Multiple Chromosomal Rearrangements Structured the Ancestral Vertebrate Hox-Bearing Protochromosomes

While the proposal that large-scale genome expansions occurred early in vertebrate evolution is widely accepted, the exact mechanisms of the expansion—such as a single or multiple rounds of whole genome duplication, bloc chromosome duplications, large-scale individual gene duplications, or some combination of these—is unclear. Gene families with a single invertebrate member but four vertebrate members, such as the Hox clusters, provided early support for Ohno's hypothesis that two rounds of genome duplication (the 2R-model) occurred in the stem lineage of extant vertebrates. However, despite extensive study, the duplication history of the Hox clusters has remained unclear, calling into question its usefulness in resolving the role of large-scale gene or genome duplications in early vertebrates. Here, we present a phylogenetic analysis of the vertebrate Hox clusters and several linked genes (the Hox “paralogon”) and show that different phylogenies are obtained for Dlx and Col genes than for Hox and ErbB genes. We show that these results are robust to errors in phylogenetic inference and suggest that these competing phylogenies can be resolved if two chromosomal crossover events occurred in the ancestral vertebrate. These results resolve conflicting data on the order of Hox gene duplications and the role of genome duplication in vertebrate evolution and suggest that a period of genome reorganization occurred after genome duplications in early vertebrates.     

Consequences of Lineage-Specific Gene Loss on Functional Evolution of Surviving Paralogs: ALDH1A and Retinoic Acid Signaling in Vertebrate Genomes

Genome duplications increase genetic diversity and may facilitate the evolution of gene subfunctions. Little attention, however, has focused on the evolutionary impact of lineage-specific gene loss. Here, we show that identifying lineage-specific gene loss after genome duplication is important for understanding the evolution of gene subfunctions in surviving paralogs and for improving functional connectivity among human and model organism genomes. We examine the general principles of gene loss following duplication, coupled with expression analysis of the retinaldehyde dehydrogenase Aldh1a gene family during retinoic acid signaling in eye development as a case study. Humans have three ALDH1A genes, but teleosts have just one or two. We used comparative genomics and conserved syntenies to identify loss of ohnologs (paralogs derived from genome duplication) and to clarify uncertain phylogenies. Analysis showed that Aldh1a1 and Aldh1a2 form a clade that is sister to Aldh1a3-related genes. Genome comparisons showed secondarily loss of aldh1a1 in teleosts, revealing that Aldh1a1 is not a tetrapod innovation and that aldh1a3 was recently lost in medaka, making it the first known vertebrate with a single aldh1a gene. Interestingly, results revealed asymmetric distribution of surviving ohnologs between co-orthologous teleost chromosome segments, suggesting that local genome architecture can influence ohnolog survival. We propose a model that reconstructs the chromosomal history of the Aldh1a family in the ancestral vertebrate genome, coupled with the evolution of gene functions in surviving Aldh1a ohnologs after R1, R2, and R3 genome duplications. Results provide evidence for early subfunctionalization and late subfunction-partitioning and suggest a mechanistic model based on altered regulation leading to heterochronic gene expression to explain the acquisition or modification of subfunctions by surviving ohnologs that preserve unaltered ancestral developmental programs in the face of gene loss.     

Genome-scale phylogenetic analysis finds extensive gene transfer among fungi

Although the role of lateral gene transfer is well recognized in the evolution of bacteria, it is generally assumed that it has had less influence among eukaryotes. To explore this hypothesis, we compare the dynamics of genome evolution in two groups of organisms: cyanobacteria and fungi. Ancestral genomes are inferred in both clades using two types of methods: first, Count, a gene tree unaware method that models gene duplications, gains and losses to explain the observed numbers of genes present in a genome; second, ALE, a more recent gene tree-aware method that reconciles gene trees with a species tree using a model of gene duplication, loss and transfer. We compare their merits and their ability to quantify the role of transfers, and assess the impact of taxonomic sampling on their inferences. We present what we believe is compelling evidence that gene transfer plays a significant role in the evolution of fungi.     

