scholarly journals The power of synteny : deep evolutionary insights from comparative genomics

2021 ◽  
Author(s):  
◽  
Richard Shawn Abrahams
Keyword(s):  
Sequence Data ◽  
Sequence Similarity ◽  
Gene Tree ◽  
Evolutionary Mechanisms ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Orthologous Locus ◽  
Orthology Detection ◽  
Insight Into

Synteny, or the order of genes in a given genome, is an emergent property of individuals and species that has only, with the implementation of next gen-sequencing, become available for evolutionary consideration. In this dissertation, I leverage syntenic information in concert with sequence data to draw connections between evolutionary mechanisms, species divergence, and trait innovation. In Chapter I, I review the major themes that ties my dissertation research together, highlighting important mechanisms at work in evolutionary complexity and introducing the system of which it will be a part. In Chapter II, I use a phylogenomic approach to better understand species relationships within the tribe. I utilize transcriptome sequences and genome derived synteny information to improve orthology detection over standard sequence similarity approaches and gain greater insight into the relationships of the tribe. I also implement differential fractionation rate orthology inference information to address gene tree-species tree incongruence. In Chapter III, as published in Abrahams et al., 2020, I utilize a microsynteny network and phylogenetic inference to investigate the origin and diversification of the MAM/IPMS gene family. I uncover unique MAM-like genes found at the orthologous locus in the Cleomaceae that shed light on the transition from IPMS to MAM. In the Brassicaceae, I identify six distinct MAM clades across Lineages I, II, and III. I characterize the evolutionary impact and consequences of local duplications, transpositions, whole genome duplications, and gene fusion events, generating several new hypotheses on the function and diversity of the MAM locus.

scholarly journals New Insights into Ligand-Receptor Pairing and Coevolution of Relaxin Family Peptides and Their Receptors in Teleosts

2012 ◽  
Vol 2012 ◽  
pp. 1-14 ◽  
Author(s):  
Sara Good ◽  
Sergey Yegorov ◽  
Joran Martijn ◽  
Jens Franck ◽  
Jan Bogerd
Keyword(s):  
Sequence Data ◽  
Gene Families ◽  
Theoretical Background ◽  
Whole Genome Duplications ◽  
Relaxin Family ◽  
Receptor Interactions ◽  
Genome Duplications ◽  
Show Evidence ◽  
Specific Receptors ◽  
Respective Function

Relaxin-like peptides (RLN/INSL) play diverse roles in reproductive and neuroendocrine processes in placental mammals and are functionally associated with two distinct types of receptors (RXFP) for each respective function. The diversification of RLN/INSL and RXFP gene families in vertebrates was predominantly driven by whole genome duplications (2R and 3R). Teleosts preferentially retained duplicates of genes putatively involved in neuroendocrine regulation, harboring a total of 10-11 receptors and 6 ligand genes, while most mammals have equal numbers of ligands and receptors. To date, the ligand-receptor relationships of teleost Rln/Insl peptides and their receptors have largely remained unexplored. Here, we use selection analyses based on sequence data from 5 teleosts and qPCR expression data from zebrafish to explore possible ligand-receptor pairings in teleosts. We find support for the hypothesis that, with the exception of RLN, which has undergone strong positive selection in mammalian lineages, the ligand and receptor genes shared between mammals and teleosts appear to have similar pairings. On the other hand, the teleost-specific receptors show evidence of subfunctionalization. Overall, this study underscores the complexity of RLN/INSL and RXFP ligand-receptor interactions in teleosts and establishes theoretical background for further experimental work in nonmammals.

scholarly journals Insights into angiosperm evolution, floral development and chemical biosynthesis from the Aristolochia fimbriata genome

Nature Plants ◽  
2021 ◽  
Author(s):  
Liuyu Qin ◽  
Yiheng Hu ◽  
Jinpeng Wang ◽  
Xiaoliang Wang ◽  
Ran Zhao ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Sequence Data ◽  
Expression Patterns ◽  
Whole Genome ◽  
Angiosperm Evolution ◽  
Aristolochic Acids ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
High Quality Genome ◽  
Angiosperm Genome

AbstractAristolochia, a genus in the magnoliid order Piperales, has been famous for centuries for its highly specialized flowers and wide medicinal applications. Here, we present a new, high-quality genome sequence of Aristolochia fimbriata, a species that, similar to Amborella trichopoda, lacks further whole-genome duplications since the origin of extant angiosperms. As such, the A. fimbriata genome is an excellent reference for inferences of angiosperm genome evolution, enabling detection of two novel whole-genome duplications in Piperales and dating of previously reported whole-genome duplications in other magnoliids. Genomic comparisons between A. fimbriata and other angiosperms facilitated the identification of ancient genomic rearrangements suggesting the placement of magnoliids as sister to monocots, whereas phylogenetic inferences based on sequence data we compiled yielded ambiguous relationships. By identifying associated homologues and investigating their evolutionary histories and expression patterns, we revealed highly conserved floral developmental genes and their distinct downstream regulatory network that may contribute to the complex flower morphology in A. fimbriata. Finally, we elucidated the genetic basis underlying the biosynthesis of terpenoids and aristolochic acids in A. fimbriata.

