and −1 positions. The plausible explanation was that the former had the worst effect on trans-splicing, whereas the latter did not completely abolish splicing. And surprisingly, the number of intronic variants that passed QC was the highest at the +9 and −9 positions, indicating a potential splicing site boundary. The proportion of variants which could not pass QC filtering (false variants) in the intronic regions flanking exons generally accord with “S”-shaped curve. At +5 and −5 positions, the number of variants predicted damaging by software was most. This was also the position at which many pathogenic variants had been reported in recent years. Our study revealed the characteristics of intronic variant in WES data for the first time, we found the +9 and −9 positions might be a potentially splicing sites boundary and +5 and −5 positions were potentially important sites affecting splicing or gene expression, the +2 and −2 positions seem more important splicing site than +1 and −1 positions, and we found variants in intronic regions flanking exons over ± 50 bps may be unreliable. This result can help researchers find more useful variants and demonstrate that WES data is valuable for intronic variants analysis.

Expression profile and association of ghrelin gene polymorphism with growth and litter traits in Indian goat breeds

Ghrelin (GHRL) is a 28 amino acid bioactive peptide influencing growth hormone secretion, regulation of energy homeostasis and appetite stimulation. The present investigation was undertaken to study the expression profile of the caprine ghrelin gene and to identify single nucleotide variations in caprine ghrelin gene to evaluate its association with production traits. Tissue samples of abomasum, lung, liver, spleen, fallopian tube and ovary were collected from six Malabari and Attappady Black adult goats to study the ghrelin gene expression pattern. Quantitative Real-Time PCR was used to find out the relative expression of ghrelin in various tissues. It was observed that there was a higher expression of ghrelin in the abomasal (3.67) tissues and the least expression in the liver (0.19) tissues. Significantly higher level of expression was noticed in Attappady Black than Malabari goats. Highly significant (p < 0.01) 4.07 fold upregulation was noticed in the ovary compared to the lung (3.85) and abomasum (3.80). A total of 176 Malabari and Attappady Black adult goats were screened for polymorphism using PCR-SSCP. Representative samples from different band patterns were sequenced. Two SNPs at the 9th position (C→A transversion) and at the 38th position (G→T transversion) in exon 4 and two SNPs at the 45th position (C→T transition) and 89th position (C→T transition) in intron 4 were identified. A significant association was observed between body measurement traits and the identified single nucleotide polymorphisms. The AB genotype demonstrated superior values over the AA genotype in body length and height for exon 4, while for intron 4 AA genotype was superior to the AB genotype. The AB genotype demonstrated higher values over the AA genotype for chest girth, CCI and TI. However, no association was found between body weight and litter size. The ghrelin gene may be used in marker-assisted selection for improving conformation traits in goats.

Identification and Analysis of the Catalase Gene Family Response to Abiotic Stress in Nicotiana tabacum L.

Catalase (CAT) is an enzyme encoded by the catalase gene family that plays an important role in the removal of reactive oxygen species. In this study, seven CAT genes were identified in Nicotiana tabacum L. and were classified into three groups. Gene structure analysis revealed that NtCAT1–6 has six or seven introns while NtCAT7 only contains one. The relative position of introns in NtCAT1 and NtCAT2 had high similarity. Tissue-specific analysis shows that NtCAT1–4 were expressed intensively in the shoot while NtCAT5 and NtCAT6 were in the root. NtCAT7 expression was influenced by circadian rhythms. NtCATs expression had the greatest change under drought stress. Additionally, expression of NtCAT5, NtCAT6 and NtCAT7 were upregulated under cold stress but downregulated under drought and salt stress. This study will help in understanding the behavior of CAT genes during environmental stress in tobacco.

New Insights into the Evolution and Gene Structure of the Mitochondrial Carrier Family Unveiled by Analyzing the Frequent and Conserved Intron Positions.

