Evidence map›Paper›PMID 32649757›Full record

ArticleGigaScience2020

Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding.

Morteza Roodgar, Afshin Babveyh, Lan H Nguyen, Wenyu Zhou, Rahul Sinha, Hayan Lee, John B Hanks, Mohan Avula, Lihua Jiang, Ruiqi Jian and 10 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing papers in PubMed
0.8field-weighted citation impact, top 29% of its field
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

9 citing papers in PubMed, 16 citations in OpenAlex.

  1. Review
  2. Article
  3. Article
  4. Article
  5. Seasonal Prevalence of Gastrointestinal Parasites in Macaques (Animals : an open access journal from MDPI · 2022
    Article
  6. Article
  7. Review
  8. Article
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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

20 authors at 8 institutions in 5 countries.

Morteza RoodgarDepartment of Genetics, 300 Pasteur Dr, Stanford University, Stanford, CA 94305, USA.
Afshin BabveyhDepartment of Genetics, 300 Pasteur Dr, Stanford University, Stanford, CA 94305, USA.
Lan H NguyenInstitute for computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA.
Wenyu ZhouDepartment of Genetics, 300 Pasteur Dr, Stanford University, Stanford, CA 94305, USA.
Rahul SinhaInstitute for Stem Cell Biology and Regenerative Medicine, 265 Campus Dr., Stanford University, Stanford, CA 94305, USA.
Hayan LeeDepartment of Genetics, 300 Pasteur Dr, Stanford University, Stanford, CA 94305, USA.
John B HanksStanford Research Computing Center, Stanford University, Stanford, CA 94305, USA.
Mohan AvulaDepartment of Genetics, 300 Pasteur Dr, Stanford University, Stanford, CA 94305, USA.
Lihua JiangDepartment of Genetics, 300 Pasteur Dr, Stanford University, Stanford, CA 94305, USA.
Ruiqi JianDepartment of Genetics, 300 Pasteur Dr, Stanford University, Stanford, CA 94305, USA.
Hoyong LeeSchool of Computer Science and Engineering, Pusan National University, Busan 46241, South Korea.
Giltae SongSchool of Computer Science and Engineering, Pusan National University, Busan 46241, South Korea.
Hassan ChaibStanford Center for Genomics and Personalized Medicine, Stanford University, 3165 Porter Dr. Palo Alto, CA 94305, USA.
Irv L WeissmanInstitute for Stem Cell Biology and Regenerative Medicine, 265 Campus Dr., Stanford University, Stanford, CA 94305, USA.
Serafim BatzoglouDepartment of Computer Science, Stanford University, Stanford, CA 94305, USA.
Susan HolmesDepartment of Statistics, Stanford University, Stanford, CA 94305, USA.
David G SmithCalifornia National Primate Research Center, University of California, Davis, CA 95616, USA.
Joseph L MankowskiDepartment of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Stefan ProstLOEWE-Centre for Translational Biodiversity Genomics, Senckenberg 25, 60325 Frankfurt am Main, Germany.
Michael P SnyderDepartment of Genetics, 300 Pasteur Dr, Stanford University, Stanford, CA 94305, USA.
Stanford University · USStanford Medicine · USCalifornia Institute for Regenerative Medicine · USPusan National University · KRInstitute of Mathematical Statistics · USJohns Hopkins University · USSouth African National Biodiversity Institute · ZAUniversity of California, Davis · US

Funding

Stanford Islet Research CoreP30DK116074 · NIDDK · STANFORD UNIVERSITY · PI Seung K Kim · 2017 to 2026
$19.5M
Viral Testing CoreU42OD013117 · OD · JOHNS HOPKINS UNIVERSITY · PI Lydia Hopper · 2017 to 2026
$10.9M
Program in Translational and Experimental HematologyT32HL120824 · NHLBI · STANFORD UNIVERSITY · PI MAJETI, RAVINDRA · 2014 to 2023
$2.4M
High-throughput sequencer for multi-scale genomic studiesS10OD020141 · OD · STANFORD UNIVERSITY · PI SNYDER, MICHAEL P. · 2015 to 2015
$600k
NHLBI NIH HHS T32 HL120824NIDDK NIH HHS P30 DK116074NIH HHS S10 OD020141NIH HHS U42 OD013117
6 · The paper itself

Abstract

backgroundMacaque species share >93% genome homology with humans and develop many disease phenotypes similar to those of humans, making them valuable animal models for the study of human diseases (e.g., HIV and neurodegenerative diseases). However, the quality of genome assembly and annotation for several macaque species lags behind the human genome effort.

resultsTo close this gap and enhance functional genomics approaches, we used a combination of de novo linked-read assembly and scaffolding using proximity ligation assay (HiC) to assemble the pig-tailed macaque (Macaca nemestrina) genome. This combinatorial method yielded large scaffolds at chromosome level with a scaffold N50 of 127.5 Mb; the 23 largest scaffolds covered 90% of the entire genome. This assembly revealed large-scale rearrangements between pig-tailed macaque chromosomes 7, 12, and 13 and human chromosomes 2, 14, and 15. We subsequently annotated the genome using transcriptome and proteomics data from personalized induced pluripotent stem cells derived from the same animal. Reconstruction of the evolutionary tree using whole-genome annotation and orthologous comparisons among 3 macaque species, human, and mouse genomes revealed extensive homology between human and pig-tailed macaques with regards to both pluripotent stem cell genes and innate immune gene pathways. Our results confirm that rhesus and cynomolgus macaques exhibit a closer evolutionary distance to each other than either species exhibits to humans or pig-tailed macaques.

conclusionsThese findings demonstrate that pig-tailed macaques can serve as an excellent animal model for the study of many human diseases particularly with regards to pluripotency and innate immune pathways.

Indexed as

ChromosomesGenomeGenomicsAnimalsComputational BiologyHumansKaryotypingMacaca nemestrinaMaleMolecular Sequence AnnotationProteomicsRepetitive Sequences, Nucleic Acidchromosome-level assemblyHiClinked-readnonhuman primatepig-tailed macaque

Identifiers

PMID32649757
PMCPMC7350979
OpenAlexW3040771989

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.