Origin Of Duplication Research Articles

Biogeography and the evolution of acoustic communication in the polyploid North American grey treefrog complex.

After polyploid species are formed, interactions between diploid and polyploid lineages may generate additional diversity in novel cytotypes and phenotypes. In anurans, mate choice by acoustic communication is the primary method by which individuals identify their own species and assess suitable mates. As such, the evolution of acoustic signals is an important mechanism for contributing to reproductive isolation and diversification in this group. Here, we estimate the biogeographical history of the North American grey treefrog complex, consisting of the diploid Hyla chrysoscelis and the tetraploid Hyla versicolor, focusing specifically on the geographical origin of whole genome duplication and the expansion of lineages out of glacial refugia. We then test for lineage-specific differences in mating signals by applying comparative methods to a large acoustic data set collected over 52 years that includes >1500 individual frogs. Along with describing the overall biogeographical history and call diversity, we found evidence that the geographical origin of H. versicolor and the formation of the midwestern polyploid lineage are both associated with glacial limits, and that the southwestern polyploid lineage is associated with a shift in acoustic phenotype relative to the diploid lineage with which they share a mitochondrial lineage. In H. chrysoscelis, we see that acoustic signals are largely split by Eastern and Western lineages, but that northward expansion along either side of the Appalachian Mountains is associated with further acoustic diversification. Overall, results of this study provide substantial clarity on the evolution of grey treefrogs as it relates to their biogeography and acoustic communication.

Whole-genome and dispersed duplication, including transposed duplication, jointly advance the evolution of TLP genes in seven representative Poaceae lineages

BackgroundIn the evolutionary study of gene families, exploring the duplication mechanisms of gene families helps researchers understand their evolutionary history. The tubby-like protein (TLP) family is essential for growth and development in plants and animals. Much research has been done on its function; however, limited information is available with regard to the evolution of the TLP gene family. Herein, we systematically investigated the evolution of TLP genes in seven representative Poaceae lineages.ResultsOur research showed that the evolution of TLP genes was influenced not only by whole-genome duplication (WGD) and dispersed duplication (DSD) but also by transposed duplication (TRD), which has been neglected in previous research. For TLP family size, we found an evolutionary pattern of progressive shrinking in the grass family. Furthermore, the evolution of the TLP gene family was at least affected by evolutionary driving forces such as duplication, purifying selection, and base mutations.ConclusionsThis study presents the first comprehensive evolutionary analysis of the TLP gene family in grasses. We demonstrated that the TLP gene family is also influenced by a transposed duplication mechanism. Several new insights into the evolution of the TLP gene family are presented. This work provides a good reference for studying gene evolution and the origin of duplication.

Applying Machine Learning to Classify the Origins of Gene Duplications.

Nearly all lineages of land plants have experienced at least one whole-genome duplication (WGD) in their history. The legacy of these ancient WGDs is still observable in the diploidized genomes of extant plants. Genes originating from WGD-paleologs-can be maintained in diploidized genomes for millions of years. These paleologs have the potential to shape plant evolution through sub- and neofunctionalization, increased genetic diversity, and reciprocal gene loss among lineages. Current methods for classifying paleologs often rely on only a subset of potential genomic features, have varying levels of accuracy, and often require significant data and/or computational time. Here, we developed a supervised machine learning approach to classify paleologs from a target WGD in diploidized genomes across a broad range of different duplication histories. We collected empirical data on syntenic block sizes and other genomic features from 27 plant species each with a different history of paleopolyploidy. Features from these genomes were used to develop simulations of syntenic blocks and paleologs to train a gradient boosted decision tree. Using this approach, Frackify (Fractionation Classify), we were able to accurately identify and classify paleologs across a broad range of parameter space, including cases with multiple overlapping WGDs. We then compared Frackify with other paleolog inference approaches in six species with paleotetraploid and paleohexaploid ancestries. Frackify provides a way to combine multiple genomic features to quickly classify paleologs while providing a high degree of consistency with existing approaches.

