Evidence map›Paper›PMID 40619359›Full record

ArticleBMC biology2025

A gap-free reference genome of Populus deltoides provides insights into karyotype evolution of Salicaceae.

Changwei Bi, Ning Sun, Zhuangwei Hou, Xiaogang Dai, Huaitong Wu, Fuchuan Han, Zefu Wang, Tongming Yin

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC biology, 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

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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. 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

8 authors.

Changwei BiState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing, 210037, China.
Ning SunCollege of Information Science and Technology & Artificial Intelligence, Nanjing Forestry University, Nanjing, 210037, China.
Zhuangwei HouShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
Xiaogang DaiState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing, 210037, China.
Huaitong WuState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing, 210037, China.
Fuchuan HanResearch Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China.
Zefu WangState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing, 210037, China.
Tongming YinState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing, 210037, China. tmyin@njfu.edu.cn.

Funding

National Key Research and Development Program of China 2021YFD2201205Natural Science Foundation of Jiangsu Province BK20220414Priority Academic Program Development of Jiangsu Higher Education Institutions PAPD
6 · The paper itself

Abstract

backgroundAs a species of poplar with significant economic and ecological value, the high-quality genome assembly of Populus deltoides (P. deltoides) is crucial for understanding its growth and development, stress resistance, and biosynthetic pathways.

resultsWe presented a gap-free telomere-to-telomere (T2T) assembly of the P. deltoides genome using PacBio HiFi and Hi-C sequencing data. The P. deltoides genome is 395.9 Mb in length and consists of 27 contigs (contig N50: 22.73 Mb), encompassing nearly all telomeres (36 out of 38). Following careful evaluations of genome accuracy and completeness, our assembly represents a substantial enhancement over the previously published genomes of P. deltoides, eliminating all gaps and rectifying numerous assembly errors. The expanded and contracted gene families of the P. deltoides genome were significantly enriched in functions crucial for stress and defense responses, as well as environmental adaptation. Additionally, our study confirms that all Salicaceae genomes have undergone at least two major whole genome duplication events. The most recent duplication event, shared by between Salicaceae and Manihot esculenta, is estimated to have occurred approximately 44.2 to 57.8 Mya. Most importantly, we reconstructed the ancestral karyotype of Salicaceae, which comprised 11 proto-chromosomes.

conclusionsThis study provides strong evidence for comprehensive understanding of the evolutionary dynamics within Salicaceae genomes and provides valuable genomic resources for the genetic improvement and biological breeding of P. deltoides.

Indexed as

Evolution, MolecularGenome, PlantKaryotypePopulusSalicaceaeChromosomes, PlantAncestral karyotype reconstructionGap-free genome assemblyGene familyGenome evolutionPopulus

Identifiers

PMID40619359
PMCPMC12232824

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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.