Gene Synteny Research Articles

PACVr: plastome assembly coverage visualization in R

BackgroundPlastid genomes typically display a circular, quadripartite structure with two inverted repeat regions, which challenges automatic assembly procedures. The correct assembly of plastid genomes is a prerequisite for the validity of subsequent analyses on genome structure and evolution. The average coverage depth of a genome assembly is often used as an indicator of assembly quality. Visualizing coverage depth across a draft genome is a critical step, which allows users to inspect the quality of the assembly and, where applicable, identify regions of reduced assembly confidence. Despite the interplay between genome structure and assembly quality, no contemporary, user-friendly software tool can visualize the coverage depth of a plastid genome assembly while taking its quadripartite genome structure into account. A software tool is needed that fills this void.ResultsWe introduce ’PACVr’, an R package that visualizes the coverage depth of a plastid genome assembly in relation to the circular, quadripartite structure of the genome as well as the individual plastome genes. By using a variable window approach, the tool allows visualizations on different calculation scales. It also confirms sequence equality of, as well as visualizes gene synteny between, the inverted repeat regions of the input genome. As a tool for plastid genomics, PACVr provides the functionality to identify regions of coverage depth above or below user-defined threshold values and helps to identify non-identical IR regions. To allow easy integration into bioinformatic workflows, PACVr can be invoked from a Unix shell, facilitating its use in automated quality control. We illustrate the application of PACVr on four empirical datasets and compare visualizations generated by PACVr with those of alternative software tools.ConclusionsPACVr provides a user-friendly tool to visualize (a) the coverage depth of a plastid genome assembly on a circular, quadripartite plastome map and in relation to individual plastome genes, and (b) gene synteny across the inverted repeat regions. It contributes to optimizing plastid genome assemblies and increasing the reliability of publicly available plastome sequences. The software, example datasets, technical documentation, and a tutorial are available with the package at https://cran.r-project.org/package=PACVr.

The complete mitochondrial and plastid genomes of the invasive marine red alga Caulacanthus okamurae (Caulacanthaceae, Rhodophyta) from Moss Landing, California, USA

Caulacanthus okamurae is an invasive red alga that forms extensive mats in sheltered marine habitats around the world. To determine its genomic structure and genetic relationship to native and other non-native populations of C. okamurae, high-throughput sequencing analysis was performed on an introduced specimen from Bennett Slough, Moss Landing, California, USA. Assembly of 23,146,595 filtered 150 bp paired-end Illumina sequencing reads yielded its complete mitogenome (GenBank accession MT193839) and plastid genome (GenBank accession MT193838). The mitogenome is 25,995 bp in length and contains 50 genes. The plastid genome is 173,516 bp and contains 234 genes. Comparison of the organellar chromosomes to other Gigartinales revealed a high-level of gene synteny. BLAST analysis of marker sequences (rbcL, cox1, cox2) of C. okamurae from Moss Landing identified four identical DNA sequences: one from a specimen from a native population of C. okamurae from South Korea and three from specimens representing invasive populations from France, Spain, and the USA. These genetic results confirm the presence of C. okamurae in central California, USA, and represent the first complete mitogenome and plastid genome from the Caulacanthaceae.

HiC-Hiker: a probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C.

