Transposable Elements Contribute to the Adaptation of Arabidopsis thaliana

Li, Zi-Wen; Hou, Xinghui; Chen, Jiafu; Xu, Yongchao; Wu, Qiong; González, Josefa; Guo, Ya‐Long

doi:10.1093/gbe/evy171

Cited by 65 publications

(64 citation statements)

References 65 publications

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“…This general expression pattern could be explained either by supergene allele‐specific gene regulation or by copy number variation of TEs between SB and Sb genomes. The general consensus is that most TE insertions are neutral or slightly deleterious; however, TEs that cause adaptive phenotypes have been described in many organisms, including insects (van't Hof et al ; Jangam, Feschotte, Betrán, ; Li et al ). Thus, it would be interesting to determine whether the differential expression of these TEs is just nonfunctional noise or adaptive gene regulation, especially for those associated with social form.…”

Section: Discussionmentioning

confidence: 99%

Has gene expression neofunctionalization in the fire ant antennae contributed to queen discrimination behavior?

Dang

Cohanim

Fontana

et al. 2019

Ecology and Evolution

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Queen discrimination behavior in the fire ant Solenopsis invicta maintains its two types of societies: colonies with one (monogyne) or many (polygyne) queens, yet the underlying genetic mechanism is poorly understood. This behavior is controlled by two supergene alleles, SB and Sb, with ~600 genes. Polygyne workers, having either the SB/SB or SB/Sb genotype, accept additional SB/Sb queens into their colonies but kill SB/SB queens. In contrast, monogyne workers, all SB/SB, reject all additional queens regardless of genotype. Because the SB and Sb alleles have suppressed recombination, determining which genes within the supergene mediate this differential worker behavior is difficult. We hypothesized that the alternate worker genotypes sense queens differently because of the evolution of differential expression of key genes in their main sensory organ, the antennae. To identify such genes, we sequenced RNA from four replicates of pooled antennae from three classes of workers: monogyne SB/SB, polygyne SB/SB, and polygyne SB/Sb. We identified 81 differentially expressed protein‐coding genes with 13 encoding potential chemical metabolism or perception proteins. We focused on the two odorant perception genes: an odorant receptor SiOR463 and an odorant‐binding protein SiOBP12. We found that SiOR463 has been lost in the Sb genome. In contrast, SiOBP12 has an Sb‐specific duplication, SiOBP12b′, which is expressed in the SB/Sb worker antennae, while both paralogs are expressed in the body. Comparisons with another fire ant species revealed that SiOBP12b′ antennal expression is specific to S. invicta and suggests that queen discrimination may have evolved, in part, through expression neofunctionalization.

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Section: Discussionmentioning

confidence: 99%

Has gene expression neofunctionalization in the fire ant antennae contributed to queen discrimination behavior?

Dang

Cohanim

Fontana

et al. 2019

Ecology and Evolution

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“…The TE content is variable in different organisms and may be used as a marker to distinguish between clonal populations of C. protrusum [70]. The TEs in C. protrusum may modify amino acids or contribute to genetic variation, thereby aiding populations to adapt successfully to changes in the environment [71,72]. Previous studies reported that the genome size, structure, and gene content are heavily influenced by natural selection, which is governed by the lifestyle and ecological niche of a species [73].…”

Section: Discussionmentioning

confidence: 99%

Advances in Single Molecule, Real-Time (SMRT) Sequencing

2019

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Infrastructure (NGI) in Sweden. He originally trained as a computer scientist and has worked in the field of next-generation sequencing (NGS) for over a decade. In 2008, he received his doctorate degree in bioinformatics from Uppsala University, Sweden, and to date, has authored over 50 scientific publications in genomics and bioinformatics. His current research is focused on technology development and novel sequencing applications for the study of human health and disease. Ongoing activities include the coordination of data analysis within the SweGen project, a national effort that aims to construct a whole genome map of genetic variation in the Swedish population, as well as the introduction of long-read single-molecule sequencing into clinical routines.

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“…This is most well-known in plants [24], but is also marked in animal lineages [25]. Sister species/strains of Arabidopsis [26][27][28][29], maize [30,31], or rice [32] differ dramatically in their TE content. Moreover, it appears that these differences arise due to the preferential expansion and contraction of different TE families in closely related lineages [33].…”

Section: The Quantitative and Qualitative Preponderance Of Non-snv Vamentioning

confidence: 98%

Substitutions are boring: some arguments about parallel mutations and repetitive DNA

Press¹,

Hall²,

Morton³

et al. 2018

Preprint

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Extant genomes are largely shaped by the global transposition, copy number fluctuation, and rearrangement of DNA sequences, rather than by the substitutions of single nucleotides. Although many of these large-scale mutations have low probabilities and are unlikely to repeat, others are recurrent or predictable in their effects, leading to stereotyped genome architectures and genetic variation in both eukaryotes and prokaryotes. Such recurrent, parallel mutation modes can profoundly shape the paths taken by evolution, and directly undermine the Wright-Fisher model of evolutionary genetics. Similar patterns are also evident at the smaller scales of individual genes or short genomic sequences. The scale and extent of this ‘non-substitution’ variation has only recently come into focus through the advent of new genomic technologies; however, it still not widely included in genotype-phenotype association studies. In this review, we identify the common features of these disparate mutational phenomena and comment on the importance and interpretation of these mutational patterns.

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Transposable Elements Contribute to the Adaptation of Arabidopsis thaliana

Cited by 65 publications

References 65 publications

Has gene expression neofunctionalization in the fire ant antennae contributed to queen discrimination behavior?

Has gene expression neofunctionalization in the fire ant antennae contributed to queen discrimination behavior?

Advances in Single Molecule, Real-Time (SMRT) Sequencing

Substitutions are boring: some arguments about parallel mutations and repetitive DNA

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