Molecular Evolution of Prolactin Gene Family in Rodents

In this study, we identified two novel members of prolactin gene family in rat by blast searches against the published genomic database. A further analysis showed that gene duplications leading to PRL gene family in rodents occurred after rodents diverged from other mammals. Major reorganization of the gene loci in rodents was largely completed before the split of rat and mouse. But PL-I and PL-II genes are the exceptions, which have clustered in a species-specific manner in the phylogenetic tree. By combining results from gene conversion testing, relative chromosomal location comparison and estimated time for gene duplication, we believe that rodent PL-I and PL-II genes are species-specific and are the results of serial duplications which occurred after the divergence of mouse and rat. Our analysis also reveals that continual gene duplication and divergence occurred during the evolution of rodent PRL gene family.     

A novel gene family NBPF: intricate structure generated by gene duplications during primate evolution

Partial and complete genome duplications occurred during evolution and resulted in the creation of new genes and gene families. We identified a novel and intricate human gene family located primarily in regions of segmental duplications on human chromosome 1. We named it NBPF, for neuroblastoma breakpoint family, because one of its members is disrupted by a chromosomal translocation in a neuroblastoma patient. The NBPF genes have a repetitive structure with high intragenic and intergenic sequence similarity in both coding and noncoding regions. These similarities might expose these genomic regions to illegitimate recombination, resulting in structural variation in the NBPF genes. The encoded proteins contain a highly conserved domain of unknown function, which we have named the NBPF repeat. In silico analysis combined with the isolation of multiple full-length cDNA clones showed that several members of this gene family are abundantly expressed in a large variety of tissues and cell lines. Strikingly, no discernable orthologues could be identified in the completed genomes of fruit fly, nematode, mouse, or rat, but sequences with low homology could be isolated from the draft canine and bovine genomes. Interestingly, this gene family shows primate-specific duplications that result in species-specific arrays of NBPF homologous sequences. Overall, this novel NBPF family reflects the continuous evolution of primate genomes that resulted in large physiological differences, and its potential role in this process is discussed.     

CrusView: A Java-Based Visualization Platform for Comparative Genomics Analyses in Brassicaceae Species