Motivation De novo assembly of reference-quality genomes used to require enormously laborious tasks. In particular, it is extremely time-consuming to build genome markers for ordering assembled contigs along chromosomes; thus, they are only available for well-established model organisms. To resolve this issue, recent studies demonstrated that Hi-C could be a powerful and cost-effective means to output chromosome-length scaffolds for non-model species with no genome marker resources, because the Hi-C contact frequency between a pair of two loci can be a good estimator of their genomic distance, even if there is a large gap between them. Indeed, state-of-the-art methods such as 3D-DNA are now widely used for locating contigs in chromosomes. However, it remains challenging to reduce errors in contig orientation because shorter contigs have fewer contacts with their neighboring contigs. These orientation errors lower the accuracy of gene prediction, read alignment, and synteny block estimation in comparative genomics.ResultsTo reduce these contig orientation errors, we propose a new algorithm, named HiC-Hiker, which has a firm grounding in probabilistic theory, rigorously models Hi-C contacts across contigs, and effectively infers the most probable orientations via the Viterbi algorithm. We compared HiC-Hiker and 3D-DNA using human and worm genome contigs generated from short reads, evaluated their performances, and observed a remarkable reduction in the contig orientation error rate from 4.3% (3D-DNA) to 1.7% (HiC-Hiker). Our algorithm can consider long-range information between distal contigs and precisely estimates Hi-C read contact probabilities among contigs, which may also be useful for determining the ordering of contigs.Availability and implementationHiC-Hiker is freely available at: https://github.com/ryought/hic_hiker.

Genome Sequencing of the Endangered Kingdonia uniflora (Circaeasteraceae, Ranunculales) Reveals Potential Mechanisms of Evolutionary Specialization.

SummaryKingdonia uniflora, an alpine herb, has an extremely narrow distribution and represents a model for studying evolutionary mechanisms of species that have adapted to undisturbed environments for evolutionarily long periods of time. We assembled a 1,004.7-Mb draft genome (encoding 43,301 genes) of K. uniflora and found significant overrepresentation in gene families associated with DNA repair, underrepresentation in gene families associated with stress response, and loss of most plastid ndh genes. During the evolutionary process, the overrepresentation of gene families involved in DNA repair could help asexual K. uniflora reduce the accumulation of deleterious mutations, while reducing genetic diversity, which is important in responding to environment fluctuations. The underrepresentation of gene families related to stress response and functional loss of ndh genes could be due to lack or loss of ability to respond to environmental changes caused by long-term adaptation to a relatively stable ecological environment.

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

Polyploidy is an evolutionary innovation for many animals and all flowering plants, but its impact on selection and domestication remains elusive. Here we analyze genome evolution and diversification for all five allopolyploid cotton species, including economically important Upland and Pima cottons. Although these polyploid genomes are conserved in gene content and synteny, they have diversified by subgenomic transposon exchanges that equilibrate genome size, evolutionary rate heterogeneities and positive selection between homoeologs within and among lineages. These differential evolutionary trajectories are accompanied by gene-family diversification and homoeolog expression divergence among polyploid lineages. Selection and domestication drive parallel gene expression similarities in fibers of two cultivated cottons, involving coexpression networks and N6-methyladenosine RNA modifications. Furthermore, polyploidy induces recombination suppression, which correlates with altered epigenetic landscapes and can be overcome by wild introgression. These genomic insights will empower efforts to manipulate genetic recombination and modify epigenetic landscapes and target genes for crop improvement.

Comparative Analyses of Mitochondrial Genomes Provide Evolutionary Insights Into Nematode-Trapping Fungi.

Predatory fungi in Orbiliaceae (Ascomycota) have evolved a diversity of trapping devices that enable them to trap and kill nematodes, other small animals, and protozoans. These trapping devices include adhesive hyphae, adhesive knobs, adhesive networks, constricting rings, and non-constricting rings. Their diversity and practical importance have attracted significant attention from biologists, making them excellent model organisms for studying adaptative evolution and as biological control agents against parasitic nematodes. The putative origins and evolutionary relationships among these carnivorous fungi have been investigated using nuclear protein-encoding genes, but their patterns of mitogenome relationships and divergences remain unknown. Here we analyze and compare the mitogenomes of 12 fungal strains belonging to eight species, including six species representing all four types of nematode trapping devices and two from related but non-predatory fungi. All 12 analyzed mitogenomes were of circular DNA molecules, with lengths ranging from 146,101 bp to 280,699 bp. Gene synteny analysis revealed several gene rearrangements and intron transfers among the mitogenomes. In addition, the number of protein coding genes (PCGs), GC content, AT skew, and GC skew varied among these mitogenomes. The increased number and total size of introns were the main contributors to the length differences among the mitogenomes. Phylogenetic analyses of the protein-coding genes indicated that mitochondrial and nuclear genomes evolved at different rates, and signals of positive selection were found in several genes involved in energy metabolism. Our study provides novel insights into the evolution of nematode-trapping fungi and shall facilitate further investigations of this ecologically and agriculturally important group of fungi.

