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9 results for “Chloroplast capture”
Multiple paternally inherited chloroplast capture events associated with Taxus speciation in the Hengduan Mountains
<p><strong>Template files and estimation files in Fastsimcoal2 for 16 models. Each model corresponded with the same name in Fig S2 and Fig S3. And SNP file, plastome matrix and transcriptome matrixes</strong></p>
Data from: Disentangling serial chloroplast captures in willows
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Data from: Intraspecific haplotype diversity in Cherleria sedoides L. (Caryophyllaceae) is best explained by chloroplast capture from an extinct species
Cherleria sedoides, a plant species widespread in alpine areas of the major European mountain ranges and in Scotland, contains two highly divergent chloroplast haplotype groups, one widespread (WH) and one present only in some populations in the Alps (AH). We investigated whether this haplotype diversity is the result of (1) intraspecific differentiation, (2) retention of an ancestral polymorphism or (3) hybridisation. For this purpose, 106 matK sequences from throughout the Caryophyllaceae and 80 trnQ-rps16 and psbD-trnT sequences of C. sedoides (51) and other species of Cherleria (29) were used for the construction of phylogenies and haplotype networks. As the two haplotype groups were never each other's closest relatives, haplotype diversity as a result of intraspecific differentiation is unlikely. Patterns of genetic differentiation within the WH and AH groups are very different. Whereas WH shows a radial pattern typical of rapid expansion, AH is divided into two divergent subgroups each containing more variation than the WH group. This suggests that the two haplotype groups have dissimilar histories and are therefore unlikely to represent an ancestral polymorphism. Instead, we conclude that the polymorphism is best interpreted as the result of hybridisation. As the WH and AH haplotype groups fall into Cherleria, but do not group with any extant species, we conclude that the rare AH group represents the original C. sedoides, and that the WH group was captured from another, now extinct, species of Cherleria.
Hybridisation and chloroplast capture between distinct Themeda triandra lineages in Australia
<p>Ecotypes are distinct populations within a species that are adapted to specific environmental conditions. Understanding how these ecotypes become established, and how they interact when reunited, is fundamental to elucidating how ecological adaptations are maintained. This study focuses on Themeda triandra, a dominant grassland species across Asia, Africa and Australia. It is the most widespread plant in Australia, where it has distinct ecotypes that are usually restricted to either wetter and cooler coastal regions or the drier and hotter interior. We generate a de novo reference genome for T. triandra and use whole genome sequencing for over 80 Themeda accessions to reconstruct the evolutionary history of T. triandra and related taxa. Organelle phylogenies confirm that Australia was colonised by T. triandra twice, with the division between ecotypes predating their arrival in Australia. The nuclear genome provides evidence of differences in the dominant ploidal level and gene-flow among the ecotypes. In northern Queensland there appears to be a hybrid zone between ecotypes with admixed nuclear genomes and shared chloroplast haplotypes. Conversely, in the cracking claypans of Western Australia, there is cytonuclear discordance with individuals possessing the coastal chloroplast and interior clade nuclear genome. This chloroplast capture is potentially a result of adaptive introgression, with selection detected in the rpoC2 gene which is associated with water use efficiency. The reason why T. triandra is the most widespread plant in Australia appears to be a result of distinct ecotypic genetic variation and genome duplication, with the importance of each depending on the geographic scale considered.</p>
Biased gene introgression and adaptation in face of chloroplast capture in Aquilegia
<p><span>Chloroplast capture</span><span>, a phenomenon that can occur through interspecific hybridization and introgression, has been frequently suggested as an explanation for cytonuclear discordance in plants. In theory, the captured donor chloroplasts may not cooperate with the recipient nuclear genome, especially chloroplast-targeted nuclear genes. However, relatively few studies have documented the mechanisms of cytonuclear coevolution and its potential species differentiation and possible functional differences in the face of chloroplast capture. To explore this crucial question, we chose the <em>Aquilegia</em> genus, which is known for having minimal sterility among the species, and we inferred that <em>A</em>. <em>amurensis</em> captured the plastome of <em>A</em>. <em>parviflora</em> based on cytonuclear discordance and gene flow between these two species. We focused on the introgression region and its differentiation with closely related species, especially its composition in a chloroplast capture scenario. We found that nuclear genes encoding cytonuclear enzyme complexes or organelle localized (CECs) were significantly enriched in the introgression regions, indicating that the CEC genes of chloroplast donor species were selectively retained and displaced the original CEC genes in chloroplast receptor species due to cytonuclear interactions during introgression. Notably, the intrinsic factor of cytonuclear compatibility may have a higher degree of evolutionary distance for the introgressed CEC genes between <em>A</em>. <em>amurensis</em> and <em>A</em>. <em>parviflora</em>. Introgression from <em>A</em>. <em>parviflora</em> promotes the differentiation of <em>A</em>. <em>amurensis</em> and <em>A</em>. <em>japonica</em>. Furthermore, we found that one of the overrepresented gene ontology terms in these introgressed genes was terpene synthase activity (GO: 0010333) in which more than one-third of the genes were CEC genes, showing that <em>A</em>. <em>amurensis</em> had similar release patterns for terpenes in flowers of <em>A</em>. <em>parviflora</em> when compared with <em>A</em>. <em>japonica</em>.</span> <span>Altogether, this study helps to clarify the mechanisms of cytonuclear coevolution, species differentiation and functional differences in face of chloroplast capture and highlights a critical role of chloroplast capture in adaptation.</span></p>
Hybridisation and chloroplast capture between distinct Themeda triandra lineages in Australia
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Biased gene introgression and adaptation in face of chloroplast capture in Aquilegia amurensis
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Data from: Intraspecific haplotype diversity in Cherleria sedoides L. (Caryophyllaceae) is best explained by chloroplast capture from an extinct species
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Data from: Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies
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