In plants and animals, chromosomal breakage and fusion events based on conserved syntenic genomic blocks lead to conserved patterns of karyotype evolution among species of the same family. However, karyotype information has not been well utilized in genomic comparison studies. We present CrusView, a Java-based bioinformatic application utilizing Standard Widget Toolkit/Swing graphics libraries and a SQLite database for performing visualized analyses of comparative genomics data in Brassicaceae (crucifer) plants. Compared with similar software and databases, one of the unique features of CrusView is its integration of karyotype information when comparing two genomes. This feature allows users to perform karyotype-based genome assembly and karyotype-assisted genome synteny analyses with preset karyotype patterns of the Brassicaceae genomes. Additionally, CrusView is a local program, which gives its users high flexibility when analyzing unpublished genomes and allows users to upload self-defined genomic information so that they can visually study the associations between genome structural variations and genetic elements, including chromosomal rearrangements, genomic macrosynteny, gene families, high-frequency recombination sites, and tandem and segmental duplications between related species. This tool will greatly facilitate karyotype, chromosome, and genome evolution studies using visualized comparative genomics approaches in Brassicaceae species. CrusView is freely available at http://www.cmbb.arizona.edu/CrusView/.The Brassicaceae (crucifer) plant family contains more than 3,700 species, including the model plant organism Arabidopsis (Arabidopsis thaliana); economically important crop species, such as Brassica rapa and Brassica napus; and close relatives of Arabidopsis used in abiotic stress research, such as Eutrema salsugineum and Schrenkiella parvula. Because Brassicaceae plants have high scientific and economic importance, several whole-genome sequencing projects of the species in this family have been recently launched (http://www.brassica.info). Moreover, Brassicaceae is also a good system for population genomics. The 1001 Arabidopsis Genomes Project (http://www.1001genomes.org/) plans to generate complete genome sequences for 1,001 Arabidopsis strains to study the associations between genetic variation and phenotypic diversity. The Value-directed Evolutionary Genomics Initiative project aims to understand the genome evolution of Brassicaceae species by sequencing several close relatives of Arabidopsis, such as Arabidopsis lyrata and Capsella rubella. Recent advances in high-throughput sequencing technology have greatly expedited these whole-genome sequencing projects of versatile nonmodel organisms. Although increasingly longer reads can now be produced from high-throughput sequencing experiments, de novo assembler tools can only generate contig and/or scaffold sequences from high-throughput sequencing reads. These tools cannot generate complete chromosome sequences without genetic and/or physical maps that typically require years to create. This limitation makes chromosome-scale structural variation (i.e. translocation, inversion, deletion and insertion, and segmental and tandem duplication) and genomic macrosynteny analyses difficult to perform.In both plants and animals, genomes of species within the same family have evolved with conserved karyotype patterns due to the rearrangements of large chromosomal segments. Chromosomal karyotypes can be obtained from comparative chromosomal painting (CCP) experiments by performing in situ hybridization experiments on bacterial artificial chromosome sequences between related species. The genome of each Brassicaceae member is composed of 24 conserved genomic blocks that have been considered as the basic units of chromosomal rearrangement during genome evolution (Lysak et al., 2006). The sizes of these conserved blocks range from several to dozens of megabases. Currently, karyotypes profiled by CCP experiments in approximately 20 Brassicaceae species are available; such karyotypes include those from Arabidopsis (n = 5), Homungia alpine (n = 6), Eutrema spp. (n = 7), A. lyrata (n = 8), B. rapa (n = 10), and Polyctenium fremontii (n = 14). By utilizing the karyotype information in Brassicaceae, we have developed a tool, KGBassembler (for Karyotype-based Genome assembler for Brassicaceae), to finalize the assembly of chromosomes from scaffolds/contigs without relying on a genetic/physical map (Ma et al., 2012).Over the past 2 years, complete whole-genome sequences of several Brassicaceae species have been released, including the aforementioned A. lyrata, S. parvula, B. rapa, and E. salsugineum (Dassanayake et al., 2011; Hu et al., 2011; Wang et al., 2011; Wright and Agren, 2011; Wu et al., 2012; Yang et al., 2013). These genomic resources have opened a new era of comparative genomics in Brassicaceae to better understand the genomic evolution (Cheng et al., 2012). Numerous tools and databases are available for performing comparative genomics analysis in plants. CoGe is a comparative genomics analysis platform that is now a part of the iPlant Collaborative Project (Goff et al., 2011). The CoGe database currently includes nearly 2,000 genome sequences of approximately 1,500 organisms, allowing users to perform online visual analyses of genome synteny and duplication events (Tang and Lyons, 2012). PLAZA and Vista are also Web-based databases that provide comparative analysis services on the genomic data deposited in the databases (Frazer et al., 2004; Van Bel et al., 2012). Other stand-alone bioinformatic applications for comparative genomic analysis, such as Easyfig and genoPlotR, are commonly used to generate synteny plots of given genome segments at a scale ranging from a single gene to one chromosome (Guy et al., 2010; Sullivan et al., 2011).In this work, we present a Java-based bioinformatic application, CrusView, for performing visualized analyses of genome synteny and karyotype evolution in Brassicaceae species. CrusView features a user-friendly graphical user interface (GUI) implemented with Standard Widget Toolkit (SWT)/Swing graphics libraries and a SQLite database used to manage local genomic data. Compared with the most commonly used tools in comparative genomics, one of the unique features of CrusView is that available karyotype data of a Brassicaceae species are incorporated to facilitate karyotype-based chromosome assembly and analyses of chromosomal structural evolution. Compared with Web-based tools, the stand-alone CrusView tool was also designed to give users higher flexibility in analyzing currently unpublished genome data and integrating self-defined genomic information based on the users’ interests, such as gene families, gene duplications, chromosomal break points, Gene Ontology terms, and groups of orthologs/paralogs, with the genomic synteny maps. In addition, CrusView can generate images representing genomic synteny between two compared genomes in PNG/SVG/PDF high-resolution formats that are suitable for publication.     

<Emphasis Type="Italic">EVG</Emphasis>, the Remnants of a Primordial Bilaterian’s Synteny of Functionally Unrelated Genes

Extant genomes are the result of repeated duplications and subsequent divergence of primordial genes that assembled the genomes of the first living beings. Increased information on genome maps of different species is revealing conserved syntenies among different vertebrate taxa, which allow to trace back the history of current chromosomes. However, inferring neighboring relationships between genes of more primitive genomes has proven to be very difficult. Most often, the ancestral arrangements of genes have been lost by multiple histories of internal duplications, chromosomal breaks, and large-scale genomic rearrangements. Here we describe a gene arrangement of nonrelated genes that seems to have endured evolution, at least from the separation of the two major clades of bilateria: deuterostomia and protostomia, approximately 1 billion years ago. In its simplest conception, this gene cluster, named EVG, groups the genes for a glucose transporter, an enolase, and a vesicle-associated membrane protein (VAMP). EVG might represent the evolutionary remnants of the gene organization of an ancient bilaterian genome.     