Characterization of the complete mitochondrial genome of the black Alpaca breed of Vicugna pacos (Mammalia, Artiodactyla, Camelidae) from Puno, Peru

The domestic South American camelid Vicugna pacos L. is distributed along Peru, Chile, Bolivia, and Argentina. Here, we contribute to the bioinformatics and evolutionary systematics of the Camelidae by performing high-throughput sequencing analysis on the black Huacaya breed of V. pacos from Puno, Peru. The black Huacaya breed mitogenome is 16,664 base pairs (bp) in length and contains 37 genes (GenBank accession MT044302). The mitogenome shares a high-level of gene synteny to other Camelidae (Camelops, Camelus, Lama, and Vicugna). The mitogenome of the black Huacaya breed of V. pacos situates it in a clade with V. vicugna Molina, sister to Lama. We anticipate that further mitogenome sequencing of different breeds from Vicugna pacos will improve our understanding of the evolutionary history of this taxon.

Analysis of the complete organellar genomes of Palmaria decipiens (Palmariaceae, Rhodophyta) from Antarctica confirms its taxonomic placement in the genus Palmaria

Palmaria decipiens (Reinsch) R.W.Ricker is a ecologically important red seaweed restricted to high latitudes of the southern hemisphere. Here, we contribute to the bioinformatics and evolutionary systematics of the Palmariales by performing high throughput sequencing analysis on a specimen of P. decipiens from the western Antarctic Peninsula. The P. decipiens mitogenome is 26,645 base pairs (bp) in length and contains 49 genes (GenBank accession MN967053) and the plastid genome is 193,007 bp and contains 245 genes (GenBank accession MN967052). The mitogenome and plastid genome of P. decipiens are similar to P. palmata from Japan in pairwise genetic distances (93.71% and 98.14%, respectively), and P. palmata from the Maine, USA (87.45% and 94.57%, respectively). The genomes of P. decipiens showed high gene synteny with P. palmata, however several tRNA differences are documented. Organellar genome content and phylogenetic analyses of P. decipiens supports its placement in the genus Palmaria.

Insights Obtained by Culturing Saccharibacteria With Their Bacterial Hosts

Oral microbiome research has moved from asking “Who’s there?” to “What are they doing?” Understanding what microbes “do” involves multiple approaches, including obtaining genomic information and examining the interspecies interactions. Recently we isolated a human oral Saccharibacteria (TM7) bacterium, HMT-952, strain TM7x, which is an ultrasmall parasite of the oral bacterium Actinomyces odontolyticus. The host-parasite interactions, such as phage-bacterium or Saccharibacteria–host bacterium, are understudied areas with large potential for insight. The Saccharibacteria phylum is a member of Candidate Phyla Radiation, a large lineage previously devoid of cultivated members. However, expanding our understanding of Saccharibacteria-host interactions requires examining multiple phylogenetically distinct Saccharibacteria-host pairs. Here we report the isolation of 3 additional Saccharibacteria species from the human oral cavity in binary coculture with their bacterial hosts. They were obtained by filtering ultrasmall Saccharibacteria cells free of other larger bacteria and inoculating them into cultures of potential host bacteria. The binary cocultures obtained could be stably passaged and studied. Complete closed genomes were obtained and allowed full genome analyses. All have small genomes (<1 Mb) characteristic of parasitic species and dramatically limited de novo synthetic pathway capabilities but include either restriction modification or CRISPR-Cas systems as part of an innate defense against foreign DNA. High levels of gene synteny exist among Saccharibacteria species. Having isolates growing in coculture with their hosts allowed time course studies of growth and parasite-host interactions by phase contrast, fluorescence in situ hybridization, and scanning electron microscopy. The cells of the 4 oral Saccharibacteria species are ultrasmall and could be seen attached to their larger Actinobacteria hosts. Parasite attachment appears to lead to host cell death and lysis. The successful cultivation of Saccharibacteria species has significantly expanded our understanding of these ultrasmall Candidate Phyla Radiation bacteria.

