A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence

Ivankovic, Mario; Brand, Jeremias N.; Pandolfini, Luca; Brown, Tom; Pippel, Martin; Rozanski, Andrei; Schubert, Til; Grohme, Markus A.; Winkler, Sylke; Robledillo, Laura; Zhang, Meng; Codino, Azzurra; Gustincich, Stefano; Vila-Farré, Miquel; Zhang, Shu; Papantonis, Argyris; Marques, André; Rink, Jochen C.

doi:10.1101/2023.12.22.572568

Cited by 9 publications

(1 citation statement)

References 113 publications

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“…In order to reduce the redundancy of the transcript set obtained, we employed an isoform pruning pipeline as described in (Ivankovic et al, 2023) . Briefly, transcripts were grouped according to the genomic locus position using gffread v0.12.7 (Pertea & Pertea, 2020) .…”

Section: Gene Model Prediction Annotation and Curationmentioning

confidence: 99%

A highly contiguous reference genome for the Alpine ibex (Capra ibex)

Çilingir,

Landuzzi,

Brambilla

et al. 2024

Preprint

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Anthropogenic hybridization, the unintentional hybridization with a non-native or domestic species in human-dominated environments, is a major concern for species conservation and a challenge for conservation management decisions. Genetically depleted species are expected to be particularly vulnerable to hybridization and introgression since hybridization can restore or introduce new adaptive genetic variation and alleviate the effects of inbreeding through hybrid vigour. However, defining the precise sets of deleterious or beneficial mutations resulting from anthropogenic hybridization is complex and limited by the quality of genomic resources. The Alpine ibex (Capra ibex), a species native to the Alps, faced near-extinction two centuries ago, but conservation programs have successfully restored its populations. Alpine ibex are known to hybridize with the domestic goat (Capra hircus) occasionally leading to hybrid swarm formation. Past introgression has been observed at immune-related genes and was suggested to have had an adaptive effect. Alpine ibex also carry deleterious mutation load from the reintroduction bottlenecks, which could be alleviated through admixture. Here, we produced a chromosome-level reference genome for Alpine ibex based on Oxford Nanopore sequencing coupled with high-throughput chromosome conformation capture. The highly contiguous assembly of 2.66 Gbp reveals 30 chromosomes and is augmented by a 98.8% complete RNAseq-assisted gene model prediction. The Alpine ibex genome presents overall a high degree of synteny compared to the domestic goat, with a number of structural variants spanning 38 Mb of insertion and deletions, as well as 49 Mb of inversions. We also identified structural variants near but not within the major histocompatibility complex (MHC), an immune-relevant gene complex, where previous studies found signals of introgression. The high degree of synteny between the Alpine ibex and domestic goat chromosomes likely facilitates recombination between haplotypes of the two species and is, therefore, in accordance with the observation of hybrid swarms. To determine the precise impact of recent admixture, we resequenced eight hybrid individuals sampled from two hybrid swarms in Northern Italy. Swarm individuals carried between 18-80% goat genome representing up to 3rd generation hybrids, including one F1 hybrid. The reference genome will facilitate quantifying maladaptive variation introduced from domestic goats and guide management efforts.

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Section: Gene Model Prediction Annotation and Curationmentioning

confidence: 99%

A highly contiguous reference genome for the Alpine ibex (Capra ibex)

Çilingir,

Landuzzi,

Brambilla

et al. 2024

Preprint

Self Cite

View full text Add to dashboard Cite

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Fusion, fission, and scrambling of the bilaterian genome in Bryozoa

Lewin,

Liao,

Chen

et al. 2024

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Genes are commonly found together on the same chromosome over vast evolutionary distances. This extensive physical gene linkage, known as macrosynteny, can be seen between bilaterian phyla as divergent as Chordata, Echinodermata, Mollusca, and Nemertea and likely reflects the importance of genome organization to gene regulatory landscapes. Here, we report a very different pattern of genome evolution in Bryozoa, an understudied yet ecologically important phylum of colonial invertebrates. Using comparative genomics, we reconstruct the chromosomal evolutionary history of five bryozoans. We infer the ancestral bryozoan genome organization and identify multiple ancient chromosome fusions followed by gene mixing, leading to the near-complete loss of bilaterian linkage groups. A second wave of rearrangements, including chromosome fission, occurred independently in two bryozoan classes, further shuffling bryozoan genomes. We also discover nine chromosomal fusion events shared between bryozoans and brachiopods, supporting the traditional yet highly debated Lophophorata hypothesis. Finally, we show that chromosome fusion and fission processes led to the separation of bryozoan Hox clusters. These findings demonstrate how the canonical bilaterian genome structure has been lost across an entire phylum, suggest a modification to gene regulatory landscapes, and provide a powerful source of phylogenetic information.

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Multiplex single-cell analysis of serotonergic neuron function in planarians reveals widespread effects in diverse cell types

Emili,

Rodríguez-Fernández,

Pérez-Posada

et al. 2024

Preprint

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Neurons function by interacting with each other and with other cell types, often exerting organism-wide regulation. Serotonergic neurons play a systemic role in processes such as appetite, sleep and motor control. Functional studies in the planarianSchmidtea mediterraneahave shown that impairment of serotonergic neurons results in systemic effects. Studying neurons and the tissues they interact with is challenging using either bulk or single-cell analysis techniques. While bulk methods merge the information from all cell types, single-cell methods show promise in overcoming this limitation. However, current single-cell approaches encounter other challenges including stress of cell dissociation, high cost, multiplexing capacity, batch effects, replication and statistical analysis. Here we used ACME and SPLiT-seq to generate a multiplex single-cell analysis of serotonergic neuron function in planarians by inhibitingpitxandlhx1/5-1, two transcription factors expressed in them. We recovered single-cell transcriptomic profiles of 47,292 cells from knockdown and control animals, including biological and technical replicates. Our results show that epidermal, muscular and the recently described parenchymal cell types are affected the most by serotonergic neuron impairment. By computationally dissecting each cell type, we elucidated gene expression changes in each, including changes in epidermis cilia genes and myofiber genes in muscle. Interestingly, parenchymal cells downregulate genes involved in neurotransmitter recycling, suggesting a glial-like function of these recently described enigmatic cell types. Our results will allow disentangling the complexity of serotonergic neuron inhibition by studying the downstream effectors and the affected tissues, and offer new data on the function of parenchymal cells in planarians. Ultimately, our results pave the way for dissecting complex phenotypes through multiplex single-cell transcriptomics.

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A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence

Cited by 9 publications

References 113 publications

A highly contiguous reference genome for the Alpine ibex (Capra ibex)

A highly contiguous reference genome for the Alpine ibex (Capra ibex)

Fusion, fission, and scrambling of the bilaterian genome in Bryozoa

Multiplex single-cell analysis of serotonergic neuron function in planarians reveals widespread effects in diverse cell types

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