What Reference Genome Assemblies Tell Us and How to Detect the Best Available Version: A Case Study in Trout

Genomic studies have largely been accelerated by the advances of next generation sequencing technologies since the beginning of the millennium. This, in turn, has motivated the generation of more reference genome assemblies not only in model organisms but also in species of scientific interest. In the present study, we employed a comparison study between the two different reference genome assemblies available for the same species, Salmo trutta, in GenBank. The results indicated an overall 90% similarity index between the two assemblies. Furthermore, the inversion regions of which assembly needs corrections were detected. Taking into account the whole genome duplication origin of the Salmonidae family, both assemblies were of good quality. However, the updated version of the Wellcome Sanger Institute assembly (fSalTru_1.2) outperformed the Norwegian assembly and was detected as the best available reference genome assembly in Salmo trutta. 

Fine-Mapping and Comparative Genomic Analysis Reveal the Gene Composition at the S and Z Self-incompatibility Loci in Grasses.

Self-incompatibility (SI) is a genetic mechanism of hermaphroditic plants to prevent inbreeding after self-pollination. Allogamous Poaceae species exhibit a unique gametophytic SI system controlled by two multi-allelic and independent loci, S and Z. Despite intense research efforts in the last decades, the genes that determine the initial recognition mechanism are yet to be identified. Here, we report the fine-mapping of the Z-locus in perennial ryegrass (Lolium perenne L.) and provide evidence that the pollen and stigma components are determined by two genes encoding DUF247 domain proteins (ZDUF247-I and ZDUF247-II) and the gene sZ, respectively. The pollen and stigma determinants are located side-by-side and were genetically linked in 10,245 individuals of two independent mapping populations segregating for Z. Moreover, they exhibited high allelic diversity as well as tissue-specific gene expression, matching the expected characteristics of SI determinants known from other systems. Revisiting the S-locus using the latest high-quality whole-genome assemblies revealed a similar gene composition and structure as found for Z, supporting the hypothesis of a duplicated origin of the two-locus SI system of grasses. Ultimately, comparative genomic analyses across a wide range of self-compatible and self-incompatible Poaceae species revealed that the absence of a functional copy of at least one of the six putative SI determinants is accompanied by a self-compatible phenotype. Our study provides new insights into the origin and evolution of the unique gametophytic SI system in one of the largest and economically most important plant families.

Chromosomal breaks at the origin of small tandem DNA duplications.

Small tandem DNA duplications in the range of 15 to 300 base-pairs play an important role in the aetiology of human disease and contribute to genome diversity. Here, we discuss different proposed mechanisms for their occurrence and argue that this type of structural variation mainly results from mutagenic repair of chromosomal breaks. This hypothesis is supported by both bioinformatical analysis of insertions occurring in the genome of different species and disease alleles, as well as by CRISPR/Cas9-based experimental data from different model systems. Recent work points to fill-in synthesis at double-stranded DNA breaks with complementary sequences, regulated by end-joining mechanisms, to account for small tandem duplications. We will review the prevalence of small tandem duplications in the population, and we will speculate on the potential sources of DNA damage that could give rise to this mutational signature. With the development of novel algorithms to analyse sequencing data, small tandem duplications are now more frequently detected in the human genome and identified as oncogenic gain-of-function mutations. Understanding their origin could lead to optimized treatment regimens to prevent therapy-induced activation of oncogenes and might expose novel vulnerabilities in cancer.

Duplicated vas deferens incidentally discovered during orchiopexy

Duplication of vas deferens is a very rare congenital anomaly usually discovered incidentally during surgery of the spermatic cord like inguinal hernia repair, orchiopexy, vasectomy, and varicocelectomy. This anomaly seems to be underrecognized or underreported due to disproportion between the low number of reported anomalies compared to the large number of surgeries requiring spermatic cord dissection. To our best of knowledge, only 47 cases were reported in the literature before our patient. The embryological origin of duplication of the vas deferens has been postulated to involve duplication or division of the mesonephric duct during organogenesis. Although preoperative diagnosis is practically impossible, intraoperative recognition is critical to avoid missing an intact vas deferens in vasectomy resulting in failed sterilization or iatrogenic trauma during other surgical procedures involving the spermatic cord.

In Silico Genome-Wide Characterisation of the Lipid Transfer Protein Multigenic Family in Sunflower (H. annuus L.).