Origins of P450 diversity

The P450 enzymes maintain a conserved P450 fold despite a considerable variation in sequence. The P450 family even includes proteins that lack the single conserved cysteine and are therefore no longer haem-thiolate proteins. The mechanisms of successive gene duplications leading to large families in plants and animals are well established. Comparisons of P450 CYP gene clusters in related species illustrate the rapid changes in CYPome sizes. Examples of CYP copy number variation with effects on fitness are emerging, and these provide an opportunity to study the proximal causes of duplication or pseudogenization. Birth and death models can explain the proliferation of CYP genes that is amply illustrated by the sequence of every new genome. Thus, the distribution of P450 diversity within the CYPome of plants and animals, a few families with many genes (P450 blooms) and many families with few genes, follows similar power laws in both groups. A closer look at some families with few genes shows that these, often single member families, are not stable during evolution. The enzymatic prowess of P450 may predispose them to switch back and forth between metabolism of critical structural or signal molecules and metabolism dedicated to environmental response.     

Genomics and expression analysis of DHHC-cysteine-rich domain S-acyl transferase protein family in apple

S-acylation is one of a group of lipid modifications that occurs on eukaryotic proteins, mediated by DHHC-CRD-containing proteins, which plays an important role in regulating the membrane association, trafficking and function of target proteins. Although genome-wide identification of PAT family has been carried out in yeast, mice, humans and Arabidopsis, little is known about apple PAT genes. In this study, a total of 33 putative apple PAT proteins, containing DHHC-CRD by domain analysis, have been identified, and were classified into three groups according to the phylogenetic analysis of PAT proteins in apple and Arabidopsis. More complex TMDs in the most MdPATs revealed the PM location of the gene family. Gene structure, gene chromosomal location and paralogs analysis of MdPAT genes within the apple genome demonstrated that tandem and segmental duplications, as well as whole genome duplications, have likely contributed to the expansion and evolution of the PAT gene family in apple. According to the microarray and expressed sequence tag (ESTs) analysis, the different expression patterns indicate that they may play different roles during fruit development and rootstock-scion interactions process. Moreover, PATs were performed expression profile analyses in different tissues, indicating that the PATs are involved in various aspects of physiological and developmental processes of apple. To our knowledge, this is the first report of a genome-wide analysis of the apple PAT gene family, and this genomic analysis of apple DHHC-CRD PAT genes provides the first step towards a functional study of this gene family in apple.     

Gene duplication as a major force in evolution

Gene duplication is an important mechanism for acquiring new genes and creating genetic novelty in organisms. Many new gene functions have evolved through gene duplication and it has contributed tremendously to the evolution of developmental programmes in various organisms. Gene duplication can result from unequal crossing over, retroposition or chromosomal (or genome) duplication. Understanding the mechanisms that generate duplicate gene copies and the subsequent dynamics among gene duplicates is vital because these investigations shed light on localized and genomewide aspects of evolutionary forces shaping intra-specific and inter-specific genome contents, evolutionary relationships, and interactions. Based on whole-genome analysis of Arabidopsis thaliana, there is compelling evidence that angiosperms underwent two whole-genome duplication events early during their evolutionary history. Recent studies have shown that these events were crucial for creation of many important developmental and regulatory genes found in extant angiosperm genomes. Recent studies also provide strong indications that even yeast (Saccharomyces cerevisiae), with its compact genome, is in fact an ancient tetraploid. Gene duplication can provide new genetic material for mutation, drift and selection to act upon, the result of which is specialized or new gene functions. Without gene duplication the plasticity of a genome or species in adapting to changing environments would be severely limited. Whether a duplicate is retained depends upon its function, its mode of duplication, (i.e. whether it was duplicated during a whole-genome duplication event), the species in which it occurs, and its expression rate. The exaptation of preexisting secondary functions is an important feature in gene evolution, just as it is in morphological evolution.     

Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes

Background

Genomes rearrangements carry valuable information for phylogenetic inference or the elucidation of molecular mechanisms of adaptation. However, the detection of genome rearrangements is often hampered by current deficiencies in data and methods: Genomes obtained from short sequence reads have generally very fragmented assemblies, and comparing multiple gene orders generally leads to computationally intractable algorithmic questions.

Results

We present a computational method, ADseq, which, by combining ancestral gene order reconstruction, comparative scaffolding and de novo scaffolding methods, overcomes these two caveats. ADseq provides simultaneously improved assemblies and ancestral genomes, with statistical supports on all local features. Compared to previous comparative methods, it runs in polynomial time, it samples solutions in a probabilistic space, and it can handle a significantly larger gene complement from the considered extant genomes, with complex histories including gene duplications and losses. We use ADseq to provide improved assemblies and a genome history made of duplications, losses, gene translocations, rearrangements, of 18 complete Anopheles genomes, including several important malaria vectors. We also provide additional support for a differentiated mode of evolution of the sex chromosome and of the autosomes in these mosquito genomes.

Conclusions

We demonstrate the method’s ability to improve extant assemblies accurately through a procedure simulating realistic assembly fragmentation. We study a debated issue regarding the phylogeny of the Gambiae complex group of Anopheles genomes in the light of the evolution of chromosomal rearrangements, suggesting that the phylogenetic signal they carry can differ from the phylogenetic signal carried by gene sequences, more prone to introgression.

     

Adaptive Evolution and the Birth of CTCF Binding Sites in the Drosophila Genome

Changes in the physical interaction between cis-regulatory DNA sequences and proteins drive the evolution of gene expression. However, it has proven difficult to accurately quantify evolutionary rates of such binding change or to estimate the relative effects of selection and drift in shaping the binding evolution. Here we examine the genome-wide binding of CTCF in four species of Drosophila separated by between ∼2.5 and 25 million years. CTCF is a highly conserved protein known to be associated with insulator sequences in the genomes of human and Drosophila. Although the binding preference for CTCF is highly conserved, we find that CTCF binding itself is highly evolutionarily dynamic and has adaptively evolved. Between species, binding divergence increased linearly with evolutionary distance, and CTCF binding profiles are diverging rapidly at the rate of 2.22% per million years (Myr). At least 89 new CTCF binding sites have originated in the Drosophila melanogaster genome since the most recent common ancestor with Drosophila simulans. Comparing these data to genome sequence data from 37 different strains of Drosophila melanogaster, we detected signatures of selection in both newly gained and evolutionarily conserved binding sites. Newly evolved CTCF binding sites show a significantly stronger signature for positive selection than older sites. Comparative gene expression profiling revealed that expression divergence of genes adjacent to CTCF binding site is significantly associated with the gain and loss of CTCF binding. Further, the birth of new genes is associated with the birth of new CTCF binding sites. Our data indicate that binding of Drosophila CTCF protein has evolved under natural selection, and CTCF binding evolution has shaped both the evolution of gene expression and genome evolution during the birth of new genes.     

Architecture and evolution of subtelomeres in the unicellular green alga Chlamydomonas reinhardtii

In most eukaryotes, subtelomeres are dynamic genomic regions populated by multi-copy sequences of different origins, which can promote segmental duplications and chromosomal rearrangements. However, their repetitive nature has complicated the efforts to sequence them, analyse their structure and infer how they evolved. Here, we use recent genome assemblies of Chlamydomonas reinhardtii based on long-read sequencing to comprehensively describe the subtelomere architecture of the 17 chromosomes of this model unicellular green alga. We identify three main repeated elements present at subtelomeres, which we call Sultan, Subtile and Suber, alongside three chromosome extremities with ribosomal DNA as the only identified component of their subtelomeres. The most common architecture, present in 27 out of 34 subtelomeres, is a heterochromatic array of Sultan elements adjacent to the telomere, followed by a transcribed Spacer sequence, a G-rich microsatellite and transposable elements. Sequence similarity analyses suggest that Sultan elements underwent segmental duplications within each subtelomere and rearranged between subtelomeres at a much lower frequency. Analysis of other green algae reveals species-specific repeated elements that are shared across subtelomeres, with an overall organization similar to C. reinhardtii. This work uncovers the complexity and evolution of subtelomere architecture in green algae.     

