Chromosomal instability in Afrotheria: fragile sites, evolutionary breakpoints and phylogenetic inference from genome sequence assemblies

Background: Extant placental mammals are divided into four major clades (Laurasiatheria, Supraprimates, Xenarthra and Afrotheria). Given that Afrotheria is generally thought to root the eutherian tree in phylogenetic analysis of large nuclear gene data sets, the study of the organization of the genomes of afrotherian species provides new insights into the dynamics of mammalian chromosomal evolution. Here we test if there are chromosomal bands with a high tendency to break and reorganize in Afrotheria, and by analyzing the expression of aphidicolin-induced common fragile sites in three afrotherian species, whether these are coincidental with recognized evolutionary breakpoints. Results: We described 29 fragile sites in the aardvark (OAF) genome, 27 in the golden mole (CAS), and 35 in the elephant-shrew (EED) genome. We show that fragile sites are conserved among afrotherian species and these are correlated with evolutionary breakpoints when compared to the human (HSA) genome. Inddition, by computationally scanning the newly released opossum (Monodelphis domestica) and chicken sequence assemblies for use as outgroups to Placentalia, we validate the HSA 3/21/5 chromosomal synteny as a rare genomic change that defines the monophyly of this ancient African clade of mammals. On the other hand, support for HSA 1/19p, which is also thought to underpin Afrotheria, is currently ambiguous. Conclusion: We provide evidence that (i) the evolutionary breakpoints that characterise human syntenies detected in the basal Afrotheria correspond at the chromosomal band level with fragile sites, (ii) that HSA 3p/21 was in the amniote ancestor (i.e., common to turtles, lepidosaurs, crocodilians, birds and mammals) and was subsequently disrupted in the lineage leading to marsupials. Its expansion to include HSA 5 in Afrotheria is unique and (iii) that its fragmentation to HSA 3p/21 + HSA 5/21 in elephant and manatee was due to a fission within HSA 21 that is probably shared by all Paenungulata

Identifiquen un nou fenomen de variació de les taxes de recombinació meiòtica com a estratègia de supervivència evolutiva de les espècies

Un estudi realitzat per investigadors de les universitats de Harvard (EUA), Shandong (Xina), Nantong (Xina) i Paris Sud (França), amb participació de la Dra. Aurora Ruiz-Herrera, professora del Departament de Biologia Cel·lular, Fisiologia i Immunologia de la UAB i investigadora de l'IBB-UAB, ha identificat un nou fenomen de variació de les taxes de recombinació meiòtica durant la formació de les cèl·lules germinals. Aquest fenomen representaria una estratègia evolutiva adaptativa conservada en espècies animals i vegetals. El treball es publica a la revista Cell.Un estudio realizado por investigadores de las universidades de Harvard (EE.UU.), Shandong (China), Nantong (China) y Paris Sud (Francia), con participación de la Dra. Aurora Ruiz-Herrera, profesora del Departamento de Biología Celular, Fisiología e Inmunología de la UAB e investigadora del IBB-UAB, ha identificado un nuevo fenómeno de variación de las tasas de recombinación meiótica durante la formación de las células germinales. Este fenómeno representaría una estrategia evolutiva adaptativa conservada en especies animales y vegetales. El trabajo se publica en la revista Cell

Implicaciones de los lugares frágiles y las secuencias teloméricas intersticiales en la evolución cromosómica de los primates