The sunflower (Helianthus annuus L.) is among the most widely cultivated crops in the world due to the oilseed production. Lipid transfer proteins (LTPs) are low molecular mass proteins encoded by a broad multigenic family in higher plants, showing a vast range of functions; these proteins have not been characterised in sunflower at the genomic level. In this work, we exploited the reliable genome sequence of sunflower to identify and characterise the LTP multigenic family in H. annuus. Overall, 101 sunflower putative LTP genes were identified using a homology search and the HMM algorithm. The selected sequences were characterised through phylogenetic analysis, exon–intron organisation, and protein structural motifs. Sunflower LTPs were subdivided into four clades, reflecting their genomic and structural organisation. This gene family was further investigated by analysing the possible duplication origin of genes, which showed the prevalence of tandem and whole genome duplication events, a result that is in line with polyploidisation events that occurred during sunflower genome evolution. Furthermore, LTP gene expression was evaluated on cDNA libraries constructed on six sunflower tissues (leaf, root, ligule, seed, stamen, and pistil) and from roots treated with stimuli mimicking biotic and abiotic stress. Genes encoding LTPs belonging to three out of four clades responded specifically to external stimuli, especially to abscisic acid, auxin, and the saline environment. Interestingly, genes encoding proteins belonging to one clade were expressed exclusively in sunflower seeds. This work is a first attempt of genome-wide identification and characterisation of the LTP multigenic family in a plant species.

Anomalous Origin of the Right Vertebral Artery

An anomalous origin of the right vertebral artery (VA) is a rare anomaly that is much rarer than that of the left VA. It can be divided into a few patterns, including aortic origin, right carotid or brachiocephalic arterial origin, and duplicated origin. In embryological development, the VA is made up of a longitudinal anastomosis between cervical segments. The mechanism of the anomalous origin of the right VA can be explained by the persistence of the cervical segmental artery and the regression point of the 4th right aortic arch. Although the anomaly is usually found incidentally on imaging modalities, it can be a potential cause of complication during surgical and interventional procedures. However, there are a lot of reports about the radiomics of the anomaly. Therefore, we discuss the potential relationship between the anomalous origin of the right VA and radiomics. As the take-home message, understanding several patterns of anomalous origin of the right VA with their embryology and imaging findings is important for surgical and endovascular interventions to avoid intraprocedural complications.

Fossilized cell structures identify an ancient origin for the teleost whole-genome duplication

Teleost fishes comprise one-half of all vertebrate species and possess a duplicated genome. This whole-genome duplication (WGD) occurred on the teleost stem lineage in an ancient common ancestor of all living teleosts and is hypothesized as a trigger of their exceptional evolutionary radiation. Genomic and phylogenetic data indicate that WGD occurred in the Mesozoic after the divergence of teleosts from their closest living relatives but before the origin of the extant teleost groups. However, these approaches cannot pinpoint WGD among the many extinct groups that populate this 50- to 100-million-y lineage, preventing tests of the evolutionary effects of WGD. We infer patterns of genome size evolution in fossil stem-group teleosts using high-resolution synchrotron X-ray tomography to measure the bone cell volumes, which correlate with genome size in living species. Our findings indicate that WGD occurred very early on the teleost stem lineage and that all extinct stem-group teleosts known so far possessed duplicated genomes. WGD therefore predates both the origin of proposed key innovations of the teleost skeleton and the onset of substantial morphological diversification in the clade. Moreover, the early occurrence of WGD allowed considerable time for postduplication reorganization prior to the origin of the teleost crown group. This suggests at most an indirect link between WGD and evolutionary success, with broad implications for the relationship between genomic architecture and large-scale evolutionary patterns in the vertebrate Tree of Life.

Multiple anterior choroidal arteries and perioperative ischemic complications in unruptured anterior choroidal artery aneurysms treated with microsurgical clipping.