scholarly journals Ancestral duplications and highly dynamic opsin gene evolution in percomorph fishes

2014 ◽  
Vol 112 (5) ◽  
pp. 1493-1498 ◽  
Author(s):  
Fabio Cortesi ◽  
Zuzana Musilová ◽  
Sara M. Stieb ◽  
Nathan S. Hart ◽  
Ulrike E. Siebeck ◽  
...  
Keyword(s):  
Gene Family ◽  
Gene Evolution ◽  
Single Gene ◽  
Gene Family Evolution ◽  
Raw Material ◽  
Opsin Gene ◽  
Evolutionary Mechanisms ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
History Of

Single-gene and whole-genome duplications are important evolutionary mechanisms that contribute to biological diversification by launching new genetic raw material. For example, the evolution of animal vision is tightly linked to the expansion of the opsin gene family encoding light-absorbing visual pigments. In teleost fishes, the most species-rich vertebrate group, opsins are particularly diverse and key to the successful colonization of habitats ranging from the bioluminescence-biased but basically dark deep sea to clear mountain streams. In this study, we report a previously unnoticed duplication of the violet-blue short wavelength-sensitive 2 (SWS2) opsin, which coincides with the radiation of highly diverse percomorph fishes, permitting us to reinterpret the evolution of this gene family. The inspection of close to 100 fish genomes revealed that, triggered by frequent gene conversion between duplicates, the evolutionary history of SWS2 is rather complex and difficult to predict. Coincidentally, we also report potential cases of gene resurrection in vertebrate opsins, whereby pseudogenized genes were found to convert with their functional paralogs. We then identify multiple novel amino acid substitutions that are likely to have contributed to the adaptive differentiation between SWS2 copies. Finally, using the dusky dottyback Pseudochromis fuscus, we show that the newly discovered SWS2A duplicates can contribute to visual adaptation in two ways: by gaining sensitivities to different wavelengths of light and by being differentially expressed between ontogenetic stages. Thus, our study highlights the importance of comparative approaches in gaining a comprehensive view of the dynamics underlying gene family evolution and ultimately, animal diversification.

scholarly journals Chromosome evolution at the origin of the ancestral vertebrate genome

2018 ◽  
Author(s):  
Christine Sacerdot ◽  
Alexandra Louis ◽  
Céline Bon ◽  
Hugues Roest Crollius
Keyword(s):  
Common Ancestor ◽  
Duplicate Gene ◽  
Vertebrate Genome ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Chromosome Fusions ◽  
The Common ◽  
Insight Into ◽  
Ancestral Vertebrate ◽  
Animal Genomes

ABSTRACTAbout 450 million years ago, a marine chordate was subject to two successive whole genome duplications (WGDs) before becoming the common ancestor of vertebrates and diversifying into the more than 60,000 species found today. Here, we reconstruct in details the evolution of chromosomes of this early vertebrate along successive steps of the two WGD. We first compared 61 extant animal genomes to build a highly contiguous order of genes in a 326 million years old ancestral Amniota genome. In this genome, we established a well-supported list of duplicated genes originating from the WGDs to link chromosomes in tetrads, a telltale signature of these events. This enabled us to reconstruct a scenario where a pre-vertebrate genome composed of 17 chromosomes duplicated into 34 chromosomes, and was subject to 7 chromosome fusions before duplicating again into 54 chromosomes. After the separation of Agnatha (jawless fish) and Gnathostomata, four more fusions took place to form the ancestral Euteleostomi genome of 50 chromosomes. These results firmly establish the occurrence of the two WGD, resolving in particular the ambiguity raised by the analysis of the lamprey genetic map. In addition, we provide insight into the origin of homologous micro-chromosomes found in the chicken and the gar genomes. This work provides a foundation for studying the evolution of vertebrate chromosomes from the standpoint of a common ancestor, and particularly the pattern of duplicate gene retention and loss that resulted in the gene composition of extant genomes.

scholarly journals Contrasting a reference cranberry genome to a crop wild relative provides insights into adaptation, domestication, and breeding