Baby Genomics: Tracing the Evolutionary Changes That Gave Rise to Placentation.

It has long been challenging to uncover the molecular mechanisms behind striking morphological innovations such as mammalian pregnancy. We studied the power of a robust comparative orthology pipeline based on gene synteny to address such problems. We inferred orthology relations between human genes and genes from each of 43 other vertebrate genomes, resulting in ∼18,000 orthologous pairs for each genome comparison. By identifying genes that first appear coincident with origin of the placental mammals, we hypothesized that we would define a subset of the genome enriched for genes that played a role in placental evolution. We thus pinpointed orthologs that appeared before and after the divergence of eutherian mammals from marsupials. Reinforcing previous work, we found instead that much of the genetic toolkit of mammalian pregnancy evolved through the repurposing of preexisting genes to new roles. These genes acquired regulatory controls for their novel roles from a group of regulatory genes, many of which did in fact originate at the appearance of the eutherians. Thus, orthologs appearing at the origin of the eutherians are enriched in functions such as transcriptional regulation by Krüppel-associated box-zinc-finger proteins, innate immune responses, keratinization, and the melanoma-associated antigen protein class. Because the cellular mechanisms of invasive placentae are similar to those of metastatic cancers, we then used our orthology inferences to explore the association between placenta invasion and cancer metastasis. Again echoing previous work, we find that genes that are phylogenetically older are more likely to be implicated in cancer development.

Ancestry and adaptive radiation of Bacteroidetes as assessed by comparative genomics

To date, the phylum Bacteroidetes comprises more than 1,500 described species with diverse ecological roles. However, there is little understanding of archetypal Bacteroidetes traits at a genomic level. In this study, a representative set of 89 Bacteroidetes genomes was compiled, and pairwise reciprocal best-match gene comparisons and gene syntenies were used to identify common traits that allowed Bacteroidetes evolution and adaptive radiation to be traced. The type IX secretion system (T9SS) was highly conserved among all studied Bacteroidetes. Class-level comparisons furthermore suggested that the ACIII-caa3COX super-complex evolved in the ancestral aerobic bacteroidetal lineage, and was secondarily lost in extant anaerobic Bacteroidetes. Another Bacteroidetes-specific respiratory chain adaptation was the sodium-pumping Nqr complex I that replaced the ancestral proton-pumping complex I in marine species. T9SS plays a role in gliding motility and the acquisition of complex macro-molecular organic compounds, and the ACIII-caa3COX super-complex allows effective control of electron flux during respiration. This combination likely provided ancestral Bacteroidetes with a decisive competitive advantage to effectively scavenge, uptake and degrade complex organic molecules, and therefore has played a pivotal role in the successful adaptive radiation of the phylum.

The complete mitochondrial genome of the chiltepin pepper (Capsicum annuum var. glabriusculum), the wild progenitor of Capsicum annuum L.

The complete mitochondrial genome of chiltepin pepper (Capsicum annuum var glabriusculum) was sequenced. The mitogenome of the American bird pepper was 505,190 bp, with 44.4% of GC content. A total of 218 genes were fully annotated, including 190 CDS (31 known genes and 158 open reading frames), three rRNA, and 25 tRNA genes. The gene synteny and number were equal to those of C. annuum var annuum, except for the partial annotation of ATP subunit 6 and the absence of ORF172 and ORF104b. The complete mt genome sequence was deposited to the GenBank (NCBI, Accession number: MN196478).

Molecular evolution and diversification of the GRF transcription factor family.

