Evidence map›Paper›PMID 38809491›Full record

ArticleGenes & genomics2024

Transcriptome sequencing of the endangered land snail Karaftohelix adamsi from the Island Ulleung: De novo assembly, annotation, valuation of fitness genes and SSR markers.

Jie Eun Park, Bharat Bhusan Patnaik, Min Kyu Sang, Dae Kwon Song, Jun Yang Jeong, Chan Eui Hong, Yong Tae Kim, Hyeon Jun Shin, Liu Ziwei, Hongray Howrelia Patnaik and 9 more

Abstract read
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In one paragraph

Article in Genes & genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0citing papers in PubMed
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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

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.

Jie Eun Park *Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea.
Bharat Bhusan Patnaik *Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea.
Min Kyu SangKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea.
Dae Kwon SongKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea.
Jun Yang JeongKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea.
Chan Eui HongKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea.
Yong Tae KimKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea.
Hyeon Jun ShinKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea.
Liu ZiweiKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea.
Hongray Howrelia PatnaikKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea.
Hee Ju HwangDepartment of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, 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.
Jung Ho KoPolice Science Institute, Korean National Police University, Asan, 31539, Chungnam, Korea.
Jun Sang LeeKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea.
Hong Seog ParkResearch Institute, GnC BIO Co., LTD, 621-6 Banseok-Dong, Yuseong-Gu, Daejeon, 34069, Korea.
Yong Hun JoKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South 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, 31538, South Korea. yslee@sch.ac.kr.ORCID 0000-0002-8687-589X

Funding

Korea Basic Science Institute 2022R1A6C101B794the National Research Foundation NRF-2017R1D1A3B06034971the National Research Foundation NRF-2021R1A6A1A03039503
6 · The paper itself

Abstract

backgroundThe Bradybaenidae snail Karaftohelix adamsi is endemic to Korea, with the species tracked from Island Ulleung in North Gyeongsang Province of South Korea. K. adamsi has been classified under the Endangered Wildlife Class II species of Korea and poses a severe risk of extinction following habitat disturbances. With no available information at the DNA (genome) or mRNA (transcriptome) level for the species, conservation by utilizing informed molecular resources seems difficult.

objectiveIn this study, we used the Illumina short-read sequencing and Trinity de novo assembly to draft the reference transcriptome of K. adamsi.

resultsAfter assembly, 13,753 unigenes were obtained of which 10,511 were annotated to public databases (a maximum of 10,165 unigenes found homologs in PANM DB). A total of 6,351, 3,535, 358, and 3,407 unigenes were ascribed to the functional categories under KOG, GO, KEGG, and IPS, respectively. The transcripts such as the HSP 70, aquaporin, TLR, and MAPK, among others, were screened as putative functional resources for adaptation. DNA transposons were found to be thickly populated in comparison to retrotransposons in the assembled unigenes. Further, 2,164 SSRs were screened with the promiscuous presence of dinucleotide repeats such as AC/GT and AG/CT.

conclusionThe transcriptome-guided discovery of molecular resources in K. adamsi will not only serve as a basis for functional genomics studies but also provide sustainable tools to be utilized for the protection of the species in the wild. Moreover, the development of polymorphic SSRs is valuable for the identification of species from newer habitats and cross-species genotyping.

Indexed as

Endangered SpeciesMicrosatellite RepeatsSnailsTranscriptomeAnimalsGenetic FitnessMolecular Sequence AnnotationRepublic of KoreaAdaptation genesEndangered speciesKaraftohelix adamsiSSR markersTranscriptome

Identifiers

PMID38809491

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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.