2021 ◽  
Author(s):  
Joseph Kawash ◽  
Kelly Colt ◽  
Nolan T Hartwick ◽  
Bradley W Abramson ◽  
Nicholi Vorsa ◽  
...  
Keyword(s):  
Reference Genome ◽  
Draft Genome ◽  
Gene Repertoire ◽  
Environmental Response ◽  
Breeding Programs ◽  
Woody Perennial ◽  
Whole Genome Duplications ◽  
Native North American ◽  
Genome Duplications ◽  
Insight Into

Cranberry (Vaccinium macrocarpon) is a member of the Heath family (Ericaceae) and is a temperate low-growing woody perennial native to North America that is both economically important and has significant health benefits. While some native varieties are still grown today, breeding programs over the past 50 years have made significant contributions to improving disease resistance, fruit quality and yield. An initial genome sequence of an inbred line of the wild selection Ben Lear, which is parent to multiple breeding programs, provided insight into the gene repertoire as well as a platform for molecular breeding. Recent breeding efforts have focused on leveraging the circumboreal V. oxycoccos, which forms interspecific hybrids with V. macrocarpon, offering to bring in novel fruit chemistry and other desirable traits. Here we present an updated, chromosome-resolved V. macrocarpon reference genome, and compare it to a high-quality draft genome of V. oxycoccos. Leveraging the chromosome resolved cranberry reference genome, we confirmed that the Ericaceae has undergone two whole genome duplications that are shared with blueberry and rhododendron. Leveraging resequencing data for Ben Lear inbred lines, as well as several wild and elite selections, we identified common regions that are targets of improvement. These same syntenic regions in V. oxycoccos, were identified and represent environmental response and plant architecture genes. These data provide insight into early genomic selection in the domestication of a native North American berry crop.

scholarly journals Molecular Phylogenetic Analysis of the AIG Family in Vertebrates

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1190
Author(s):  
Yuqi Huang ◽  
Minghao Sun ◽  
Lenan Zhuang ◽  
Jin He
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Functional Characterization ◽  
Vertebrate Evolution ◽  
Molecular Phylogenetic Analysis ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Molecular Phylogenetic ◽  
Duplication Events ◽  
Inducible Genes

Androgen-inducible genes (AIGs), which can be regulated by androgen level, constitute a group of genes characterized by the presence of the AIG/FAR-17a domain in its protein sequence. Previous studies on AIGs demonstrated that one member of the gene family, AIG1, is involved in many biological processes in cancer cell lines and that ADTRP is associated with cardiovascular diseases. It has been shown that the numbers of AIG paralogs in humans, mice, and zebrafish are 2, 2, and 3, respectively, indicating possible gene duplication events during vertebrate evolution. Therefore, classifying subgroups of AIGs and identifying the homologs of each AIG member are important to characterize this novel gene family further. In this study, vertebrate AIGs were phylogenetically grouped into three major clades, ADTRP, AIG1, and AIG-L, with AIG-L also evident in an outgroup consisting of invertebrsate species. In this case, AIG-L, as the ancestral AIG, gave rise to ADTRP and AIG1 after two rounds of whole-genome duplications during vertebrate evolution. Then, the AIG family, which was exposed to purifying forces during evolution, lost or gained some of its members in some species. For example, in eutherians, Neognathae, and Percomorphaceae, AIG-L was lost; in contrast, Salmonidae and Cyprinidae acquired additional AIG copies. In conclusion, this study provides a comprehensive molecular phylogenetic analysis of vertebrate AIGs, which can be employed for future functional characterization of AIGs.

scholarly journals Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidates for targeted treatment

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Hua Sun ◽  
Song Cao ◽  
R. Jay Mashl ◽  
Chia-Kuei Mo ◽  
Simone Zaccaria ◽  
...  
Keyword(s):  
Human Tumors ◽  
Multiple Time ◽  
Cancer Treatments ◽  
Whole Genome Duplications ◽  
Patient Derived Xenograft ◽  
Genome Duplications ◽  
Genomic Characterization ◽  
Cancer Types ◽  
Multiple Time Points ◽  
Pdx Models

AbstractDevelopment of candidate cancer treatments is a resource-intensive process, with the research community continuing to investigate options beyond static genomic characterization. Toward this goal, we have established the genomic landscapes of 536 patient-derived xenograft (PDX) models across 25 cancer types, together with mutation, copy number, fusion, transcriptomic profiles, and NCI-MATCH arms. Compared with human tumors, PDXs typically have higher purity and fit to investigate dynamic driver events and molecular properties via multiple time points from same case PDXs. Here, we report on dynamic genomic landscapes and pharmacogenomic associations, including associations between activating oncogenic events and drugs, correlations between whole-genome duplications and subclone events, and the potential PDX models for NCI-MATCH trials. Lastly, we provide a web portal having comprehensive pan-cancer PDX genomic profiles and source code to facilitate identification of more druggable events and further insights into PDXs’ recapitulation of human tumors.

