Evidence map›Paper›PMID 36864388›Full record

ArticleBMC genomics2023

Transcriptome analysis of the endangered dung beetle Copris tripartitus (Coleoptera: Scarabaeidae) and characterization of genes associated to immunity, growth, and reproduction.

Hee Ju Hwang, Bharat Bhusan Patnaik, Snigdha Baliarsingh, Hongray Howrelia Patnaik, Min Kyu Sang, Jie Eun Park, Hang Chul Cho, Dae Kwon Song, Jun Yang Jeong, Chan Eui Hong and 9 more

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

Article in BMC genomics, 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
4.8field-weighted citation impact, top 7% 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

3 citing papers in PubMed, 6 citations in OpenAlex.

  1. miR-let-7 TargetingInsects · 2026
    Article
  2. Comparative Transcriptome Analysis ofInternational journal of molecular sciences · 2024
    Article
  3. Review
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

19 authors at 6 institutions in 2 countries.

Hee Ju HwangKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea.
Bharat Bhusan PatnaikKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea.
Snigdha BaliarsinghPG Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore-, Odisha, 756089, India.
Hongray Howrelia PatnaikKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea.
Min Kyu SangResearch Support Center (Core-Facility) for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Asan, Chungnam, South Korea.
Jie Eun ParkKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea.
Hang Chul ChoiLAB, INSILICOGEN, INC. #2901~2904, Tower-Dong A, HEUNGDEOK IT VALLEY, 13, Heungdeok 1-Ro, Giheung-Gu, Yongin-Si, 16954, Gyeonggi-do, Korea.
Dae Kwon SongKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea.
Jun Yang JeongKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea.
Chan Eui HongKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea.
Yong Tae KimKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea.
Hyeon Jun SinDepartment of Biology, College of Natural Sciences, Soonchunhyang University, Asan, Chungnam, South Korea.
Liu ZiweiDepartment of Biology, College of Natural Sciences, Soonchunhyang University, Asan, Chungnam, South Korea.
So Young ParkBiodiversity Research Team, Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Gyeongbuk, South Korea.
Se Won KangBiological Resource Center (BRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeonbuk, South Korea.
Heon Cheon JeongKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea.
Hong Seog ParkResearch Institute, GnC BIO Co., LTD., 621-6 Banseok-Dong, Yuseong-Gu, Daejeon, 34069, Korea.
Yeon Soo HanCollege of Agriculture and Life Science, Chonnam National University, 77 Yongbong-Ro, Buk-Gu, Gwangju, 61186, South Korea.
Yong Seok LeeKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea. yslee@sch.ac.kr.
Soonchunhyang University · KRChonnam National University · KRFakir Mohan University · INInsilicogen (South Korea) · KRKorea Research Institute of Bioscience and Biotechnology · KRNational Institute of Biological Resources · KR

Funding

Kore Basic Science Institute (National research Facilitues and Equipment Center) 2022R1A6C101B794National Research Foundation of Korea NRF-2021R1A6A1A03039503
6 · The paper itself

Abstract

backgroundDung beetles recycle organic matter through the decomposition of feces and support ecological balance. However, these insects are threatened by the indiscriminate use of agrochemicals and habitat destruction. Copris tripartitus Waterhouse (Coleoptera: Scarabaeidae), a dung beetle, is listed as a class-II Korean endangered species. Although the genetic diversity of C. tripartitus populations has been investigated through analysis of mitochondrial genes, genomic resources for this species remain limited. In this study, we analyzed the transcriptome of C. tripartitus to elucidate functions related to growth, immunity and reproduction for the purpose of informed conservation planning.

resultsThe transcriptome of C. tripartitus was generated using next-generation Illumina sequencing and assembled de novo using a Trinity-based platform. In total, 98.59% of the raw sequence reads were processed as clean reads. These reads were assembled into 151,177 contigs, 101,352 transcripts, and 25,106 unigenes. A total of 23,450 unigenes (93.40%) were annotated to at least one database. The largest proportion of unigenes (92.76%) were annotated to the locally curated PANM-DB. A maximum of 5,512 unigenes had homologous sequences in Tribolium castaneum. Gene Ontology (GO) analysis revealed a maximum of 5,174 unigenes in the Molecular function category. Further, in Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, a total of 462 enzymes were associated with established biological pathways. Based on sequence homology to known proteins in PANM-DB, representative immunity, growth, and reproduction-related genes were screened. Potential immunity-related genes were categorized into pattern recognition receptors (PRRs), the Toll-like receptor signaling pathway, the MyD88- dependent pathway, endogenous ligands, immune effectors, antimicrobial peptides, apoptosis, and adaptation-related transcripts. Among PRRs, we conducted detailed in silico characterization of TLR-2, CTL, and PGRP_SC2-like. Repetitive elements such as long terminal repeats, short interspersed nuclear elements, long interspersed nuclear elements and DNA elements were enriched in the unigene sequences. A total of 1,493 SSRs were identified among all unigenes of C. tripartitus.

conclusionsThis study provides a comprehensive resource for analysis of the genomic topography of the beetle C. tripartitus. The data presented here clarify the fitness phenotypes of this species in the wild and provide insight to support informed conservation planning.

Indexed as

ColeopteraTriboliumAnimalsGene Expression ProfilingGenes, MitochondrialReproductionTranscriptomeC. tripartitusIllumina sequencingImmunity-related genesInformed conservation planningSimple sequence repeatsTranscriptome

Identifiers

PMID36864388
PMCPMC9979532
OpenAlexW4322769696

What Socratic 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 Socratic graph.