- Growth Regulating Factors (GRFs) comprise a transcription factor family with important functions in plant growth and development. They are characterized by the presence of QLQ and WRC domains, responsible for interaction with proteins and DNA, respectively. The QLQ domain is named due to the similarity to a protein interaction domain found in the SWI2/SNF2 chromatin remodeling complex. Despite the occurrence of the QLQ domain in both families, the divergence between them had not been further explored. Here, we show evidence for GRF origin and determined its diversification in angiosperm species. Phylogenetic analysis revealed 11 well-supported groups of GRFs in flowering plants. These groups were supported by gene structure, synteny, and protein domain composition. Synteny and phylogenetic analyses allowed us to propose different sets of probable orthologs in the groups. Besides, our results, together with functional data previously published, allowed us to suggest candidate genes for engineering agronomic traits. In addition, we propose that the QLQ domain of GRF genes evolved from the eukaryotic SNF2 QLQ domain, most likely by a duplication event in the common ancestor of the Charophytes and land plants. Altogether, our results are important for advancing the origin and evolution of the GRF family in Streptophyta.

Identification and Characterization of Carnitine Palmitoyltransferase 1 (cpt 1) Genes in Nile Tilapia, Oreochromis niloticus.

Four cpt 1 genes (cpt 1α1a, cpt 1α2a, cpt 1α2b, and cpt 1β) were identified in the Nile tilapia genome. Two transmembrane helix domains (TMH) were identified for Cpt 1α1a, Cpt 1α2a, and Cpt 1β, while Cpt 1α2b had only one TMH domain. Evidence was found of conserved gene synteny between cpt 1 genes from Nile tilapia and the cpt 1/CPT 1 genes of zebrafish and human. Phylogenetic analysis showed that Nile tilapia Cpt 1 sequences clustered in distinct clades with their orthologous Cpt 1/CPT 1 from other vertebrates. Nile tilapia cpt 1α1a, cpt 1α2a, cpt 1α2b, and cpt 1β contain 18 coding exons encoding polypeptides of 771, 784, 788, and 786 amino acids in length, respectively. The cpt 1 genes were determined in all the tested tissues with varying tissue distribution patterns. These findings suggest that (1) cpt 1α1a, cpt 1α2a, and cpt 1α2b arose in the Nile tilapia genome as a result of the teleost-specific whole-genome duplication; (2) nonfunctionalization is the most likely cause of the loss of cpt 1α1b in the Nile tilapia genome; (3) the different tissue-specific transcription of cpt 1α2a and cpt 1α2b may be either due to the sub- or the neo-functionalization of transcriptional control side.

Reconstruction of the Carbohydrate 6-O Sulfotransferase Gene Family Evolution in Vertebrates Reveals Novel Member, CHST16, Lost in Amniotes.

Glycosaminoglycans are sulfated polysaccharide molecules, essential for many biological processes. The 6-O sulfation of glycosaminoglycans is carried out by carbohydrate 6-O sulfotransferases (C6OSTs), previously named Gal/GalNAc/GlcNAc 6-O sulfotransferases. Here, for the first time, we present a detailed phylogenetic reconstruction, analysis of gene synteny conservation and propose an evolutionary scenario for the C6OST family in major vertebrate groups, including mammals, birds, nonavian reptiles, amphibians, lobe-finned fishes, ray-finned fishes, cartilaginous fishes, and jawless vertebrates.The C6OST gene expansion likely started early in the chordate lineage, giving rise to four ancestral genes after the divergence of tunicates and before the emergence of extant vertebrates. The two rounds of whole-genome duplication in early vertebrate evolution (1R/2R) only contributed two additional C6OST subtype genes, increasing the vertebrate repertoire from four genes to six, divided into two branches. The first branch includes CHST1 and CHST3 as well as a previously unrecognized subtype, CHST16 that was lost in amniotes. The second branch includes CHST2, CHST7, and CHST5. Subsequently, local duplications of CHST5 gave rise to CHST4 in the ancestor of tetrapods, and to CHST6 in the ancestor of primates.The teleost-specific gene duplicates were identified for CHST1, CHST2, and CHST3 and are result of whole-genome duplication (3R) in the teleost lineage. We could also detect multiple, more recent lineage-specific duplicates. Thus, the vertebrate repertoire of C6OST genes has been shaped by gene duplications and gene losses at several stages of vertebrate evolution, with implications for the evolution of skeleton, nervous system, and cell–cell interactions.