scholarly journals Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dimitri Boeckaerts ◽  
Michiel Stock ◽  
Bjorn Criel ◽  
Hans Gerstmans ◽  
Bernard De Baets ◽  
...  
Keyword(s):  
Machine Learning ◽  
Predictive Model ◽  
Receptor Binding ◽  
Bacterial Infections ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Area Under The Curve ◽  
Local Alignment ◽  
Search Tool ◽  
Different Levels

AbstractNowadays, bacteriophages are increasingly considered as an alternative treatment for a variety of bacterial infections in cases where classical antibiotics have become ineffective. However, characterizing the host specificity of phages remains a labor- and time-intensive process. In order to alleviate this burden, we have developed a new machine-learning-based pipeline to predict bacteriophage hosts based on annotated receptor-binding protein (RBP) sequence data. We focus on predicting bacterial hosts from the ESKAPE group, Escherichia coli, Salmonella enterica and Clostridium difficile. We compare the performance of our predictive model with that of the widely used Basic Local Alignment Search Tool (BLAST). Our best-performing predictive model reaches Precision-Recall Area Under the Curve (PR-AUC) scores between 73.6 and 93.8% for different levels of sequence similarity in the collected data. Our model reaches a performance comparable to that of BLASTp when sequence similarity in the data is high and starts outperforming BLASTp when sequence similarity drops below 75%. Therefore, our machine learning methods can be especially useful in settings in which sequence similarity to other known sequences is low. Predicting the hosts of novel metagenomic RBP sequences could extend our toolbox to tune the host spectrum of phages or phage tail-like bacteriocins by swapping RBPs.

scholarly journals Chromosome Distribution of Highly Conserved Tandemly Arranged Repetitive DNAs in the Siberian Sturgeon (Acipenser baerii)

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1375
Author(s):  
Larisa S. Biltueva ◽  
Dmitry Yu. Prokopov ◽  
Svetlana A. Romanenko ◽  
Elena A. Interesova ◽  
Manfred Schartl ◽  
...  
Keyword(s):  
Duplication Event ◽  
Siberian Sturgeon ◽  
Genome Duplication Event ◽  
Acipenser Baerii ◽  
Whole Genome Duplications ◽  
Sturgeon Species ◽  
Genome Duplications ◽  
Size Groups ◽  
Genomic Studies ◽  
Syntenic Regions

Polyploid genomes present a challenge for cytogenetic and genomic studies, due to the high number of similar size chromosomes and the simultaneous presence of hardly distinguishable paralogous elements. The karyotype of the Siberian sturgeon (Acipenser baerii) contains around 250 chromosomes and is remarkable for the presence of paralogs from two rounds of whole-genome duplications (WGD). In this study, we applied the sterlet-derived acipenserid satDNA-based whole chromosome-specific probes to analyze the Siberian sturgeon karyotype. We demonstrate that the last genome duplication event in the Siberian sturgeon was accompanied by the simultaneous expansion of several repetitive DNA families. Some of the repetitive probes serve as good cytogenetic markers distinguishing paralogous chromosomes and detecting ancestral syntenic regions, which underwent fusions and fissions. The tendency of minisatellite specificity for chromosome size groups previously observed in the sterlet genome is also visible in the Siberian sturgeon. We provide an initial physical chromosome map of the Siberian sturgeon genome supported by molecular markers. The application of these data will facilitate genomic studies in other recent polyploid sturgeon species.

scholarly journals perfectphyloR: An R package for reconstructing perfect phylogenies

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Charith B. Karunarathna ◽  
Jinko Graham
Keyword(s):  
Binary Tree ◽  
Sequence Data ◽  
R Package ◽  
Binary Sequences ◽  
Ancestral Haplotype ◽  
Perfect Phylogeny ◽  
Nested Partitions ◽  
Genetic Sequence ◽  
Insight Into ◽  
Rooted Binary Tree

Abstract Background A perfect phylogeny is a rooted binary tree that recursively partitions sequences. The nested partitions of a perfect phylogeny provide insight into the pattern of ancestry of genetic sequence data. For example, sequences may cluster together in a partition indicating that they arise from a common ancestral haplotype. Results We present an R package to reconstruct the local perfect phylogenies underlying a sample of binary sequences. The package enables users to associate the reconstructed partitions with a user-defined partition. We describe and demonstrate the major functionality of the package. Conclusion The package should be of use to researchers seeking insight into the ancestral structure of their sequence data. The reconstructed partitions have many applications, including the mapping of trait-influencing variants.

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