Frontiers in Plant Science | Functional and Applied Plant Genomics

Original Research

Published on 30 Jun 2025

Mitochondrial genome assembly and comparative analysis of decaploid Camellia hainanica

in Functional and Applied Plant Genomics

Shihui Zhang
Yuyan Zhang
Sheng Luo
Jie Gao
Haiyan Hu
Jinping Liu
Wenqiang Wu
Jian Wang
Xiaolong Huang
Hanggui Lai

Frontiers in Plant Science

doi 10.3389/fpls.2025.1556379

2,416 views
3 citations

Editorial

Published on 27 Jun 2025

Editorial: Genetic resources and conservation strategies for neotropical plant biodiversity

in Functional and Applied Plant Genomics

Enéas Ricardo Konzen
Miklos Maximiliano Bajay
Jorge Carlos Berny Mier y Teran
Marcos Vinícius Bohrer Monteiro Siqueira

Frontiers in Plant Science

doi 10.3389/fpls.2025.1629546

1,467 views

Original Research

Published on 25 Jun 2025

Improving Soybean Seed Sucrose Content using TILLING by Sequencing Analyses of The Soybean Sucrose Synthase Gene Family

in Functional and Applied Plant Genomics

Dounya Knizia
Erdem Anil
Yasser Salhi
Haiying Shi
Abdelhalim El Baze
My Abdelmajid Kassem
Naoufal Lakhssassi
Henry T. Nguyen
Khalid Meksem

Frontiers in Plant Science

doi 10.3389/fpls.2025.1606321

2,076 views

Original Research

Published on 25 Jun 2025

Identification of DNA N6-methyladenine modifications in the rice genome with a fine-tuned large language model

in Functional and Applied Plant Genomics

Yichi Zhang
Hao Chen
Shicheng Xiang
Zhibin Lv

Frontiers in Plant Science

doi 10.3389/fpls.2025.1626539

1,889 views
1 citation

Original Research

Published on 20 Jun 2025

Screening and identification of grain sorghum germplasm for salt tolerance at seedling stage

in Functional and Applied Plant Genomics

Yu Wang
Dongyang Li
Chunjuan Liu
Xiaolong Shi
Yan Huang
Chang Liu
Yufei Zhou

Frontiers in Plant Science

doi 10.3389/fpls.2025.1610685

2,312 views
4 citations

Data Report

Published on 20 Jun 2025

Whole genome sequencing of Neolamarckia macrophylla (Roxb.) Bosser and Neolamarckia cadamba (Roxb.) Bosser from Indonesia: a vital resource for completing chloroplast genomes and mining microsatellite markers

in Functional and Applied Plant Genomics

Fifi Gus Dwiyanti
Irsyad Kamal
Rahadian Pratama
Dhika Syaputra
Evayusvita Rustam
Ratna Uli Damayanti
Iskandar Z. Siregar
Dede J. Sudrajat

Frontiers in Plant Science

doi 10.3389/fpls.2025.1608577

2,167 views
1 citation

Original Research

Published on 19 Jun 2025

Genome-wide identification, transcriptional profiling, and miRNA-binding site analysis of the LBD gene family in the camphor tree

in Functional and Applied Plant Genomics

Jiaqi Zhang
Luyang Shan
Haoran Qi
Caihui Chen
Yongda Zhong
Meng Xu

Frontiers in Plant Science

doi 10.3389/fpls.2025.1591736

1,768 views

Original Research

Published on 13 Jun 2025

Genome-wide identification and characterization of soybean GH9 endo-1,4-β-glucanases

in Functional and Applied Plant Genomics

Weimin Zhan
Huijuan Huang
Zaipan Cai
Zhenwei Zhao
Xuefu Lin
Yize Peng
Zhicheng Dong
Di Qin
Li Jiang

Frontiers in Plant Science

doi 10.3389/fpls.2025.1597668

2,417 views
1 citation

Original Research

Published on 13 Jun 2025

Complete sequencing of the mitochondrial genome of tea plant Camellia sinensis cv. ‘Baihaozao’: multichromosomal structure, phylogenetic relationships, and adaptive evolutionary analysis

in Functional and Applied Plant Genomics

Zhiyin Chen
Zixu Wang
Wei Zhou
Sijie Liu
Yuxin Xiao
Yihui Gong

Frontiers in Plant Science

doi 10.3389/fpls.2025.1604404

2,427 views
4 citations

Editorial

Published on 10 Jun 2025

Editorial: Improving yield and quality of cereal crops: exploring and utilizing genes for green and efficient traits

