Evidence map›Paper›PMID 40082317›Full record

ArticleRice (New York, N.Y.)2025

Revealing Genomic Traits and Evolutionary Insights of Oryza officinalis from Southern China Through Genome Assembly and Transcriptome Analysis.

Can Chen, Haifei Hu, Hui Guo, Xiuzhong Xia, Zongqiong Zhang, Baoxuan Nong, Rui Feng, Shuhui Liang, Boheng Liu, Jianhui Liu and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Rice (New York, N.Y.), 2025. 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
–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

1 citing paper in PubMed.

  1. Chromosome-Level Genome Assembly ofPlants (Basel, Switzerland) · 2026
    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

13 authors.

Can Chen *Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
Haifei Hu *Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Rice Science and Technology, Guangdong Rice Engineering Laboratory, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
Hui Guo *Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
Xiuzhong XiaGuangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
Zongqiong ZhangGuangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
Baoxuan NongGuangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
Rui FengGuangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
Shuhui LiangGuangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
Boheng LiuInstitute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
Jianhui LiuGuangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
Danting LiGuangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China. ricegl@163.com.
Junliang ZhaoKey Laboratory of Genetics and Breeding of High Quality Rice in Southern China, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Rice Science and Technology, Guangdong Rice Engineering Laboratory, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China. zhao_junliang@gdaas.cn.
Xinghai YangGuangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China. yangxinghai514@163.com.

Funding

Guangxi Academy of Agricultural Sciences 2023YM62, 2025YP032Guangxi Department of Science and Technology GuikeAA22068087-2National Key Research and Development Program of China 2021YFD1200505National Natural Science Foundation of China 32360519, 3226047, 32160436, 32060476 and 31860371
6 · The paper itself

Abstract

Wild rice, as the ancestor of cultivated rice, has accumulated a wide range of beneficial traits through prolonged natural selection and evolution. Oryza officinalis, belonging to the CC genome, differs significantly from the AA genome. In this study, we utilized second- and third-generation sequencing, along with Hi-C technology, to assemble the genome of MT10 (O. officinalis). The assembled genome is 552.58 Mb, with contigs and scaffold N50 values of 40.04 and 44.48 Mb, respectively, and 96.73% of the sequences anchored to 12 chromosomes. A total of 33,813 genes were annotated, and repetitive sequences account for 54.24% of the MT10 genome. The number of unique genes in MT10 exceeds that in the O. officinalis genome from Thailand, and their divergence time is estimated at 1.6 million years ago. The MT10 genome exhibits fewer expanded gene families compared to contracted ones, with the expanded families predominantly associated with disease and pest resistance. Comparative genomic analysis of MT10 and Nipponbare reveals sequence variations in biotic and abiotic resistance-related genes. In particular, the presence of R genes and cystatin gene families in MT10 may contribute to its unique insect resistance. Transcriptome analyses indicate that flavonoid biosynthesis and MAPK-related genes are expressed in response to brown planthopper infestation. This study represents the first chromosome-level genome assembly of MT10, providing a reference sequence for the efficient cloning of beneficial genes from O. officinalis, which holds significant potential for the genetic improvement of cultivated rice.

Indexed as

CC genomeEvolutionGenome sequencingOryza officinalisResistance

Identifiers

PMID40082317
PMCPMC11906960

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.