Evidence map›Paper›PMID 40161681›Full record

ArticlebioRxiv : the preprint server for biology2025

Hi-reComb: constructing recombination maps from bulk gamete Hi-C sequencing.

Milan Malinsky, Marion Talbi, Chenxi Zhou, Nicholas Maurer, Samuel Sacco, Beth Shapiro, Catherine L Peichel, Ole Seehausen, Walter Salzburger, Jesse N Weber and 3 more

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PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

13 authors.

Milan MalinskyInstitute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.ORCID 0000-0002-1462-6317
Marion TalbiInstitute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.
Chenxi ZhouDepartment of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.ORCID 0000-0002-1735-2630
Nicholas MaurerDepartment of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
Samuel SaccoDepartment of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
Beth ShapiroDepartment of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
Catherine L PeichelInstitute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.ORCID 0000-0002-7731-8944
Ole SeehausenInstitute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.
Walter SalzburgerDepartment of Environmental Sciences, Zoological Institute, University of Basel, 4051 Basel, Switzerland.
Jesse N WeberDepartment of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA.ORCID 0000-0003-4839-6684
Daniel I BolnickDepartment of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA.
Richard E GreenDepartment of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.ORCID 0000-0003-0516-5827
Richard DurbinDepartment of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA.ORCID 0000-0002-9130-1006

Funding

Reciprocal genetics of recently-evolved vertebrate immunity and peritoneal helminth counter-adaptationR01AI123659 · NIAID · UNIVERSITY OF TEXAS AT AUSTIN · PI Daniel Imara Bolnick · 2017 to 2026
$3.8M
Mining natural infection variation to find the genetic basis of coevolution between vertebrate hosts and helminth parasitesR35GM142891 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI WEBER, JESSE NATHANIEL · 2021 to 2025
$1.9M
NIAID NIH HHS R01 AI123659NIGMS NIH HHS R35 GM142891
6 · The paper itself

Abstract

Recombination is central to genetics and to evolution of sexually reproducing organisms. However, obtaining accurate estimates of recombination rates, and of how they vary along chromosomes, continues to be challenging. To advance our ability to estimate recombination rates, we present Hi-reComb, a new method and software for estimation of recombination maps from bulk gamete chromosome conformation capture sequencing (Hi-C). Simulations show that Hi-reComb produces robust, accurate recombination landscapes. With empirical data from sperm of five fish species we show the advantages of this approach, including joint assessment of recombination maps and large structural variants, map comparisons using bootstrap, and workflows with trio phasing vs. Hi-C phasing. With off-the-shelf library construction and a straightforward rapid workflow, our approach will facilitate routine recombination landscape estimation for a broad range of studies and model organisms in genetics and evolutionary biology. Hi-reComb is open-source and freely available at https://github.com/millanek/Hi-reComb.

Indexed as

cichlidsgametesgeneticsHi-CRecombination mapsoftwarespermstickleback

Identifiers

PMID40161681
PMCPMC11952307

What OpenQuestion holds

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LicenceCC BY-NC
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.