This study aimed to identify the association between the number of anterior choroidal arteries (AchoAs) and procedure-related ischemic complications in microsurgical clipping of unruptured AchoA aneurysms. We retrospectively reviewed the clinical, radiological, and intraoperative findings of 153 patients with unruptured AchoA aneurysms treated with microsurgical clipping between January 2012 and November 2020 in a single tertiary institution. Intraoperative video clips were reviewed, and the AchoA type was categorized into two according to the number of AchoAs: (1) single-type group with single origin and single branch and (2) multiple-type group with duplicated origin or divided multiple branches. Uni- and multivariate analyses were performed to assess the relationship between clinical and radiological factors and perioperative ischemic complications. Of the 153 patients, 52 (34%) were categorized as multiple-type group. The frequency of perioperative ischemic complications, including decreased intraoperative motor evoked potential (MEP), silent infarction, and postoperative ischemic symptoms, was significantly higher in the multiple-type group than in the single-type group (13 [25%] vs 6 [5.9%], p = 0.001). Multivariate logistic regression analysis showed that multiple-type group (odds ratio [OR], 3.725; 95% confidence interval [CI], 1.171-11.845, p = 0.026) and multilobulated shape (OR, 9.512; 95% CI, 2.093-43.224; p = 0.004) were significantly associated with perioperative ischemic complications. Among 9 patients with decreased MEP, postoperative ischemic symptoms developed in 2 patients after clip adjustment. Multiple-type AchoA aneurysms and multilobulated shape are significantly correlated with perioperative ischemic complications. Postoperative ischemic complications can be minimized by recognizing these variations and using multimodal approach with MEP monitoring.

A Comprehensive Multi-Omic Approach Reveals a Relatively Simple Venom in a Diet Generalist, the Northern Short-Tailed Shrew, Blarina brevicauda.

Animals that use venom to feed on a wide diversity of prey may evolve a complex mixture of toxins to target a variety of physiological processes and prey-defense mechanisms. Blarina brevicauda, the northern short-tailed shrew, is one of few venomous mammals, and is also known to eat evolutionarily divergent prey. Despite their complex diet, earlier proteomic and transcriptomic studies of this shrew’s venom have only identified two venom proteins. Here, we investigated with comprehensive molecular approaches whether B. brevicauda venom is more complex than previously understood. We generated de novo assemblies of a B. brevicauda genome and submaxillary-gland transcriptome, as well as sequenced the salivary proteome. Our findings show that B. brevicauda’s venom composition is simple relative to their broad diet and is likely limited to seven proteins from six gene families. Additionally, we explored expression levels and rate of evolution of these venom genes and the origins of key duplications that led to toxin neofunctionalization. We also found three proteins that may be involved in endogenous self-defense. The possible synergism of the toxins suggests that vertebrate prey may be the main target of the venom. Further functional assays for all venom proteins on both vertebrate and invertebrate prey would provide further insight into the ecological relevance of venom in this species.

Phylogenomics Identifies an Ancestral Burst of Gene Duplications Predating the Diversification of Aphidomorpha.

Aphids (Aphidoidea) are a diverse group of hemipteran insects that feed on plant phloem sap. A common finding in studies of aphid genomes is the presence of a large number of duplicated genes. However, when these duplications occurred remains unclear, partly due to the high relatedness of sequenced species. To better understand the origin of aphid duplications we sequenced and assembled the genome of Cinara cedri, an early branching lineage (Lachninae) of the Aphididae family. We performed a phylogenomic comparison of this genome with 20 other sequenced genomes, including the available genomes of five other aphids, along with the transcriptomes of two species belonging to Adelgidae (a closely related clade to the aphids) and Coccoidea. We found that gene duplication has been pervasive throughout the evolution of aphids, including many parallel waves of recent, species-specific duplications. Most notably, we identified a consistent set of very ancestral duplications, originating from a large-scale gene duplication predating the diversification of Aphidomorpha (comprising aphids, phylloxerids, and adelgids). Genes duplicated in this ancestral wave are enriched in functions related to traits shared by Aphidomorpha, such as association with endosymbionts, and adaptation to plant defenses and phloem-sap-based diet. The ancestral nature of this duplication wave (106–227 Ma) and the lack of sufficiently conserved synteny make it difficult to conclude whether it originated from a whole-genome duplication event or, alternatively, from a burst of large-scale segmental duplications. Genome sequencing of other aphid species belonging to different Aphidomorpha and related lineages may clarify these findings.

