Evidence map›Paper›PMID 38438864›Full record

ArticleBMC genomic data2024

De novo genome assembly of a high-protein soybean variety HJ117.

Zhi Liu, Qing Yang, Bingqiang Liu, Chenhui Li, Xiaolei Shi, Yu Wei, Yuefeng Guan, Chunyan Yang, Mengchen Zhang, Long Yan

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

Article in BMC genomic data, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
2.4field-weighted citation impact, top 12% 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

1 citing paper in PubMed, 4 citations in OpenAlex.

  1. 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 at 3 institutions in 1 country.

Zhi Liu *Hebei Key Laboratory of Crop Genetics and Breeding, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, National Soybean Improvement Center Shijiazhuang Sub- Center, Hebei Academy of Agricultural and Forestry Sciences, 050035, Shijiazhuang, Hebei, China.
Qing Yang *Hebei Key Laboratory of Crop Genetics and Breeding, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, National Soybean Improvement Center Shijiazhuang Sub- Center, Hebei Academy of Agricultural and Forestry Sciences, 050035, Shijiazhuang, Hebei, China.
Bingqiang Liu *Hebei Key Laboratory of Crop Genetics and Breeding, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, National Soybean Improvement Center Shijiazhuang Sub- Center, Hebei Academy of Agricultural and Forestry Sciences, 050035, Shijiazhuang, Hebei, China.
Chenhui LiHebei Key Laboratory of Crop Genetics and Breeding, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, National Soybean Improvement Center Shijiazhuang Sub- Center, Hebei Academy of Agricultural and Forestry Sciences, 050035, Shijiazhuang, Hebei, China.
Xiaolei ShiHebei Key Laboratory of Crop Genetics and Breeding, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, National Soybean Improvement Center Shijiazhuang Sub- Center, Hebei Academy of Agricultural and Forestry Sciences, 050035, Shijiazhuang, Hebei, China.
Yu WeiHebei Key Laboratory of Crop Genetics and Breeding, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, National Soybean Improvement Center Shijiazhuang Sub- Center, Hebei Academy of Agricultural and Forestry Sciences, 050035, Shijiazhuang, Hebei, China.
Yuefeng GuanGuangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006, Guangzhou, Guangdong, China.
Chunyan YangHebei Key Laboratory of Crop Genetics and Breeding, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, National Soybean Improvement Center Shijiazhuang Sub- Center, Hebei Academy of Agricultural and Forestry Sciences, 050035, Shijiazhuang, Hebei, China.
Mengchen ZhangHebei Key Laboratory of Crop Genetics and Breeding, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, National Soybean Improvement Center Shijiazhuang Sub- Center, Hebei Academy of Agricultural and Forestry Sciences, 050035, Shijiazhuang, Hebei, China. zhangmengchen@hotmail.com.
Long YanHebei Key Laboratory of Crop Genetics and Breeding, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, National Soybean Improvement Center Shijiazhuang Sub- Center, Hebei Academy of Agricultural and Forestry Sciences, 050035, Shijiazhuang, Hebei, China. dragonyan1979@163.com.
Ministry of Agriculture and Rural Affairs · CNHebei Academy of Agriculture and Forestry Sciences · CNGuangzhou University · CN

Funding

National Key Research and Development Program of China 2021YFD1201602National Natural Science Foundation of China 31871652Natural Science Foundation of Hebei Province C2020301020
6 · The paper itself

Abstract

objectivesSoybean is an important feed and oil crop in the world due to its high protein and oil content. China has a collection of more than 43,000 soybean germplasm resources, which provides a rich genetic diversity for soybean breeding. However, the rich genetic diversity poses great challenges to the genetic improvement of soybean. This study reports on the de novo genome assembly of HJ117, a soybean variety with high protein content of 52.99%. These data will prove to be valuable resources for further soybean quality improvement research, and will aid in the elucidation of regulatory mechanisms underlying soybean protein content. DATA DESCRIPTION: We generated a contiguous reference genome of 1041.94 Mb for HJ117 using a combination of Illumina short reads (23.38 Gb) and PacBio long reads (25.58 Gb), with high-quality sequence coverage of approximately 22.44× and 24.55×, respectively. HJ117 was developed through backcross breeding, using Jidou 12 as the recurrent parent and Chamoshidou as the donor parent. The assembly was further assisted by 114.5 Gb Hi-C data (109.9×), resulting in a contig N50 of 19.32 Mb and scaffold N50 of 51.43 Mb. Notably, Core Eukaryotic Genes Mapping Approach (CEGMA) assessment and Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment results indicated that most core eukaryotic genes (97.18%) and genes in the BUSCO dataset (99.4%) were identified, and 96.44% of the genomic sequences were anchored onto twenty pseudochromosomes.

Indexed as

Glycine maxPlant BreedingChinaSoybean ProteinsSoybean ProteinsDe novo assemblyGenome featureHigh protein contentSoybean

Identifiers

PMID38438864
PMCPMC10913422
OpenAlexW4392380526

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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.