Descripció del recurs: el 13 de juliol de 2004El objetivo principal de la presente tesis doctoral ha consistido en la comprobación de la siguiente hipótesis de trabajo: las bandas cromosómicas implicadas en reorganizaciones cromosómicas evolutivas podrían ser la expresión de regiones cromosómicas inestables, como son los lugares frágiles. Al mismo tiempo, las secuencias teloméricas en regiones internes de los cromosomas podrían ser el resultado de reorganizaciones cromosómicas evolutivas. Para cumplir dicho objetivo se han descrito, en primer lugar la descripción de homologías cromosómicas entre cariotipos de diferentes especies de Primates, y determinar las reorganizaciones cromosómicas que explican dichas homologías, así como las bandas cromosómicas implicadas en dichas reorganizaciones. Las especies de Primates estudiadas han sido: Macaca fascicularis, Macaca arctoides, Mandrillus sphinx, Cebus apella, Cebus nigrivittatus y Homo sapiens. En segundo lugar, se ha analizado la expresión citogenética de los lugares frágiles en las especies de Primates caracterizadas y se ha comparado su localización con los lugares frágiles descritos en la especie humana en la literatura con la finalidad de determinar si dichas regiones se han conservado durante el proceso evolutivo. Al mismo tiempo se ha estudiado la distribución de las secuencias teloméricas en posiciones internas de los cromosomas de las especies Macaca fascicularis, Cebus apella. Y por último, se ha relacionado la localización de lugares frágiles y la distribución de las secuencias teloméricas intersticiales con las bandas cromosómicas implicadas en reorganizaciones evolutivas. Por tanto, el uso combinado de las técnicas de citogenética clásica e hibridación in situ fluorescente (FISH) ha permitido: (1) la caracterización citogenética de la especies de Primates estudiadas en el presente trabajo, (2) establecer las homologías cromosómicas entre sus cariotipos y el cariotipo humano, (3) determinar las reorganizaciones que explicarían dichas homologías y (4) identificar las bandas cromosómicas implicadas en dichas reorganizaciones. El estudio comparativo de la localización de los lugares frágiles muestra que existe una conservación entre las especies de primates estudiadas. Como resultado significativo, cabe destacar que las reorganizaciones cromosómicas evolutivas no se distribuyen al azar, ya que existe una correlación positiva con la localización de los lugares frágiles. Como conclusión final, hemos podido establecer una clara relación entre puntos de rotura evolutivos, bandas cromosómicas que expresan lugares frágiles y la localización de secuencias teloméricas intersticiales

Is mammalian chromosomal evolution driven by regions of genome fragility?

BACKGROUND: A fundamental question in comparative genomics concerns the identification of mechanisms that underpin chromosomal change. In an attempt to shed light on the dynamics of mammalian genome evolution, we analyzed the distribution of syntenic blocks, evolutionary breakpoint regions, and evolutionary breakpoints taken from public databases available for seven eutherian species (mouse, rat, cattle, dog, pig, cat, and horse) and the chicken, and examined these for correspondence with human fragile sites and tandem repeats. RESULTS: Our results confirm previous investigations that showed the presence of chromosomal regions in the human genome that have been repeatedly used as illustrated by a high breakpoint accumulation in certain chromosomes and chromosomal bands. We show, however, that there is a striking correspondence between fragile site location, the positions of evolutionary breakpoints, and the distribution of tandem repeats throughout the human genome, which similarly reflect a non-uniform pattern of occurrence. CONCLUSION: These observations provide further evidence that certain chromosomal regions in the human genome have been repeatedly used in the evolutionary process. As a consequence, the genome is a composite of fragile regions prone to reorganization that have been conserved in different lineages, and genomic tracts that do not exhibit the same levels of evolutionary plasticity