Comparative genomics reveals the origin of fungal hyphae and multicellularity

Hyphae represent a hallmark structure of multicellular fungi. The evolutionary origins of hyphae and of the underlying genes are, however, hardly known. By systematically analyzing 72 complete genomes, we here show that hyphae evolved early in fungal evolution probably via diverse genetic changes, including co-option and exaptation of ancient eukaryotic (e.g. phagocytosis-related) genes, the origin of new gene families, gene duplications and alterations of gene structure, among others. Contrary to most multicellular lineages, the origin of filamentous fungi did not correlate with expansions of kinases, receptors or adhesive proteins. Co-option was probably the dominant mechanism for recruiting genes for hypha morphogenesis, while gene duplication was apparently less prevalent, except in transcriptional regulators and cell wall - related genes. We identified 414 novel gene families that show correlated evolution with hyphae and that may have contributed to its evolution. Our results suggest that hyphae represent a unique multicellular organization that evolved by limited fungal-specific innovations and gene duplication but pervasive co-option and modification of ancient eukaryotic functions.

Organization and evolution of the chalcone synthase gene family in bread wheat and relative species

BackgroundFlavonoid compounds are secondary plant metabolites, having a functional importance in plant development, protection from pathogens and unfavorable environmental factors. Chalcone synthase (CHS) is a key enzyme in the biosynthesis of flavonoids; it is involved in biosynthesis of all classes of flavonoid compounds. Nevertheless, the Chs gene family in bread wheat (Triticum aestivum L.) has been not characterized yet. The aim of the current study was to investigate structural and functional organization of the Chs genes and evolution of this gene family in bread wheat and relative species.ResultsThe nucleotide sequences of the eight Chs copies in T. aestivum were identified. Among them, two homoeologous sets of the Chs genes were located on the short (Chs-A1, −B1, −D1) and the long (Chs-A4, −B4, −D4) arms of homoeologous group 2 chromosomes. Two paralogous gene copies in the B-genome (Chs-B2, −B3) were located in the distal regions of 2BS chromosome. To clarify the origin of Chs duplications in the B-genome the phylogenetic analysis with the Chs sequences of Triticum and Aegilops species carrying ancestral genomes was conducted. It was estimated that the first duplication event occurred in the genome of the common ancestor of Triticum and Aegilops genera about 10–12 million years ago (MYA), then another copy was formed in the ancestor of the B-genome about 6–7 MYA. A homology modeling revealed high sequence similarity of bread wheat CHS enzymes. A number of short deletions in coding regions of some Chs sequences are not expected to have any significant functional effects. Estimation of transcriptional activity of the Chs copies along with a comparative analysis of their promoters structure suggested their functional specialization, which likely contributed to the maintaining of the duplicated Chs genes in wheat genome.ConclusionsFrom possible ten Chs copies in bread wheat genome, eight members of this family retained their intact structure and activity, while two copies appear to be lost at the level of diploid and tetraploid ancestors. Transcriptional assay along with a comparative analysis of the cis-regulatory elements revealed their functional diversification. The multiple functions supported by the Chs family are assumed to be a driving force for duplications of the Chs gene and their retention in plant genome.

SVIM: structural variant identification using mapped long reads.

MotivationStructural variants are defined as genomic variants larger than 50 bp. They have been shown to affect more bases in any given genome than single-nucleotide polymorphisms or small insertions and deletions. Additionally, they have great impact on human phenotype and diversity and have been linked to numerous diseases. Due to their size and association with repeats, they are difficult to detect by shotgun sequencing, especially when based on short reads. Long read, single-molecule sequencing technologies like those offered by Pacific Biosciences or Oxford Nanopore Technologies produce reads with a length of several thousand base pairs. Despite the higher error rate and sequencing cost, long-read sequencing offers many advantages for the detection of structural variants. Yet, available software tools still do not fully exploit the possibilities.ResultsWe present SVIM, a tool for the sensitive detection and precise characterization of structural variants from long-read data. SVIM consists of three components for the collection, clustering and combination of structural variant signatures from read alignments. It discriminates five different variant classes including similar types, such as tandem and interspersed duplications and novel element insertions. SVIM is unique in its capability of extracting both the genomic origin and destination of duplications. It compares favorably with existing tools in evaluations on simulated data and real datasets from Pacific Biosciences and Nanopore sequencing machines.Availability and implementationThe source code and executables of SVIM are available on Github: github.com/eldariont/svim. SVIM has been implemented in Python 3 and published on bioconda and the Python Package Index.Supplementary information Supplementary data are available at Bioinformatics online.