Organellar Genome Variation and Genetic Diversity of Chinese Pyropia yezoensis

Pyropia yezoensis is an economically important marine algae crop that, due to its large economic value, has generated considerable interest in the development of breeding programs to improve its production rates. Here, we sequenced the complete mitochondrial and plastid genomes of the P. yezoensis strain RZ-58 using PacBio RS II sequencing technology. The mitochondrial genome (mtDNA) is 41,692 bp in size with an overall GC content of 32.72%, and the plastid genome (ptDNA) is 191,977 bp with a GC content of 33.09%. The complete mitochondrial and plastid genomes of 53 individuals from 3 geographical populations were then resequenced using NGS technology to characterize their molecular features. When compared, the plastid genomes displayed similar genomic lengths and conserved gene synteny. However, mitochondrial genomes were quite different in length, which was mainly due to the different patterns of intron distributions. Single nucleotide polymorphisms (SNPs) were examined to evaluate the genetic diversity of different geographical populations. High diversity was observed across the whole collection with moderate genetic variation between populations. In total, there were 463 and 366 high-quality SNPs detected in the mtDNA and ptDNA, respectively. The Qingdao wild group has the highest diversity with a mean pi of 0.00348 for mtDNA and 0.000388 for ptDNA, while the Yantai group had the lowest diversity. Cluster based grouping and principal component analysis revealed three subpopulations in the whole collections. However, a genetic break of organellar DNA was observed in populations at sympatric localities, which was inferred as the result of historic biogeographic events. Our findings provide important information to guide the marker-assisted selective breeding of Chinese P. yezoensis in the future.

Isolation and Characterization of a Novel Klebsiella pneumoniae N4-like Bacteriophage KP8.

Klebsiella pneumoniae is a common pathogen, associated with a wide spectrum of infections, and clinical isolates of K. pneumoniae often possess multiple antibiotic resistances. Here, we describe a novel lytic N4-like bacteriophage KP8, specific to K. pneumoniae, including its genome, partial structural proteome, biological properties, and proposed taxonomy. Electron microscopy revealed that KP8 belongs to the Podoviridae family. The size of the KP8 genome was 73,679 bp, and it comprised 97 putative open reading frames. Comparative genome analysis revealed that the KP8 genome possessed the highest similarity to the genomes of Enquatrovirus and Gamaleyavirus phages, which are N4-like podoviruses. In addition, the KP8 genome showed gene synteny typical of the N4-like podoviruses and contained the gene encoding a large virion-encapsulated RNA polymerase. Phylogenetic analysis of the KP8 genome revealed that the KP8 genome formed a distinct branch within the clade, which included the members of Enquatrovirus and Gamaleyavirus genera besides KP8. The average evolutionary divergences KP8/Enquatrovirus and KP8/Gamaleyavirus were 0.466 and 0.447 substitutions per site (substitutes/site), respectively, similar to that between Enquatrovirus and Gamaleyavirus genera (0.468 substitutes/site). The obtained data suggested that Klebsiella phage KP8 differs from other similar phages and may represent a new genus within the N4-like phages.

Identification and modulation of expression of a TNF receptor superfamily member 25 homologue in grass carp (Ctenopharyngodon idella)

The TNF receptor superfamily member 25 (TNFRSF25) is part of the tumor necrosis factor receptor superfamily and contains a typical death domain. It is also known as DR3, TRAMP, LARD, WSL-1, Apo-3 and TR3, and has a vital role in regulating cell proliferation, differentiation and apoptosis. In this study, a homologue of the TNFRSF25 gene was identified in grass carp (Ctenopharyngodon idella). It encodes a transmembrane protein with an extracellular domain containing a cysteine-rich domain and an intracellular domain containing a death domain. It is an orthologue of fish TNFRSF1ALs and shares conserved gene synteny with human TNFRSF25. Expression studies showed that CiTNFRSF25 was constitutively expressed in the majority of fish tissues and can be modulated by interleukin 4/13B and infection by F. columnare. To our knowledge, this is the first report describing the existence of a TNFRSF25 homologue in teleost fish.