Turvapaikkatutkinnan sanasto

Sanglakhi, Fahima. Turvapaikkatutkinnan sanasto, suomi-persia-englanti. Helsinki, kevät 2015, 37 s., liitteitä 1. Diakonia-ammattikorkeakoulu, Diak Etelä. Asioimistulkkauksen koulutusohjelma, Tulkki (AMK) Kaksikielisten sanastojen puutteen vuoksi, varsinkin kieliparilla suomi-persia, tunsin tarvetta sanaston laatimiseen. Opinnäytetyö on kehittämispainotteinen eli toiminnallinen, jonka tuloksena syntyy uusi tuote. Tämän opinnäytetyön tavoitteena oli tehdä suppea turvapaikkatutkinnan sanasto työkielissä suomi-persia-englanti. Sanasto voi auttaa persian- ja darinkielistä tulkkia valmistautumisessa toimeksiantoihin. Uudistetun asioimistulkkien ammattisäännöstön viidennen kohdan mukaan valmistautumisella tarkoitetaan sitä, että tulkin on perehdyttävä tulkkausaiheeseen ja sen edellyttämään sanastoon ja terminologiaan molemmilla työkielillä. Opinnäytetyön tarkoitus oli helpottaa persian ja darin kielen tulkkien työtä turvapaik-katutkinnassa ja auttaa heitä välittämään viestiä paremmin vaikeista termeistä huolimatta. Opinnäytetyössä aineistona on käytetty Suomen maahanmuuttoviraston kotisivuilla olevaa sanastoa ja pakolaisneuvonnan ja maahanmuuttoviraston yhteistyössä julkistamaa Opas tulkeille -kirjan sanastoa. Sanastoa laadin ensin keräämällä suomenkielisiä termejä ja myöhemmin etsimällä niiden vastineita persiaksi ja englanniksi. Aineisto koostu 157 suomenkielisestä termistä ja niiden vastineista persian ja englannin kielellä. Sanastosta on hyötyä tulkeille, kääntäjille ja opiskelijoille, jotka työskentelevät maahanmuuttoalalla tai ovat muutenkin kiinnostuneita tästä aiheesta. Asiasanat: sanastotyö, persian kieli, suomen kieli, sanastot, maahanmuutto, turvapaikanhakijat, asioimistulkkausSanglakhi, Fahima. Asylum investigation glossary in Finnish, Persian and English. Helsinki, spring 2015, p 37, 1 appendix Diaconia University of Applied Sciences, Diak South. Degree Programme in Community Interpreting, Degree: Interpreter Due to the lack of multilingual glossaries especially in the language pairs of Finnish- Persian, it was necessary to draft a glossary in the field of migration. Aim of this thesis was to make a concise asylum investigation glossary in language pairs of Finnish-Persian-English, which could help Persian and Dari language interpreters in preparing for their assignments. The purpose of this thesis was to facilitate Persian and Dari language interpreters' work in asylum investigation field and help them to forward the messages better, despite the tough terms. The thesis material consisted of glossary of Finnish immigration website and glossary of Interpretation in the asylum processes which were published by collaboration of the Finnish Immigration and Refugee advice centre. I found 157 terms. The glossary was compiled first by collecting Finnish terms and later looking for their equivalents in Persian and English. A glossary is useful for all Persian and Dari language interpreters, translators and students who work and study in the field of immigration or are otherwise interested in this topic

Molecular cytogenetic and genomic insights to chromosomal evolution

This review summarizes aspects of the extensive literature on the patterns and processes underpinning chromosomal evolution in vertebrates and especially placental mammals. It highlights the growing synergy between molecular cytogenetics and comparative genomics, particularly with respect to fully or partially sequenced genomes, and provides novel insights into changes in chromosome number and structure across deep division of the vertebrate tree of life. The examination of basal numbers in the deeper branches of the vertebrate tree suggest a haploid (n) chromosome number of 10–13 in an ancestral vertebrate, with modest increases in tetrapods and amniotes most probably by chromosomal fissioning. Information drawn largely from cross-species chromosome painting in the data-dense Placentalia permits the confident reconstruction of an ancestral karyotype comprising n=23 chromosomes that is similarly retained in Boreoeutheria. Using in silico genome-wide scans that include the newly released frog genome we show that of the nine ancient syntenies detected in conserved karyotypes of extant placentals (thought likely to reflect the structure of ancestral chromosomes), the human syntenic segmental associations 3p/21, 4pq/8p, 7a/16p, 14/15, 12qt/22q and 12pq/22qt predate the divergence of tetrapods. These findings underscore the enhanced quality of ancestral reconstructions based on the integrative molecular cytogenetic and comparative genomic approaches that collectively highlight a pattern of conserved syntenic associations that extends back ∼360 million years ago

Recombination rates and genomic shuffling in human and chimpanzee – a new twist in the chromosomal speciation theory

