Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax

Fang, Xiaodong; Nevo, Eviatar; Han, Lijuan; Levanon, Erez Y.; Zhao, Jing; Avivi, Aaron; Larkin, Denis M.; Jiang, Xuanting; Feranchuk, Sergey; Zhu, Yabing; Fishman, Ayelet; Feng, Yue; Sher, Noa; Xiong, Zhiqiang; Hankeln, Thomas; Huang, Zhiyong; Gorbunova, Vera; Zhang, Lu; Zhao, Wei; Wildman, Derek E.; Xiong, Yingqi; Gudkov, Andrei V.; Zheng, Qiumei; Rechavi, Gideon; Liu, Sanyang; Bazak, Lily; Chen, Jie; Knisbacher, Binyamin A.; Lu, Yao; Shams, Imad; Gajda, Krzysztof; Farré, Marta; Kim, Jaebum; Lewin, Harris A.; Ma, Jian; Band, Mark; Bicker, Anne; Kranz, Angela; Mattheus, Tobias; Schmidt, Hanno; Seluanov, Andrei; Azpurua, Jorge; McGowen, Michael R.; Jacob, Eshel Ben; Li, Kexin; Peng, Shaoliang; Zhu, Xinhua; Liao, Xiangke; Li, Shuai Cheng; Krogh, Anders; Zhou, Xin; Brodsky, Leonid; Wang, Jun

doi:10.1038/ncomms4966

Cited by 131 publications

(147 citation statements)

References 68 publications

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“…S11). This coincides with the previous observations of increased genetic diversity in molecular markers (AFLP), mtDNA, and whole genome in the ancestral chalk population (21). To identify soil population-specific differences in RNA editing, two analyses were conducted-one of the major retroelement families (B1, B2, and B4) and the other of sites in mRNA known to be evolutionarily conserved RNA-editing targets in mammals (23) (SI Appendix).…”

Section: Dna-and Rna-editing Comparison Between Spalax Chalk and Basaltmentioning

confidence: 85%

Transcriptome, genetic editing, and microRNA divergence substantiate sympatric speciation of blind mole rat, Spalax

Wang

Knisbacher³

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Incipient sympatric speciation in blind mole rat, Spalax galili, in Israel, caused by sharp ecological divergence of abutting chalkbasalt ecologies, has been proposed previously based on mitochondrial and whole-genome nuclear DNA. Here, we present new evidence, including transcriptome, DNA editing, microRNA, and codon usage, substantiating earlier evidence for adaptive divergence in the abutting chalk and basalt populations. Genetic divergence, based on the previous and new evidence, is ongoing despite restricted gene flow between the two populations. The principal component analysis, neighbor-joining tree, and genetic structure analysis of the transcriptome clearly show the clustered divergent two mole rat populations. Gene-expression level analysis indicates that the population transcriptome divergence is displayed not only by soil divergence but also by sex. Gene ontology enrichment of the differentially expressed genes from the two abutting soil populations highlights reproductive isolation. Alternative splicing variation of the two abutting soil populations displays two distinct splicing patterns. L-shaped F ST distribution indicates that the two populations have undergone divergence with gene flow. Transcriptome divergent genes highlight neurogenetics and nutrition characterizing the chalk population, and energetics, metabolism, musculature, and sensory perception characterizing the abutting basalt population. Remarkably, microRNAs also display divergence between the two populations. The GC content is significantly higher in chalk than in basalt, and stress-response genes mostly prefer nonoptimal codons. The multiple lines of evidence of ecologicalgenomic and genetic divergence highlight that natural selection overrules the gene flow between the two abutting populations, substantiating the sharp ecological chalk-basalt divergence driving sympatric speciation.natural selection | ecological adaptive speciation | DNA editing | microRNA regulation | nonoptimal codon usage

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Section: Dna-and Rna-editing Comparison Between Spalax Chalk and Basaltmentioning

confidence: 85%

Transcriptome, genetic editing, and microRNA divergence substantiate sympatric speciation of blind mole rat, Spalax