in Functional and Applied Plant Genomics

Hao Zhou
Yuqing He
Ming Luo

Frontiers in Plant Science

doi 10.3389/fpls.2025.1617702

1,480 views

Original Research

Published on 09 Jun 2025

A BERT-based rice enhancer identification model combined with sequence-representation differential entropy interpretation

in Functional and Applied Plant Genomics

Yajing Pu
Xintong Hao
Zhaoqi Zheng
Huiyan Ma
Zhibin Lv

Frontiers in Plant Science

doi 10.3389/fpls.2025.1618174

2,615 views

Original Research

Published on 06 Jun 2025

GWAS and RNA-seq reveal novel loci and genes of low-nitrogen tolerance in cucumber (Cucumis sativus L.)

in Functional and Applied Plant Genomics

Huaxiang Wu
Huiming Yan
Bowen Li
Yike Han
Nan Liu
Mengyu Fan
Yahan Liu
Mingjie Lyu
Shengli Du
Aimin Wei

Frontiers in Plant Science

doi 10.3389/fpls.2025.1602360

3,488 views
2 citations

Original Research

Published on 05 Jun 2025

Comparative transcriptomics in B73-teosinte near-isogenic maize lines reveals key defense signaling and phytoalexins in response to Cercospora zeina infection

in Functional and Applied Plant Genomics

Xiaomeng Sun
Ruiyu Zhang
Zongping Wang
Haotian Zhang
Hairun Wen
Junli Zhang
Naibin Yu
Zhe Wang
Huanhuan Tai
Qin Yang

Frontiers in Plant Science

doi 10.3389/fpls.2025.1580016

2,203 views
1 citation

Original Research

Published on 05 Jun 2025

IRGL-RRI: interpretable graph representation learning for plant RNA–RNA interaction discovery

in Functional and Applied Plant Genomics

Qingquan Liao
Xuchong Liu
Wei Zhao
Yu Tong
Fangzheng Xu
Xinxin Liu
Yifan Chen

Frontiers in Plant Science

doi 10.3389/fpls.2025.1617495

2,017 views

Review

Published on 04 Jun 2025

Research progress of NAC transcription factors in woody plants

in Functional and Applied Plant Genomics

Huan Zhang
Jia Zhao
Tongxing Zhang
Guiying Wang
Zhixiao Han
Yuemei Meng
Jingran Bi
Yachao Ren
Minsheng Yang

Frontiers in Plant Science

doi 10.3389/fpls.2025.1592898

3,291 views
6 citations

Mini Review

Published on 03 Jun 2025

Foundation models in plant molecular biology: advances, challenges, and future directions

in Functional and Applied Plant Genomics

Feng Xu
Tianhao Wu
Qian Cheng
Xiangfeng Wang
Jun Yan

Frontiers in Plant Science

doi 10.3389/fpls.2025.1611992

8,430 views
4 citations

Original Research

Published on 30 May 2025

Systematic identification and analysis of WRKY transcription factors reveals the role of MrWRKY14 in Myrica rubra

in Functional and Applied Plant Genomics

Xiurun Fan
Minghui Chen
Huiling Zhang
Yumeng Liu
Meng Yang
Chengyang Ye
Hailing Gu
Kai Xu
Boping Wu

Frontiers in Plant Science

doi 10.3389/fpls.2025.1602750

2,825 views
4 citations

Original Research

Published on 30 May 2025

Intensifying cropping sequences in the US Central Great Plains: an in silico analysis of a sorghum–wheat sequence

in Functional and Applied Plant Genomics

Lucia Marziotte
Ana J. P. Carcedo
Daniel Rodriguez
Laura Mayor
P. V. Vara Prasad
Ignacio A. Ciampitti

Frontiers in Plant Science

doi 10.3389/fpls.2025.1525128

1,898 views

Original Research

Published on 23 May 2025

Genome-wide identification and development of SSR molecular markers for genetic diversity studies in Ilex asprella

in Functional and Applied Plant Genomics

Jingchun Li
Changqian Quan
Rongchang Wei
Fan Wei
Qing Ma
Yuquan Huang
Meihua Xu
Danfeng Tang

Frontiers in Plant Science

doi 10.3389/fpls.2025.1582154

2,929 views
4 citations

Original Research

Published on 21 May 2025

Integrated metabolome-transcriptome analyses reveal key pathways regulating staminate catkin development and pollen maturation in Betula platyphylla

in Functional and Applied Plant Genomics

Xinying Liu
Jiayuan Shi
Jingyun Zhang
Bello Hassan Jakada
HuiLing Guo
Kehao Zeng
Xingguo Lan