A long-standing question in evolutionary biology concerns the effect of recombination in shaping the genomic architecture of organisms and, in particular, how this impacts the speciation process. Despite efforts employed in the last decade, the role of chromosomal reorganizations in the human–chimpanzee speciation process remains unresolved. Through whole-genome comparisons, we have analyzed the genome-wide impact of genomic shuffling in the distribution of human recombination rates during the human–chimpanzee speciation process. We have constructed a highly refined map of the reorganizations and evolutionary breakpoint regions in the human and chimpanzee genomes based on orthologous genes and genome sequence alignments. The analysis of the most recent human and chimpanzee recombination maps inferred from genome-wide single-nucleotide polymorphism data revealed that the standardized recombination rate was significantly lower in rearranged than in collinear chromosomes. In fact, rearranged chromosomes presented significantly lower recombination rates than chromosomes that have been maintained since the ancestor of great apes, and this was related with the lineage in which they become fixed. Importantly, inverted regions had lower recombination rates than collinear and noninverted regions, independently of the effect of centromeres. Our observations have implications for the chromosomal speciation theory, providing new evidences for the contribution of inversions in suppressing recombination in mammals.This work was supported by the Ministerio de Ciencia y Tecnologia (CGL-2010-20170) and the Universitat Autònoma de Barcelona (PhD fellowship to M.F.).Peer reviewe

Assessing the Role of Tandem Repeats in Shaping the Genomic Architecture of Great Apes

Background: Ancestral reconstructions of mammalian genomes have revealed that evolutionary breakpoint regions are clustered in regions that are more prone to break and reorganize. What is still unclear to evolutionary biologists is whether these regions are physically unstable due solely to sequence composition and/or genome organization, or do they represent genomic areas where the selection against breakpoints is minimal. Methodology and Principal Findings: Here we present a comprehensive study of the distribution of tandem repeats in great apes. We analyzed the distribution of tandem repeats in relation to the localization of evolutionary breakpoint regions in the human, chimpanzee, orangutan and macaque genomes. We observed an accumulation of tandem repeats in the genomic regions implicated in chromosomal reorganizations. In the case of the human genome our analyses revealed that evolutionary breakpoint regions contained more base pairs implicated in tandem repeats compared to synteny blocks, being the AAAT motif the most frequently involved in evolutionary regions. We found that those AAAT repeats located in evolutionary regions were preferentially associated with Alu elements. Significance: Our observations provide evidence for the role of tandem repeats in shaping mammalian genome architecture. We hypothesize that an accumulation of specific tandem repeats in evolutionary regions can promote genome instability by altering the state of the chromatin conformation or by promoting the insertion of transposable elements

Unraveling the effect of genomic structural changes in the rhesus macaque - implications for the adaptive role of inversions

Background: By reshuffling genomes, structural genomic reorganizations provide genetic variation on which natural selection can work. Understanding the mechanisms underlying this process has been a long-standing question in evolutionary biology. In this context, our purpose in this study is to characterize the genomic regions involved in structural rearrangements between human and macaque genomes and determine their influence on meiotic recombination as a way to explore the adaptive role of genome shuffling in mammalian evolution. Results: We first constructed a highly refined map of the structural rearrangements and evolutionary breakpoint regions in the human and rhesus macaque genomes based on orthologous genes and whole-genome sequence alignments. Using two different algorithms, we refined the genomic position of known rearrangements previously reported by cytogenetic approaches and described new putative micro-rearrangements (inversions and indels) in both genomes. A detailed analysis of the rhesus macaque genome showed that evolutionary breakpoints are in gene-rich regions, being enriched in GO terms related to immune system. We also identified defense-response genes within a chromosome inversion fixed in the macaque lineage, underlying the relevance of structural genomic changes in evolutionary and/or adaptation processes. Moreover, by combining in silico and experimental approaches, we studied the recombination pattern of specific chromosomes that have suffered rearrangements between human and macaque lineages. Conclusions: Our data suggest that adaptive alleles – in this case, genes involved in the immune response – might have been favored by genome rearrangements in the macaque lineage