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111 results for “genome duplications”

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dryad28/100

Chromosome-level genome of Capitulum mitella reveals an ancient whole-genome duplication event and intertidal adaptation of barnacles

Barnacles are the only sessile crustaceans inhabiting intertidal zone, an extremely stressful environment for sessile organisms. Herein, we report the chromosome-level genome of a stalked barnacle, Capitulum mitella, which is a dominant intertidal cirripede of the west Pacific Ocean coast. After comprehensive comparative genomic analyses, it is the first time to find an ancient whole-genome duplication (WGD) event that preceded the divergence of Lepadomorpha and Sessilia approximately 237 million years ago. The retained duplicated genes of WGD are primarily enriched in many environmental information processing pathways, shedding light on its adaptive evolution of intertidal sessile life. In addition, transcriptomic and metabolomic sequencing and analyses of C. mitella indicated that the upregulation of some expanded anti-stress factors and accumulation of acyl-carnitines help barnacles adapt to stressful intertidal conditions. Therefore, this study provides a valuable resource for understanding the unique intertidal adaptation mechanism of sessile crustaceans and reveals novel WGD events in invertebrates.

opencc-zeroOct 2022View details →

zenodo28/100

Repeated shifts out of tropical climates preceded by whole genome duplication

Inputs, outputs and scripts for performing anayses in the above mentioned article.

opencc-by-4.0Feb 2024View details →

dryad28/100

Data from: Ancestral whole genome duplication in the marine chelicerate horseshoe crabs

Whole-genome duplication (WGD) results in new genomic resources that can be exploited by evolution for rewiring genetic regulatory networks in organisms. In metazoans, WGD occurred before the last common ancestor of vertebrates, and has been postulated as a major evolutionary force that contributed to their speciation and diversification of morphological structures. Here, we have sequenced genomes from three of the four extant species of horseshoe crabs—Carcinoscorpius rotundicauda, Limulus polyphemus and Tachypleus tridentatus. Phylogenetic and sequence analyses of their Hox and other homeobox genes, which encode crucial transcription factors and have been used as indicators of WGD in animals, strongly suggests that WGD happened before the last common ancestor of these marine chelicerates >135 million years ago. Signatures of subfunctionalisation of paralogues of Hox genes are revealed in the appendages of two species of horseshoe crabs. Further, residual homeobox pseudogenes are observed in the three lineages. The existence of WGD in the horseshoe crabs, noted for relative morphological stasis over geological time, suggests that genomic diversity need not always be reflected phenotypically, in contrast to the suggested situation in vertebrates. This study provides evidence of ancient WGD in the ecdysozoan lineage, and reveals new opportunities for studying genomic and regulatory evolution after WGD in the Metazoa.

opencc-zeroDec 2014View details →

zenodo28/100

Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole-genome duplications in Brassica

Plant cells arose through the endosymbiotic engulfment of a cyanobacterium that subsequently formed the chloroplast genome, enabling plants to develop new critical functions. Almost all chloroplast proteins are now encoded in the nucleus, but some chloroplast protein complexes are jointly encoded by both nuclear and chloroplast genes, which interact to facilitate essential plant functions, such as the photosystems. Allopolyploidy, resulting from the hybridization and genome doubling of two divergent species, can disrupt these fine-tuned cytonuclear interactions, as newly formed allopolyploid species confront biparental nuclear chromosomes with a uniparental organelle inheritance. Such unequal genome inheritance may affect the conformation of the five cytonuclear complexes in allopolyploids. We used Brassica as a model to study the effects of paleopolyploidy and dichotomic divergence in parental species, as well as the effects of recent allopolyploidy in Brassica napus, on genes implicated in cytonuclear complexes. Because the B. napus parental diploid species are paleohexaploids, we first identified paleologous copies of cytonuclear complex genes. We found that these genes are preferentially retained in duplicates, are nearly all transcribed and are undergoing strong purifying selection, in accordance with the ‘gene balance hypothesis’. Subsequently, we compared expression patterns of cytonuclear complex homoeolog genes between resynthesized B. napus individuals and their respective diploid parents. The neo-polyploids showed neither biased sub-genome expression nor homogenization of homoeologs, due to highly conserved parental chloroplast genomes. These findings provide new insights and an innovative framework to understand the impact of cytonuclear interactions on interspecific hybridization and allopolyploid speciation.

opencc-by-4.0Jan 2019View details →

dryad28/100