Mitochondrial carriers (MCs) belong to a eukaryotic protein family of transporters that in higher organisms is called the solute carrier family 25 (SLC25). All MCs have characteristic triplicated sequence repeats forming a 3-fold symmetrical structure of a six-transmembrane α-helix bundle with a centrally located substrate-binding site. Biochemical characterization has shown that MCs altogether transport a wide variety of substrates but can be divided into subfamilies, each transporting a few specific substrates. We have investigated the intron positions in the human MC genes and their orthologs of highly diversified organisms. The results demonstrate that several intron positions are present in numerous MC sequences at the same specific points, of which some are 3-fold symmetry related. Many of these frequent intron positions are also conserved in subfamilies or in groups of subfamilies transporting similar substrates. The analyses of the frequent and conserved intron positions in MCs suggest phylogenetic relationships not only between close but also distant homologs as well as a possible involvement of the intron positions in the evolution of the substrate specificity diversification of the MC family members.

Molecular Study of ACE2 Gene Polymorphism of COVID-19 Infection among the Kurdish Population in Kurdistan Region- Iraq.

Coronavirus Disease 2019 (COVID-19) is a current pandemic infection of the human respiratory system, which is caused by which caused by Sever Acute respiratory syndrome virus 2 (SARS-CoV-2). The infection was classified by World Health Organization (WHO) as a universal pandemic in February 2020; there have been 494.587.638 confirmed cases and 6.170.283 deaths. The present study investigated the molecular genetics of the Angiotensin Converting Enzyme 2 (ACE2) gene in correlation to COVID-19 patients in the Kurdish population. Eighty-six individuals were clinically diagnosed with COVID-19 and control groups. After the genomic DNA extraction these participants the target 1, 2 and 8 exons of the ACE2 gene were amplified using the PCR technique, and then the Sanger sequencing technique was performed to analyze genetic variants of the ACE2 gene in 70 DNA samples of COVID-19 hospital patients at Emergency Hospital in Erbil city, Sarchnar Hospital in Sulaymaniyah city, Lalav Hospital in Duhok city and Wafa Hospital in Halabja city from Kurdistan Region of Iraq. The current study was designed into two groups control group and a patient group. The patient group was divided into two subgroups, severe and mild patients of different ages and genders. As a result, there were no mutations at the positions 1, 2 and 8 exons sequences, while single nucleotide polymorphisms (SNPs) were detected and identified three different types of mutation at intron position: twenty-six of c.12405 del T, two of c.12407 T>G, and two of c.12406 G>A in a total 86 participants. This result shows that genetic difference does not impact the COVID-19 infection severity among the Kurdish population regarding ACE2 gene polymorphism.

The position of the longest intron is related to biological functions in some human genes.

The evidence that introns can influence different levels of transfer of genetic information between DNA and the final product is increasing. Longer first introns were found to be a general property of eukaryotic gene structure and shown to contain a higher fraction of conserved sequence and different functional elements. Our work brings more precise information about the position of the longest introns in human protein-coding genes and possible connection with biological function and gene expression. According to our results, the position of the longest intron can be localized to the first third of introns in 64%, the second third in 19%, and the third in 17%, with notable peaks at the middle and last introns of approximately 5% and 6%, respectively. The median lengths of the longest introns decrease with increasing distance from the start of the gene from approximately 15,000 to 5,000bp. We have shown that the position of the longest intron is in some cases linked to the biological function of the given gene. For example, DNA repair genes have the longest intron more often in the second or third. In the distribution of gene expression according to the position of the longest intron, tissue-specific profiles can be traced with the highest expression usually at the absolute positions of intron 1 and 2. In this work, we present arguments supporting the hypothesis that the position of the longest intron in a gene is another biological factor modulating the transmission of genetic information. The position of the longest intron is related to biological functions in some human genes.

Integrating Phylogenetics With Intron Positions Illuminates the Origin of the Complex Spliceosome.

Eukaryotic genes are characterized by the presence of introns that are removed from pre-mRNA by a spliceosome. This ribonucleoprotein complex is comprised of multiple RNA molecules and over a hundred proteins, which makes it one of the most complex molecular machines that originated during the prokaryote-to-eukaryote transition. Previous works have established that these introns and the spliceosomal core originated from self-splicing introns in prokaryotes. Yet, how the spliceosomal core expanded by recruiting many additional proteins remains largely elusive. In this study, we use phylogenetic analyses to infer the evolutionary history of 145 proteins that we could trace back to the spliceosome in the last eukaryotic common ancestor. We found that an overabundance of proteins derived from ribosome-related processes was added to the prokaryote-derived core. Extensive duplications of these proteins substantially increased the complexity of the emerging spliceosome. By comparing the intron positions between spliceosomal paralogs, we infer that most spliceosomal complexity postdates the spread of introns through the proto-eukaryotic genome. The reconstruction of early spliceosomal evolution provides insight into the driving forces behind the emergence of complexes with many proteins during eukaryogenesis.