Dual origin of the right vertebral artery from the right common carotid and aberrant right subclavian arteries

This report describes a case of duplicated origin of the right vertebral artery incidentally found in a young patient. Computed tomographic angiography and digital subtraction angiography showed a dominant branch derived from the right common carotid artery and an accessory branch that derived from the right subclavian artery, which aberrantly originated from the far left aortic arch, and adjoined the dominant branch at the C5 level. We discuss angiographic findings, clinical implications and embryological basis for this rare anomaly.

Parental origin of deletions and duplications \u2013 about the necessity to check for cryptic inversions

BackgroundCopy number variants (CNVs) are the genetic bases for microdeletion/ microduplication syndromes (MMSs). Couples with an affected child and desire to have further children are routinely tested for a potential parental origin of a specific CNV either by molecular karyotyping or by two color fluorescence in situ hybridization (FISH), yet. In the latter case a critical region probe (CRP) is combined with a control probe for identification of the chromosome in question. However, CNVs can arise also due to other reasons, like a recombination-event based on a submicroscopic, cryptic inversion in one of the parents.ResultsSeventy-four patients with different MMSs and overall 81 CNVs were studied here by a novel three color FISH approach. The way how three locus-specific probes are selected (one is the CRP and two are flanking it in a distance of 5-10 Mb) enables to detect or exclude two possible parental conditions as origins of the CNV seen in the index: (i) direct parental origin of the CNV (deletion or duplication) or (ii) a parental cryptic inversion. Thus, for overall 51/81 CNVs (63%) a parental origin could be determined. 36/51 (70.5%) inherited the CNV directly from one of the parents, but 15/51 (29.5%) were due to an exclusively by three color FISH detectable parental inversion. A 2:1 ratio of maternal versus paternal inheritance was found. Also almost two times more male than female were among the index patients.ConclusionThe new, here suggested three color FISH approach is suited for more comprehensive parental studies of patients with MMS. The detection rate for parental origin was increased by 140% in this study. Still, for 30/81 cases (37%) no reason for the ‘de novo’ MMS in the affected index patient could be found by the here suggested FISH-probe set.

A new type of hyperplastic anterior choroidal artery

Hyperplastic anomaly of the anterior choroidal artery (hyperplastic AchA) and posterior communicating artery of duplicate origin (duplicated Pcom) are rare vessel anomalies. With some literature review, we here report three cases of hyperplastic AchA, one of which was considered a new type of hyperplastic AchA. This case was not categorized into Takahashi classification.

Duplicated middle cerebral artery origin with an aneurysm

Rationale:Middle cerebral artery (MCA) anomalies are relatively rare and often related to aneurysms. Familiarity with these anomalies is important in resolving problems that arise in the complex angioarchitecture. Reports often describe that aneurysms that are related to accessory or duplicated MCA are often located at its origin.Patient concerns:A 59-year-old man presented with a headache for 10 days, without nausea and vomiting. The physical examination was negative.Diagnosis:A computed tomography (CT) scan revealed an intracerebral hematoma in the deep right frontal lobe, near the caudate nucleus. Digital subtraction angiography (DSA) revealed an anomalous duplicated origin of the right MCA, with occlusion of the main MCA trunk as well as twisting and dilation of the accessory MCA trunk. A wide-necked aneurysm was located at a sharp curve of the tortuous accessory MCA trunk. A ruptured aneurysm related to a duplicated MCA origin was diagnosed.Interventions:Open surgery was rejected by the patient; hence, palliative endovascular coil embolization of the larger daughter sac was performed.Outcomes:The postoperative course was uneventful. There was no rebleeding at 8-months follow-up.Lessons:MCA anomalies are relatively rare and often related to aneurysms. It is important to be familiar with these anomalies as related lesions often manifest within a complex angioarchitecture. Aneurysms at the trunk of an anomalous MCA are a rare entity and open surgery may be recommended.