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

Ruiz‐Herrera, Aurora; Robinson, Terence J.

doi:10.1186/1471-2148-7-199

Cited by 39 publications

(24 citation statements)

References 89 publications

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“…This synteny appears not to exist in opossum, but it is present in chicken (Ruiz-Herrera & Robinson 2007) and both the pufferfish and zebrafish genomes (Kohn et al 2006 and their supplementary data) making it a symplesiomorphy for Eutheria. Opossum has a synteny (21/Xp/3q/Xp/3q) in chromosome 4 and another (3p/3q/Xp) in chromosome 7, implying breakpoints different from those of the eutherian synteny (Ruiz-Herrera & Robinson 2007). These data suggest that 3p/21 was present in the common ancestor of vertebrates (õ450 Mya) and amniotes (õ310 Mya) (turtles, lepidosaurs, crocodilians, birds and mammals), but was subsequently disrupted in the lineage leading to marsupials.…”

Section: Human Segment 3/21mentioning

confidence: 92%

Defining the ancestral eutherian karyotype: A cladistic interpretation of chromosome painting and genome sequence assembly data

Robinson

Ruiz‐Herrera

2008

Chromosome Res

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A cladistic analysis of genome assemblies (syntenic associations) for eutherian mammals against two distant outgroup species--opossum and chicken--permitted a refinement of the 46-chromosome karyotype formerly inferred in the ancestral eutherian. We show that two intact chromosome pairs (corresponding to human chromosomes 13 and 18) and three conserved chromosome segments (10q, 19p and 8q in the human karyotype) are probably symplesiomorphic for Eutheria because they are also present as unaltered orthologues in one or both outgroups. Seven additional syntenies (4q/8p/4pq, 3p/21, 14/15, 10p/12pq/22qt, 19q/16q, 16p/7a and 12qt/22q), each involving human chromosomal segments that in various combinations correspond to complete chromosomes in the ancestral eutherian karyotype, are also present in one or both outgroup taxa and thus are probable symplesiomorphies for Eutheria. Interestingly, several of the symplesiomorphic characters identified in chicken and/or opossum are present in more distant outgroups such as pufferfish and zebrafish (for example 3p/21, 14/15, 19q/16q and 16p/7a), suggesting their retention since vertebrate common ancestry approximately 450 million years ago. However, eight intact pairs (corresponding to human chromosomes 1, 5, 6, 9, 11, 17, 20 and the X) and three chromosome segments (7b, 2p-q13 and 2q13-qter) are derived characters potentially consistent with eutherian monophyly. Our analyses clarify the distinction between shared-ancestral and shared-derived homology in the eutherian ancestral karyotype.

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Section: Human Segment 3/21mentioning

confidence: 92%

Defining the ancestral eutherian karyotype: A cladistic interpretation of chromosome painting and genome sequence assembly data

Robinson

Ruiz‐Herrera

2008

Chromosome Res

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“…see Refs 12-14, but also see Ref. 15). It was, however, the development of molecular cytogenetics in the 1990s that revolutionized the field providing a new dimension to comparative genomic studies.…”

Section: Introductionmentioning

confidence: 95%

Evolutionary plasticity and cancer breakpoints in human chromosome 3

Ruiz‐Herrera

Robinson

2008

BioEssays

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In this review, we focus on the evolutionary and biomedical aspects of the architecture of human chromosome 3 (HSA3) by analyzing chromosomal regions that have been conserved during the evolutionary process, compared to those that have been involved in the genomic restructuring of different placental lineages. Given that the organization of human chromosome 3 is derived when compared to the ancestral primate karyotype, and is an autosome that is commonly implicated in human tumour formation, we examined the patterns of change and the genomic consequences that have resulted from its complex evolutionary history. The data show four discrete chromosomal regions that are frequently implicated in chromosomal rearrangements (3p25, 3p22, 3p12 and 3q21). These are rich in repetitive elements and are commonly implicated in structural rearrangements that underpin human genomic disorders and neoplasias. Additional Supporting Information may be found in the online version of this article.

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“…Although some ambiguity and points of contention remain, (13,14) the trend of genomic-scale phylogenetics for living mammals continues. (15,16) Extended taxon sampling applied to mitochondrial genomes, (17,18) together with analyses of chromosomal data, (19) are largely consistent with the nuclear-genomic phylogenies that sample across placental mammal orders, supporting the basic topology first made explicit at the turn of this century. (20)(21)(22)(23) While this consensus has yielded some ambiguous is now resolved into a well-supported, high-level phylogeny ( Fig.…”

Section: Introductionmentioning

confidence: 98%

The new framework for understanding placental mammal evolution

2009

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An unprecedented level of confidence has recently crystallized around a new hypothesis of how living placental mammals share a pattern of common descent. The major groups are afrotheres (e.g., aardvarks, elephants), xenarthrans (e.g., anteaters, sloths), laurasiatheres (e.g., horses, shrews), and euarchontoglires (e.g., humans, rodents). Compared with previous hypotheses this tree is remarkably stable; however, some uncertainty persists about the location of the placental root, and (for example) the position of bats within laurasiatheres, of sea cows and aardvarks within afrotheres, and of dermopterans within euarchontoglires. A variety of names for sub‐clades within the new placental mammal tree have been proposed, not all of which follow conventions regarding priority and stability. More importantly, the new phylogenetic framework enables the formulation of new hypotheses and testing thereof, for example regarding the possible developmental dichotomy that seems to distinguish members of the newly identified southern and northern radiations of living placental mammals.

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

Cited by 39 publications

References 89 publications

Defining the ancestral eutherian karyotype: A cladistic interpretation of chromosome painting and genome sequence assembly data

Defining the ancestral eutherian karyotype: A cladistic interpretation of chromosome painting and genome sequence assembly data

Evolutionary plasticity and cancer breakpoints in human chromosome 3

The new framework for understanding placental mammal evolution

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