Intron-rich dinoflagellate genomes driven by Introner transposable elements of unprecedented diversity

Spliceosomal introns, which interrupt nuclear genes, are ubiquitous features of eukaryotic nuclear genes.1 Spliceosomal intron evolution is complex, with different lineages ranging from virtually zero to thousands of newly created introns.2,3,4,5 This punctate phylogenetic distribution could be explained if intron creation is driven by specialized transposable elements ("Introners"), with Introner-containing lineages undergoing frequent intron gain.6,7,8,9,10 Fragmentation of nuclear genes by spliceosomal introns reaches its apex in dinoflagellates, which have some twenty introns per gene11,12; however, little is known about dinoflagellate intron evolution. We reconstructed intron evolution in five dinoflagellate genomes, revealing a dynamic history of intron gain. We find evidence for historical creation of introns in all five species and identify recently active Introners in 4/5 studied species. In one species, Polarella glacialis, we find an unprecedented diversity of Introners, with recent Introner insertion leading to creation of some 12,253 introns, and with 15 separate families of Introners accounting for at least 100 introns each. These Introner families show diverse mechanisms of moblization and intron creation. Comparison within and between Introner families provides evidence that biases in the so-called intron phase, intron position relative to codon periodicity, could be driven by Introner insertion site requirements.9,13,14 Finally, we report additional transformations of the spliceosomal system in dinoflagellates, including widespread loss of ancestral introns, and novelties of tolerated and favored donor sequence motifs. These results reveal unappreciated diversity of intron-creating elements and spliceosomal evolutionary capacity and highlight the complex evolutionary dependencies shaping genome structures.

Emergence of the ABC Transporter Antibiotic Resistant Gene in Pathogenic Fungi Using In Silico Analysis

Adenosine triphosphate binding cassette proteins (ATP-ABC) transporters belong to a broad superfamily of proteins in all living organisms that have essential physiological functions. They are necessary for transporting a wide range of substrates across lipid membranes. ABC transport proteins share two conserved domain architectures: the multiple transmembrane helices (TMD) nucleotide binding protein domain (NBD). Fungi have evolved active transport pathways through endogenous and exogenous toxicants. Drug efflux from ABC transporters lowers the concentration of intracellular drugs, in many pathogens and cancer cells; therefore, efflux is subjected to extensive studies in pathogens. ABC transporter gene of aspergillus versicolor as reference and evaluated metadata of ABC transporter gene in comparison from dermatophyte and non-dermatophyte fungi using fungi DB and NCBI databases. ABC transporters gene was studied using gene homology via phylogenetic analysis. Study evaluated ABC transporters sub families, number of transcripts, exon, intron numbers sizes and position using gene sequence analysis by NCBI. The evolutionary history of ABC gene analyzed by using 12 proteins of both dermatophytes. Study also explored the single nucleotide polymorphism (SNPs) homology in dermatophytes using the NCBI SNP tool. ABC protein examined five sub-families which include ABC-B, ABC-C, ABC-D, ABC-F. Phylogenetic studies on ABC transporter genes showed its emergence in three major groups of dermatophytes and non- dermatophyte. Exon number of ABC transporter gene varies from 2 to 18 and one transcript number in dermatophytes and non-dermatophytes. The evolutionary history of ABC-B was analyzed by using 12 proteins of both dermatophytes and non-dermatophytes. ABC genes in dermatophytes were found in five subfamilies ABC-B, ABC-C, ABC-D, ABC-F and ABC-G. However, ABC transporter gene family survey suggested that ABC- C family is a highly emerged sub family in dermatophytes and non-dermatophytes. Study revealed that ABC protein has been found in five sub-families of ABC transporter gene in dermatophytes. It has one transcript number in dermatophytes and non-dermatophytes. Whereas, the exon numbers are varied from 2 to 18. Moreover, ABC transporter gene phylogenetic family survey suggested that ABC- C family is highly emerged in both fungal types.

