Human inversions and their functional consequences

Puig, Marta; Casillas, Sònia; Villatoro, Sergi; Cáceres, Mario

doi:10.1093/bfgp/elv020

Cited by 114 publications

(118 citation statements)

References 106 publications

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“…A direct effect of inversions is that they suppress recombination in heterozygotes, causing inverted regions to evolve independently. Selection can act to maintain an inversion when it carries one or more advantageous alleles or when an inversion breakpoint causes gene disruption or expression changes that are adaptive (Kirkpatrick, ; Puig et al ., ). Two of the three landraces carrying the inversion (B‐301 and B‐171) originated from Botswana, while the third (TVu‐53) is a Nigerian landrace.…”

Section: Resultsmentioning

confidence: 97%

The genome of cowpea (Vigna unguiculata [L.] Walp.)

et al. 2019

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SummaryCowpea (Vigna unguiculata [L.] Walp.) is a major crop for worldwide food and nutritional security, especially in sub‐Saharan Africa, that is resilient to hot and drought‐prone environments. An assembly of the single‐haplotype inbred genome of cowpea IT97K‐499‐35 was developed by exploiting the synergies between single‐molecule real‐time sequencing, optical and genetic mapping, and an assembly reconciliation algorithm. A total of 519 Mb is included in the assembled sequences. Nearly half of the assembled sequence is composed of repetitive elements, which are enriched within recombination‐poor pericentromeric regions. A comparative analysis of these elements suggests that genome size differences between Vigna species are mainly attributable to changes in the amount of Gypsy retrotransposons. Conversely, genes are more abundant in more distal, high‐recombination regions of the chromosomes; there appears to be more duplication of genes within the NBS‐LRR and the SAUR‐like auxin superfamilies compared with other warm‐season legumes that have been sequenced. A surprising outcome is the identification of an inversion of 4.2 Mb among landraces and cultivars, which includes a gene that has been associated in other plants with interactions with the parasitic weed Striga gesnerioides. The genome sequence facilitated the identification of a putative syntelog for multiple organ gigantism in legumes. A revised numbering system has been adopted for cowpea chromosomes based on synteny with common bean (Phaseolus vulgaris). An estimate of nuclear genome size of 640.6 Mbp based on cytometry is presented.

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Section: Resultsmentioning

confidence: 97%

The genome of cowpea (Vigna unguiculata [L.] Walp.)

et al. 2019

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show abstract

“…A direct effect of inversions is that they suppress recombination in heterozygotes, causing inverted regions to evolve independently. Selection can act to maintain an inversion when it carries one or more advantageous alleles or when an inversion breakpoint causes gene disruption or expression changes that are adaptive (Kirkpatrick, 2010;Puig et al, 2015). Two of the three landraces carrying the inversion (B-301 and B-171) originated from Botswana, while the third (TVu-53) is a Nigerian landrace.…”

Section: Cowpea Genetic Diversitymentioning

confidence: 99%

The genome of cowpea (Vigna unguiculata[L.] Walp.)

Lonardi

Muñoz‐Amatriaín

Liang

et al. 2019

Preprint

103

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Cowpea (Vigna unguiculata [L.] Walp.) is a major crop for worldwide food and nutritional security, especially in sub-Saharan Africa, that is resilient to hot and drought-prone environments. An assembly of the singlehaplotype inbred genome of cowpea IT97K-499-35 was developed by exploiting the synergies between single-molecule real-time sequencing, optical and genetic mapping, and an assembly reconciliation algorithm. A total of 519 Mb is included in the assembled sequences. Nearly half of the assembled sequence is composed of repetitive elements, which are enriched within recombination-poor pericentromeric regions. A comparative analysis of these elements suggests that genome size differences between Vigna species are mainly attributable to changes in the amount of Gypsy retrotransposons. Conversely, genes are more abundant in more distal, high-recombination regions of the chromosomes; there appears to be more duplication of genes within the NBS-LRR and the SAUR-like auxin superfamilies compared with other warm-season legumes that have been sequenced. A surprising outcome is the identification of an inversion of 4.2 Mb among landraces and cultivars, which includes a gene that has been associated in other plants with interactions with the parasitic weed Striga gesnerioides. The genome sequence facilitated the identification of a putative syntelog for multiple organ gigantism in legumes. A revised numbering system has been adopted for cowpea chromosomes based on synteny with common bean (Phaseolus vulgaris). An estimate of nuclear genome size of 640.6 Mbp based on cytometry is presented.

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“…Inversions can create large areas of restricted recombination as they prevent proper chromatid pairing, although gene conversion and double cross-overs may allow some genetic exchange between inverted and non-inverted haplotypes (Andoflatto, Depaulis, & Navarro, 2001). Empirical studies have inversions contributing to local adaptation for instance in D. melanogaster (Kapun & Flatt, 2018), sticklebacks (Jones et al, 2012), yellow monkeyflower (Gould, Chen, & Lowry, 2018), teosinte (Tanja Pyhäjärvi, Hufford, Mezmouk, & Ross-Ibarra, 2013), humans (Puig, Casillas, Villatoro, & Cáceres, 2015) and in many others (Wellenreuther & Bernatchez, 2018).…”

Section: Linkage Disequilibrium Patterns and Putative Large Inversionmentioning

confidence: 99%

Genomics of clinal local adaptation inPinus sylvestrisunder continuous environmental and spatial genetic setting

Tyrmi

Vuosku

Acosta

et al. 2019

Preprint

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Understanding the consequences of local adaptation at the genomic diversity is a central goal in evolutionary genetics of natural populations. In species with large continuous geographical distributions the phenotypic signal of local adaptation is frequently clear, but the genetic background often remains elusive. We examined the patterns of genetic diversity in Pinus sylvestris, a keystone species in many Eurasian ecosystems with a huge distribution range and decades of forestry research showing that it is locally adapted to the vast range of environmental conditions. Making P. sylvestris an even more attractive subject of local adaptation study, population structure has been shown to be weak previously and in this study. However, little is known about the molecular genetic basis of adaptation, as the massive size of gymnosperm genomes has prevented large scale genomic surveys. We generated a both geographically and genomically extensive dataset using a targeted sequencing approach. By applying divergence-based and landscape genomics methods we found that several coding loci contribute to local adaptation. We also discovered a very large (ca. 300 Mbp) putative inversion with a signal of local adaptation, which to our knowledge is the first such discovery in conifers. Our results call for more detailed analysis of structural variation in relation to genomic basis of local adaptation, emphasize the lack of large effect loci contributing to local adaptation in the coding regions and thus point out to the need for more attention towards multi-locus analysis of polygenic adaptation.

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Human inversions and their functional consequences

Cited by 114 publications

References 106 publications

The genome of cowpea (Vigna unguiculata [L.] Walp.)

The genome of cowpea (Vigna unguiculata [L.] Walp.)

The genome of cowpea (Vigna unguiculata[L.] Walp.)

Genomics of clinal local adaptation inPinus sylvestrisunder continuous environmental and spatial genetic setting

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