Different patterns of evolution for duplicated DNA repair genes in bacteria of the Xanthomonadales group

Background

DNA repair genes encode proteins that protect organisms against genetic damage generated by environmental agents and by-products of cell metabolism. The importance of these genes in life maintenance is supported by their high conservation, and the presence of duplications of such genes may be easily traced, especially in prokaryotic genomes.

Results

The genome sequences of two Xanthomonas species were used as the basis for phylogenetic analyses of genes related to DNA repair that were found duplicated. Although 16S rRNA phylogenetic analyses confirm their classification at the basis of the gamma proteobacteria subdivision, differences were found in the origin of the various genes investigated. Except for lexA, detected as a recent duplication, most of the genes in more than one copy are represented by two highly divergent orthologs. Basically, one of such duplications is frequently positioned close to other gamma proteobacteria, but the second is often positioned close to unrelated bacteria. These orthologs may have occurred from old duplication events, followed by extensive gene loss, or were originated from lateral gene transfer (LGT), as is the case of the uvrD homolog.

Conclusions

Duplications of DNA repair related genes may result in redundancy and also improve the organisms' responses to environmental challenges. Most of such duplications, in Xanthomonas, seem to have arisen from old events and possibly enlarge both functional and evolutionary genome potentiality.

     

Species-Specific Expansion and Molecular Evolution of the 3-hydroxy-3-methylglutaryl Coenzyme A Reductase (HMGR) Gene Family in Plants

The terpene compounds represent the largest and most diverse class of plant secondary metabolites which are important in plant growth and development. The 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR; EC 1.1.1.34) is one of the key enzymes contributed to terpene biosynthesis. To better understand the basic characteristics and evolutionary history of the HMGR gene family in plants, a genome-wide analysis of HMGR genes from 20 representative species was carried out. A total of 56 HMGR genes in the 14 land plant genomes were identified, but no genes were found in all 6 algal genomes. The gene structure and protein architecture of all plant HMGR genes were highly conserved. The phylogenetic analysis revealed that the plant HMGRs were derived from one ancestor gene and finally developed into four distinct groups, two in the monocot plants and two in dicot plants. Species-specific gene duplications, caused mainly by segmental duplication, led to the limited expansion of HMGR genes in Zea mays, Gossypium raimondii, Populus trichocarpa and Glycine max after the species diverged. The analysis of Ka/Ks ratios and expression profiles indicated that functional divergence after the gene duplications was restricted. The results suggested that the function and evolution of HMGR gene family were dramatically conserved throughout the plant kingdom.     

Pinaceae show elevated rates of gene turnover that are robust to incomplete gene annotation

Gene duplications and gene losses are major determinants of genome evolution and phenotypic diversity. The frequency of gene turnover (gene gains and gene losses combined) is known to vary between organisms. Comparative genomic analyses of gene families can highlight such variation; however, estimates of gene turnover may be biased when using highly fragmented genome assemblies resulting in poor gene annotations. Here, we address potential biases introduced by gene annotation errors in estimates of gene turnover frequencies in a dataset including both well‐annotated angiosperm genomes and the incomplete gene sets of four Pinaceae, including two pine species, Norway spruce and Douglas‐fir. We show that Pinaceae experienced higher gene turnover rates than angiosperm lineages lacking recent whole‐genome duplications. This finding is robust to both known major issues in Pinaceae gene sets: missing gene models and erroneous annotation of pseudogenes. A separate analysis limited to the four Pinaceae gene sets pointed to an accelerated gene turnover rate in pines compared with Norway spruce and Douglas‐fir. Our results indicate that gene turnover significantly contributes to genome variation and possibly to speciation in Pinaceae, particularly in pines. Moreover, these findings indicate that reliable estimates of gene turnover frequencies can be discerned in incomplete and potentially inaccurate gene sets. Because gymnosperms are known to exhibit low overall substitution rates compared with angiosperms, our results suggest that the rate of single‐base pair mutations is uncoupled from the rate of large DNA duplications and deletions associated with gene turnover in Pinaceae.