The evolution of pre-mRNA splicing and its machinery revealed by reduced extremophilic red algae.

The Cyanidiales are a group of mostly thermophilic and acidophilic red algae that thrive near volcanic vents. Despite their phylogenetic relationship, the reduced genomes of Cyanidioschyzon merolae and Galdieria sulphuraria are strikingly different with respect to pre-mRNA splicing, a ubiquitous eukaryotic feature. Introns are rare and spliceosomal machinery is extremely reduced in C.merolae, in contrast to G.sulphuraria. Previous studies also revealed divergent spliceosomes in the mesophilic red alga Porphyridium purpureum and the red algal derived plastid of Guillardia theta (Cryptophyta), along with unusually high levels of unspliced transcripts. To further examine the evolution of splicing in red algae, we compared C.merolae and G.sulphuraria, investigating splicing levels, intron position, intron sequence features, and the composition of the spliceosome. In addition to identifying 11 additional introns in C. merolae, our transcriptomic analysis also revealed typical eukaryotic splicing in G. sulphuraria, whereas most transcripts in C. merolae remain unspliced. The distribution of intron positions within their host genes was examined to provide insight into patterns of intron loss in red algae. We observed increasing variability of 5' splice sites and branch donor regions with increasing intron richness. We also found these relationships to be connected to reductions in and losses of corresponding parts of the spliceosome. Our findings highlight patterns of intron and spliceosome evolution in related red algae under the pressures of genome reduction.

Characterization of P450 monooxygenase gene family in the cotton aphid, Aphis gossypii Glover

• A total of 49 CYP sequences were classified into 13 families and 21 subfamilies. • 47 genes were found to be functional and P450-encoding genes are conserved in gene structure and organization in cotton aphids. • The cotton aphid P450 family has evolutionary differentiation. • The distribution across the genome and phylogenetic clustering analysis indicated past occurrence of gene duplication events. Cytochrome P450 monooxygenases play an important role in the biosynthesis and detoxification of endogenous compounds. In this study, we analyzed a number of P450 genes through transcriptome-wide and genome analyses in Aphis gossypii Glover, the most notorious cotton pests. A total of 49 CYP-putative sequences were identified and classified into 13 families and 21 subfamilies. We identified a putative P450 motif (FXXGXXXCXG), and further analyzed other conserved sequences, which indicate that forty-seven of the forty-nine genes seem to be functional, but one is likely non-functional and one is predicted pseudogenes. We found that P450-encoding genes are conserved in gene structure and organization (number, position, and phase of introns) in cotton aphids. The size, transcription orientation, and comparison with other insects of the cotton aphid P450 family suggested that it has evolutionary differentiation. The distribution across the genome and phylogenetic clustering analysis indicated past occurrence of gene duplication events. These results may provide valuable clues for understanding the evolution of the aphid genome, studying the functions of P450s in cotton aphid, and further selecting candidate genes for novel insect control methods.

The spread of the first introns in proto-eukaryotic paralogs

Spliceosomal introns are a unique feature of eukaryotic genes. Previous studies have established that many introns were present in the protein-coding genes of the last eukaryotic common ancestor (LECA). Intron positions shared between genes that duplicated before LECA could in principle provide insight into the emergence of the first introns. In this study we use ancestral intron position reconstructions in two large sets of duplicated families to systematically identify these ancient paralogous intron positions. We found that 20–35% of introns inferred to have been present in LECA were shared between paralogs. These shared introns, which likely preceded ancient duplications, were wide spread across different functions, with the notable exception of nuclear transport. Since we observed a clear signal of pervasive intron loss prior to LECA, it is likely that substantially more introns were shared at the time of duplication than we can detect in LECA. The large extent of shared introns indicates an early origin of introns during eukaryogenesis and suggests an early origin of a nuclear structure, before most of the other complex eukaryotic features were established.