Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs

O'Connor, Rebecca E; Romanov, Michael N; Kiazim, Lucas G.; Barrett, Paul M.; Farré, Marta; Damas, Joana; Ferguson‐Smith, Malcolm A.; Valenzuela, Nicole; Larkin, Denis M.; Griffin, Darren K.

doi:10.1038/s41467-018-04267-9

Cited by 68 publications

(99 citation statements)

References 51 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…S4). Further, the presence of microchromosomes in most extant diapsids (Olmo 2005;Organ et al 2008), the ancestral diapsid genome (O'Connor et al 2018), amphibians (Voss et al 2011), and fish (Braasch et al 2015) broadly suggest that the majority of vertebrate evolution has been shaped by the distinctive but poorly understood biology of microchromosomes.…”

Section: Synteny and Chromosomal Compositionmentioning

confidence: 99%

The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes

et al. 2019

View full text Add to dashboard Cite

Here we use a chromosome-level genome assembly of a prairie rattlesnake (Crotalus viridis), together with Hi-C, RNA-seq, and whole-genome resequencing data, to study key features of genome biology and evolution in reptiles. We identify the rattlesnake Z Chromosome, including the recombining pseudoautosomal region, and find evidence for partial dosage compensation driven by an evolutionary accumulation of a female-biased up-regulation mechanism. Comparative analyses with other amniotes provide new insight into the origins, structure, and function of reptile microchromosomes, which we demonstrate have markedly different structure and function compared to macrochromosomes. Snake microchromosomes are also enriched for venom genes, which we show have evolved through multiple tandem duplication events in multiple gene families. By overlaying chromatin structure information and gene expression data, we find evidence for venom gene-specific chromatin contact domains and identify how chromatin structure guides precise expression of multiple venom gene families. Further, we find evidence for venom gland-specific transcription factor activity and characterize a complement of mechanisms underlying venom production and regulation. Our findings reveal novel and fundamental features of reptile genome biology, provide insight into the regulation of snake venom, and broadly highlight the biological insight enabled by chromosome-level genome assemblies.

show abstract

Section: Synteny and Chromosomal Compositionmentioning

confidence: 99%

The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes

et al. 2019

View full text Add to dashboard Cite

show abstract

“…Chromosome-level assemblies also inform studies of evolution and speciation given that inter-species differences arise from chromosomal changes fixed during evolution [ 29 – 35 ]. In recent studies, we have used (near) chromosome-level assemblies to reconstruct ancestral karyotypes and trace inter- and intrachromosomal changes that have occurred to generate the karyotypes of extant species [ 28 , 36 ]. Theories explaining the mechanisms of chromosomal change in vertebrates include a role for repetitive sequences used for non-allelic homologous recombination (NAHR) in evolutionary breakpoint regions (EBRs) [ 37 ] and the proximity of DNA regions in chromatin [ 38 ].…”

Section: Introductionmentioning

confidence: 99%

Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes

et al. 2018

Self Cite

View full text Add to dashboard Cite

BackgroundThe number of de novo genome sequence assemblies is increasing exponentially; however, relatively few contain one scaffold/contig per chromosome. Such assemblies are essential for studies of genotype-to-phenotype association, gross genomic evolution, and speciation. Inter-species differences can arise from chromosomal changes fixed during evolution, and we previously hypothesized that a higher fraction of elements under negative selection contributed to avian-specific phenotypes and avian genome organization stability. The objective of this study is to generate chromosome-level assemblies of three avian species (saker falcon, budgerigar, and ostrich) previously reported as karyotypically rearranged compared to most birds. We also test the hypothesis that the density of conserved non-coding elements is associated with the positions of evolutionary breakpoint regions.ResultsWe used reference-assisted chromosome assembly, PCR, and lab-based molecular approaches, to generate chromosome-level assemblies of the three species. We mapped inter- and intrachromosomal changes from the avian ancestor, finding no interchromosomal rearrangements in the ostrich genome, despite it being previously described as chromosomally rearranged. We found that the average density of conserved non-coding elements in evolutionary breakpoint regions is significantly reduced. Fission evolutionary breakpoint regions have the lowest conserved non-coding element density, and intrachromomosomal evolutionary breakpoint regions have the highest.ConclusionsThe tools used here can generate inexpensive, efficient chromosome-level assemblies, with > 80% assigned to chromosomes, which is comparable to genomes assembled using high-density physical or genetic mapping. Moreover, conserved non-coding elements are important factors in defining where rearrangements, especially interchromosomal, are fixed during evolution without deleterious effects.Electronic supplementary materialThe online version of this article (10.1186/s13059-018-1550-x) contains supplementary material, which is available to authorized users.

show abstract

“…A typical avian karyotype has a 2n of 76-80, consisting of a few large-tointermediate-sized chromosomes and many small (<10 Mb) chromosomes. Also, avian karyotypes are more stable because interchromosomal rearrangements are rare, except in certain groups (e.g., Psittaciformes and Falconiformes) where it is clear that karyotypes are highly rearranged [7][8][9]. Domestic Galloanserae (ducks, fowls and relatives) are one of the bird groups with lower rates of chromosomal rearrangements [10], with chicken chromosomes closely resembling the putative ancestral karyotype (PAK) of birds [11,12].…”

Section: Introductionmentioning

confidence: 99%

MLH1 focus mapping in the guinea fowl (Numida meleagris) give insights into the crossover landscapes in birds

Priore

Pigozzi

2020

PLoS ONE

View full text Add to dashboard Cite

Crossover rates and localization are not homogeneous throughout the genomes. Along the chromosomes of almost all species, domains with high crossover rates alternate with domains where crossover rates are significantly lower than the genome-wide average. The distribution of crossovers along chromosomes constitutes the recombination landscape of a given species and can be analyzed at broadscale using immunostaining of the MLH1 protein, a component of mature recombination nodules found on synaptonemal complexes during pachytene. We scored the MLH1 foci in oocytes of the chicken and the guinea fowl and compared their frequencies in the largest bivalents. The average autosomal number of foci is 62 in the chicken and 44 in the guinea fowl. The lower number in the guinea fowl responds to the occurrence of fewer crossovers in the six largest bivalents, where most MLH1 foci occur within one-fifth of the chromosome length with high polarization towards opposite ends. The skewed distribution of foci in the guinea fowl contrast with the more uniform distribution of numerous foci in the chicken, especially in the four largest bivalents. The crossover distribution observed in the guinea fowl is unusual among Galloanserae and also differs from other, more distantly related birds. We discussed the current evidence showing that the shift towards crossover localization, as observed in the guinea fowl, was not a unique event but also occurred at different moments of bird evolution. A comparative analysis of genome-wide average recombination rates in birds shows variations within narrower limits compared to mammals and the absence of a phylogenetic trend.

show abstract

Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs

Cited by 68 publications

References 51 publications

The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes

The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes

Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes

MLH1 focus mapping in the guinea fowl (Numida meleagris) give insights into the crossover landscapes in birds

Contact Info

Product

Resources

About