Basic helix–loop–helix (bHLH) gene family in Tartary buckwheat (Fagopyrum tataricum): Genome-wide identification, phylogeny, evolutionary expansion and expression analyses

Tartary buckwheat (Fagopyrum tataricum) a kind of edible and medicinal plant, is of great nutritional value. It is difficult to remove the hull of Tartary buckwheat fruit and breeding new easy-dehulled varieties has been one of the major breeding objectives. The bHLH gene family plays a vital role in plant growth and fruit dehiscence. In order to improve Tartary buckwheat breeding, we need to study the bHLH gene family for excavating genes with potential regulation of fruit development and dehiscence. Here, 164 Fagopyrum tataricum bHLH (FtbHLH) genes were identified. Analyses of gene structure and motif composition illustrate that the members of specific FtbHLH subfamily are relatively conserved. Synteny and phylogenetic analyses of bHLH genes in Tartary buckwheat and other plants lay a foundation for further exploring the evolutionary characteristic of the FtbHLH genes (FtbHLHs). qRT-PCR experiments showed that FtbHLHs expression patterns were different in plant organs, indicating that they may perform diverse functions. In addition, some genes that potentially regulate flower and fruit development and easy dehulling were screened out. Overall, this study will be helpful for further analyzing the biological function of FtbHLHs and provides clues for improving the genetic breeding and economic value of the Tartary buckwheat.

Screening for mouse genes lost in mammals with long lifespans

BackgroundGerontogenes include those that modulate life expectancy in various species and may be the actual longevity genes. We believe that a long (relative to body weight) lifespan in individual rodent and primate species can be due, among other things, to the loss of particular genes that are present in short-lived species of the same orders. These genes can also explain the widely different rates of aging among diverse species as well as why similarly sized rodents or primates sometimes have anomalous life expectancies (e.g., naked mole-rats and humans). Here, we consider the gene loss in the context of the prediction of Williams’ theory that concerns the reallocation of physiological resources of an organism between active reproduction (r-strategy) and self-maintenance (K-strategy). We have identified such lost genes using an original computer-aided approach; the software considers the loss of a gene as disruptions in gene orthology, local gene synteny or both.ResultsA method and software identifying the genes that are absent from a predefined set of species but present in another predefined set of species are suggested. Examples of such pairs of sets include long-lived vs short-lived, homeothermic vs poikilothermic, amniotic vs anamniotic, aquatic vs terrestrial, and neotenic vs nonneotenic species, among others. Species are included in one of two sets according to the property of interest, such as longevity or homeothermy. The program is universal towards these pairs, i.e., towards the underlying property, although the sets should include species with quality genome assemblies. Here, the proposed method was applied to study the longevity of Euarchontoglires species. It largely predicted genes that are highly expressed in the testis, epididymis, uterus, mammary glands, and the vomeronasal and other reproduction-related organs. This agrees with Williams’ theory that hypothesizes a species transition from r-strategy to K-strategy. For instance, the method predicts the mouse gene Smpd5, which has an expression level 20 times greater in the testis than in organs unrelated to reproduction as experimentally demonstrated elsewhere. At the same time, its paralog Smpd3 is not predicted by the program and is widely expressed in many organs not specifically related to reproduction.ConclusionsThe method and program, which were applied here to screen for gene losses that can accompany increased lifespan, were also applied to study reduced regenerative capacity and development of the telencephalon, neoteny, etc. Some of these results have been carefully tested experimentally. Therefore, we assume that the method is widely applicable.