Wang

Knisbacher³

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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“…Explanations may perhaps be sought in the restrictions inevitably connected with the methods used in the genetic studies of Table 2 and in the incompleteness inherent to the fossil record. New insights may be obtained through the application of advanced molecular genetic techniques (genome and transcriptome sequencing) such as those which have already been used for rhizomyine and spalacine species by Zhao et al (2013), Fang et al (2014) and Lin et al (2014). Although the fossil record of the Rhizomyinae and Spalacinae is relatively good, it is clear that much of the earliest history of these subfamilies is not documented.…”

Section: Discussionmentioning

confidence: 99%

Are the Rhizomyinae and the Spalacinae closely related? Contradistinctive conclusions between genetics and palaeontology

Bruijn

Bosma

Wessels

2015

Palaeobio Palaeoenv

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The reconstruction of the evolutionary history of the Rhizomyinae and the Spalacinae based on the fossil record strongly suggests that these do not share the same murid ancestor and developed separately since the early Oligocene. This conclusion is supported by the difference in evolutionary dynamics between these groups during the Miocene and Pliocene. Molecular genetic studies of extant representatives of the Rhizomyinae, Spalacinae and Myospalacinae, however, suggest that these subfamilies share similarities that distinguish them from all other Muridae. As a result, geneticists unite these subfamilies into the family Spalacidae and consider the Spalacidae and the Muridae to be sister lineages. Until the conflict between the two disciplines is resolved we prefer to maintain the Rhizomyinae and the Spalacinae as two subfamilies within the family Muridae (superfamily Muroidea).

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“…It is worth mentioning that, unlike RACA, other reference-assisted assembly algorithms, e.g., Ragout (Kolmogorov et al 2014) or Chromosomer (Tamazian et al 2016), do not use the target genome short-and long-range paired-read data to verify synteny breaks in/between scaffolds, meaning that the target species-specific rearrangements could be missed from the reconstructed PCFs/pseudochromosomes, making the reconstructed target chromosome structures more heavily biased to the reference genome(s) than when using RACA. RACA algorithm applied to the Tibetan antelope and blind mole rat genomes significantly improved continuities of these assemblies, but they still contain more than one large PCF for most chromosomes (Kim et al 2013;Fang et al 2014). Therefore, a novel, integrative approach that would allow de novo assembled genomes to retain structures of the target species karyotypes is a necessity.…”

Section: [Supplemental Materials Is Available For This Article]mentioning

confidence: 99%

Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set

et al. 2016

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Most recent initiatives to sequence and assemble new species' genomes de novo fail to achieve the ultimate endpoint to produce contigs, each representing one whole chromosome. Even the best-assembled genomes (using contemporary technologies) consist of subchromosomal-sized scaffolds. To circumvent this problem, we developed a novel approach that combines computational algorithms to merge scaffolds into chromosomal fragments, PCR-based scaffold verification, and physical mapping to chromosomes. Multigenome-alignment-guided probe selection led to the development of a set of universal avian BAC clones that permit rapid anchoring of multiple scaffolds to chromosomes on all avian genomes. As proof of principle, we assembled genomes of the pigeon (Columbia livia) and peregrine falcon (Falco peregrinus) to chromosome levels comparable, in continuity, to avian reference genomes. Both species are of interest for breeding, cultural, food, and/or environmental reasons. Pigeon has a typical avian karyotype (2n = 80), while falcon (2n = 50) is highly rearranged compared to the avian ancestor. By using chromosome breakpoint data, we established that avian interchromosomal breakpoints appear in the regions of low density of conserved noncoding elements (CNEs) and that the chromosomal fission sites are further limited to long CNE "deserts." This corresponds with fission being the rarest type of rearrangement in avian genome evolution. High-throughput multiple hybridization and rapid capture strategies using the current BAC set provide the basis for assembling numerous avian (and possibly other reptilian) species, while the overall strategy for scaffold assembly and mapping provides the basis for an approach that (provided metaphases can be generated) could be applied to any animal genome.

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Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax

Cited by 131 publications

References 68 publications

Transcriptome, genetic editing, and microRNA divergence substantiate sympatric speciation of blind mole rat, Spalax

Transcriptome, genetic editing, and microRNA divergence substantiate sympatric speciation of blind mole rat, Spalax

Are the Rhizomyinae and the Spalacinae closely related? Contradistinctive conclusions between genetics and palaeontology

Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set

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