Frontiers in Plant Science

doi 10.3389/fpls.2025.1581560

1,753 views
1 citation

Original Research

Published on 16 May 2025

Selection and validation of reference genes for quantitative real-time PCR during the developmental stages of seeds in Sophora davidii

in Functional and Applied Plant Genomics

Jingjing Li
Shanrong Han
Zongren Xu
Bin Deng
Na Zheng
Yaqiong Su
Ziyao Qiao
Yun Yang
Hong Zhang
Zongsuo Liang

Frontiers in Plant Science

doi 10.3389/fpls.2025.1485586

1,953 views

Data Report

Published on 16 May 2025

Transcriptome map and genome annotation of flax line 3896

in Functional and Applied Plant Genomics

Daiana A. Zhernova
Alexander A. Arkhipov
Tatiana A. Rozhmina
Alexander A. Zhuchenko
Nadezhda L. Bolsheva
Elizaveta A. Sigova
Ekaterina M. Dvorianinova
Elena V. Borkhert
Elena N. Pushkova
Nataliya V. Melnikova

Frontiers in Plant Science

doi 10.3389/fpls.2025.1520832

2,434 views
2 citations

Original Research

Published on 14 May 2025

Characterization analyses of MADS-box genes highlighting their functions with seed development in Ricinus communis

in Functional and Applied Plant Genomics

Jing Sun
Zekun Zhou
Fanqing Meng
Mengyun Wen
Aizhong Liu
Anmin Yu

Frontiers in Plant Science

doi 10.3389/fpls.2025.1589915

2,249 views
2 citations

Original Research

Published on 13 May 2025

Identification of key genes associated with mesocotyl length through a genome-wide association study in rice

in Functional and Applied Plant Genomics

Li Xue
Sen Wang
Qiuyu Zhang
Bing Han
Di Cui
Longzhi Han
Jianxin Deng
Xiaoding Ma

Frontiers in Plant Science

doi 10.3389/fpls.2025.1546580

2,924 views
1 citation

654 articles

articles

Mitochondrial genome assembly and comparative analysis of decaploid Camellia hainanica

Editorial: Genetic resources and conservation strategies for neotropical plant biodiversity

Improving Soybean Seed Sucrose Content using TILLING by Sequencing Analyses of The Soybean Sucrose Synthase Gene Family

Identification of DNA N6-methyladenine modifications in the rice genome with a fine-tuned large language model

Screening and identification of grain sorghum germplasm for salt tolerance at seedling stage

Whole genome sequencing of Neolamarckia macrophylla (Roxb.) Bosser and Neolamarckia cadamba (Roxb.) Bosser from Indonesia: a vital resource for completing chloroplast genomes and mining microsatellite markers

Genome-wide identification, transcriptional profiling, and miRNA-binding site analysis of the LBD gene family in the camphor tree

Genome-wide identification and characterization of soybean GH9 endo-1,4-β-glucanases

Complete sequencing of the mitochondrial genome of tea plant Camellia sinensis cv. ‘Baihaozao’: multichromosomal structure, phylogenetic relationships, and adaptive evolutionary analysis

Editorial: Improving yield and quality of cereal crops: exploring and utilizing genes for green and efficient traits

A BERT-based rice enhancer identification model combined with sequence-representation differential entropy interpretation

GWAS and RNA-seq reveal novel loci and genes of low-nitrogen tolerance in cucumber (Cucumis sativus L.)

Comparative transcriptomics in B73-teosinte near-isogenic maize lines reveals key defense signaling and phytoalexins in response to Cercospora zeina infection

IRGL-RRI: interpretable graph representation learning for plant RNA–RNA interaction discovery

Research progress of NAC transcription factors in woody plants

Foundation models in plant molecular biology: advances, challenges, and future directions

Systematic identification and analysis of WRKY transcription factors reveals the role of MrWRKY14 in Myrica rubra

Intensifying cropping sequences in the US Central Great Plains: an in silico analysis of a sorghum–wheat sequence

Genome-wide identification and development of SSR molecular markers for genetic diversity studies in Ilex asprella

Integrated metabolome-transcriptome analyses reveal key pathways regulating staminate catkin development and pollen maturation in Betula platyphylla

Selection and validation of reference genes for quantitative real-time PCR during the developmental stages of seeds in Sophora davidii

Transcriptome map and genome annotation of flax line 3896

Characterization analyses of MADS-box genes highlighting their functions with seed development in Ricinus communis

Identification of key genes associated with mesocotyl length through a genome-wide association study in rice