Evidence map›Paper›PMID 37428819›Full record

ArticleThe Journal of heredity2023

A draft reference genome assembly of the Pipevine Swallowtail butterfly, Battus philenor hirsuta.

Samridhi Chaturvedi, Merly Escalona, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Colin W Fairbairn, William Seligmann, Courtney Miller, H Bradley Shaffer, Noah K Whiteman

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in The Journal of heredity, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Samridhi ChaturvediDepartment of Integrative Biology, University of California, 142 Weill Hall #3200, Berkeley, CA 94720, United States.ORCID 0000-0002-9181-4338
Merly EscalonaDepartment of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, United States.ORCID 0000-0003-0213-4777
Mohan P A MarimuthuDNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States.
Oanh NguyenDNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States.ORCID 0000-0003-1492-2084
Noravit ChumchimDNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States.ORCID 0000-0003-1139-9427
Colin W FairbairnDepartment of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, United States.
William SeligmannDepartment of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, United States.ORCID 0000-0002-5762-3095
Courtney MillerDepartment of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095-7239, United States.ORCID 0000-0002-4347-6629
H Bradley ShafferDepartment of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095-7239, United States.ORCID 0000-0002-5795-9242
Noah K WhitemanDepartment of Integrative Biology, University of California, 142 Weill Hall #3200, Berkeley, CA 94720, United States.ORCID 0000-0003-1448-4678

Funding

Co-evolutionary Genetics of Host-Parasite InteractionsR35GM119816 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI NOAH K WHITEMAN · 2016 to 2026
$4.7M
Pacific Biosciences PacBio RS Single Molecule Real Time SequencerS10OD018174 · OD · UNIVERSITY OF CALIFORNIA BERKELEY · PI ROKHSAR, DANIEL SOLEYMAN · 2014 to 2014
$600k
Acquisition of Covaris E220 and Sciclone G3 systems for high throughput sequencinS10OD010786 · OD · UNIVERSITY OF CALIFORNIA AT DAVIS · PI COMAI, LUCA · 2012 to 2012
$311k
NIGMS NIH HHS R35 GM119816NIGMS NIH HHS R35GM119816NIH HHS S10 OD010786NIH HHS S10 OD018174
6 · The paper itself

Abstract

The California Pipevine Swallowtail Butterfly, Battus philenor hirsuta, and its host plant, the California Pipevine or Dutchman's Pipe, Aristolochia californica Torr., are an important California endemic species pair. While this species pair is an ideal system to study co-evolution, genomic resources for both are lacking. Here, we report a new, chromosome-level assembly of B. philenor hirsuta as part of the California Conservation Genomics Project (CCGP). Following the sequencing and assembly strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin proximity sequencing technology to produce a de novo assembled genome. Our genome assembly, the first for any species in the genus, contains 109 scaffolds spanning 443 mega base (Mb) pairs, with a contig N50 of 14.6 Mb, a scaffold N50 of 15.2 Mb, and BUSCO complete score of 98.9%. In combination with the forthcoming A. californica reference genome, the B. philenor hirsuta genome will be a powerful tool for documenting landscape genomic diversity and plant-insect co-evolution in a rapidly changing California landscape.

Indexed as

AristolochiaButterfliesAnimalsChromosomesGenomeGenomicsCalifornia Conservation Genomics ProjectgenomicsLepidopteraPapilionidae

Identifiers

PMID37428819
PMCPMC10650949

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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.