Evidence map›Paper›PMID 39840553›Full record

ArticleAdvanced science (Weinheim, Baden-Wurttemberg, Germany)2025

Global Protein Interactome Mapping in Rice Using Barcode-Indexed PCR Coupled with HiFi Long-Read Sequencing.

Xixi Liu, Dandan Xia, Jinjin Luo, Mengyuan Li, Lijuan Chen, Yiting Chen, Jie Huang, Yanan Li, Huayu Xu, Yang Yuan and 19 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Advanced science (Weinheim, Baden-Wurttemberg, Germany), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  1. Article
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  3. Review
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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

29 authors.

Xixi LiuState Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China.
Dandan XiaNational Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
Jinjin LuoState Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China.
Mengyuan LiNational Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
Lijuan ChenState Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China.
Yiting ChenState Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China.
Jie HuangState Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China.
Yanan LiState Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China.
Huayu XuState Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China.
Yang YuanState Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China.
Yu ChengState Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China.
Zhiyong LiState Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China.
Guanghao LiState Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China.
Shiyi WangState Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China.
Xinyong LiuState Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China.
Wanning LiuState Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China.
Fengyong ZhangState Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China.
Zhichao LiuState Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China.
Xiaohong TongState Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China.
Yuxuan HouState Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China.
Yifeng WangState Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China.
Jiezheng YingState Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China.
Abdullaev Mirtemir Baxodir UgliRice Research Institute of Uzbekistan, Tashkent, 111506, Uzbekistan.
Mukhammadjon Arabboevich ErgashevRice Research Institute of Uzbekistan, Tashkent, 111506, Uzbekistan.
Sanqiang ZhangHubei Agricultural Machinery Engineering Research and Design Institute, Hubei University of Technology, Wuhan, 430068, China.
Wenya YuanState Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China.
Dawei XueCollege of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China.
Jianwei ZhangNational Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
Jian ZhangState Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China.ORCID https://orcid.org/0000-0003-2804-0162

Funding

ASTIP program of CAASCentral Public-interest Scientific Institution Basal Research Fund Y2023PT17China Postdoctoral Science Foundation 2024M763606Major Program of Natural Science Foundation of Zhejiang LD24C130001Major Project of Hubei Hongshan Laboratory 2022HSZD031National Key R&D Program of China 2020YFE0202300National Key R&D Program of China 2022YFE0125600National Natural Science Foundation of China 32072050National Natural Science Foundation of China U22A20456National Natural Science Foundation of China W2412006Special support plan for high-level talents in Zhejiang 2022R52020
6 · The paper itself

Abstract

Establishing the protein-protein interaction network sheds light on functional genomics studies by providing insights from known counterparts. However, the rice interactome has barely been studied due to the lack of massive, reliable, and cost-effective methodologies. Here, the development of a barcode-indexed PCR coupled with HiFi long-read sequencing pipeline (BIP-seq) is reported for high throughput Protein Protein Interaction (PPI)identification. BIP-seq is essentially built on the integration of library versus library Y2H mating strategy to facilitate the efficient acquisition of random PPI colonies, semi-mechanized dual barcode-indexed yeast colony PCR for the large-scale indexed amplification of bait and prey cDNAs, and massive pac-bio sequencing of PCR amplicon pools. It is demonstrated that BIP-seq could map over 15 000 high-confidence (≈62.5% could be verified by Bimolecular fluorescence Complementation (BiFC)) rice PPIs within 2 months, outperforming the other reported methods. In addition, the obtained 23 032 rice PPIs, including 22,665 newly identified PPIs, greatly expanded the current rice PPI dataset, provided a comprehensive overview of the rice PPIs networks, and could be a valuable asset in facilitating functional genomics research in rice.

Indexed as

OryzaPlant ProteinsPolymerase Chain ReactionProtein Interaction MappingProtein Interaction MapsHigh-Throughput Nucleotide SequencingPlant Proteinsbarcode‐indexed PCRHiFi sequencingprotein–protein interactomerice

Identifiers

PMID39840553
PMCPMC11923860

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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.