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Plants
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Crop Genome Sequencing and Analysis
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Crop Genome Sequencing and Analysis

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 30 November 2025 | Viewed by 2231

Special Issue Editor

Dr. Juan J. Gutierrez-Gonzalez

E-Mail Website
Guest Editor
Department of Molecular Biology, University of Leon, Leon, Spain
Interests: genomics; bioinformatics; genetics; plant breeding; biotechnology; gene expression; legumes; plant diseases
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

With the reduction in sequencing prices brought about by new technologies, tasks like genome-wide sequencing or resequencing and subsequent whole genome analysis have become routine. At the same time, with more fully annotated and ordered reference genome sequences in place, researchers and breeders can now easily access or generate high-quality sequence-level information to precisely define the necessary changes in the genomes for breeding programs. This Special Issue of Plants will highlight contributions in which high-throughput genomic methods are used to drive information on aspects such as, but not limited to, crop sequencing and assembly, crop genome and transcriptome analyses, gene expression, high-throughput marker identification, genomics-aided breeding, genomic selection, and targeted breeding technologies, including genome editing. Priority will be given to crops. Manuscripts on orphan crops are welcome.

I hope you may find this Special Issue of interest for submitting your manuscripts.

Dr. Juan J. Gutierrez-Gonzalez
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • crop breeding
  • genome sequencing
  • resequencing
  • genome-wide analysis
  • high-throughput markers

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Published Papers (4 papers)

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Research

19 pages, 14469 KB  
Article
Genome-Wide Identification of the AP2/ERF Gene Family and Functional Analysis of PgAP2/ERF187 Under Cold Stress in Panax ginseng C. A. Meyer
by Yihan Wang, Shurui Wang, Xiangru Meng, Ping Wang, Hongmei Lin, Peng Di and Yingping Wang
Plants 2025, 14(18), 2922; https://doi.org/10.3390/plants14182922 - 20 Sep 2025
Viewed by 283
Abstract
Panax ginseng C. A. Meyer (P. ginseng) is a medicinal plant rich in bioactive components such as ginsenosides, polysaccharides, and volatile oils and is widely used in both the pharmaceutical and food industries. While the AP2/ERF gene family is well-documented to [...] Read more.
Panax ginseng C. A. Meyer (P. ginseng) is a medicinal plant rich in bioactive components such as ginsenosides, polysaccharides, and volatile oils and is widely used in both the pharmaceutical and food industries. While the AP2/ERF gene family is well-documented to play crucial roles in plant growth, development, and defense responses, functional studies on this gene family in P. ginseng remain unreported. Our genome-wide analysis identified 318 PgAP2/ERF family members, which are classified into five subfamilies: AP2, DREB, ERF, RAV, and Soloist. Homology analysis revealed that segmental duplication serves as the primary evolutionary driver for the PgAP2/ERF gene family in P. ginseng. RT-qPCR analysis demonstrated that all PgAP2/ERF members in the DREB-A1 subgroup respond to cold stress. Specifically, we found that the DREB-A1 member PgAP2/ERF187 plays a pivotal role in the cold stress response, with its expression specifically induced by ABA. Overexpression of PgAP2/ERF187 in Arabidopsis significantly enhanced the expression of cold tolerance-related genes. Subcellular localization analysis confirmed the co-localization of PgABF and PgAP2/ERF187 in the nucleus. Combining transcription factor interaction predictions and yeast one-hybrid experiments, we propose that PgABF likely regulates PgAP2/ERF187 expression by directly binding to its promoter region. These findings unveil the potential mechanism of the “PgABF-PgAP2/ERF187” regulatory module within the ABA signaling pathway during P. ginseng’s cold stress adaptation, thereby providing novel theoretical insights into the molecular mechanisms underlying P. ginseng’s cold resistance. Full article
(This article belongs to the Special Issue Crop Genome Sequencing and Analysis)
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17 pages, 1073 KB  
Article
Association Mapping Analysis of Morphological Characteristics in F2 Population of Perilla (Perilla frutescens L.) Using SSR Markers
by Tae Hyeon Heo, Hyeon Park, Jungeun Cho, Da Hyeon Lee and Ju Kyong Lee
Plants 2025, 14(17), 2799; https://doi.org/10.3390/plants14172799 - 6 Sep 2025
Viewed by 497
Abstract
To identify SSR markers associated with both quantitative and qualitative traits in Perilla, we analyzed a total of 68 individuals from an F2 population derived from a cross between WPC06-339 (weedy var. crispa) and WPF17-049 (weedy var. frutescens) using [...] Read more.
To identify SSR markers associated with both quantitative and qualitative traits in Perilla, we analyzed a total of 68 individuals from an F2 population derived from a cross between WPC06-339 (weedy var. crispa) and WPF17-049 (weedy var. frutescens) using 40 SSR primer sets. The genetic diversity of these markers ranged from 0.464 to 0.676, with a mean value of 0.607. Correlation analysis of 13 morphological traits (4 qualitative, 9 quantitative) revealed significant positive correlations among three leaf-related traits and two inflorescence-related traits. Association analysis involving 40 SSR markers and the 13 morphological traits identified 39 significant marker–trait associations, comprising 18 SSR markers associated with 11 morphological traits. Among these SSR markers, 12 were associated with two to five quantitative or qualitative traits. Additionally, 10 SSR markers were significantly associated with three qualitative traits, while 15 SSR markers were associated with eight quantitative traits. Notably, GBPFM179, KNUPF59, and KNUPF167 were significantly associated with multiple quantitative or qualitative traits. GBPFM179 and KNUPF182 exhibited the highest R2 values, of 0.38, for stem color and days to maturity, respectively. These SSR markers demonstrate the potential for use in marker-assisted selection in Perilla breeding programs aimed at enhancing leaf or seed productivity through the selection of both quantitative and qualitative traits. Full article
(This article belongs to the Special Issue Crop Genome Sequencing and Analysis)
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16 pages, 3551 KB  
Article
Transcriptome Analysis of Developmental Gene Expression in Thesium chinense Turcz
by Sijia Liang, Qiongqiong Wang, Qin Han, Xinmin Zhang, Yiyuan Liu, Miaosheng Chen, Chengcai Zhang, Zhaoyang Wang, Junxiao Li, Di Yu, Hao Zhan, Yubin Zhang and Zhongping Xu
Plants 2025, 14(16), 2549; https://doi.org/10.3390/plants14162549 - 16 Aug 2025
Viewed by 510
Abstract
Thesium chinense Turcz. (T. chinense), a perennial herb in the Santalaceae family, exhibits potent antibacterial and anti-inflammatory properties. Transcriptome sequencing was performed on one- and two-year-old T. chinense plants across seedling, flowering, and fruiting stages (all sampled from the same location) [...] Read more.
Thesium chinense Turcz. (T. chinense), a perennial herb in the Santalaceae family, exhibits potent antibacterial and anti-inflammatory properties. Transcriptome sequencing was performed on one- and two-year-old T. chinense plants across seedling, flowering, and fruiting stages (all sampled from the same location) using the illumina NovaSeq 6000 platform. A total of 58,706 unigenes were identified, including 1656 transcription factors (TFs). Further analysis classified these TFs into seven functional categories, enabling the reconstruction of a representative TF regulatory network. Differential expression analysis revealed that the number of differentially expressed genes (DEGs) ranged from 2000 to 5000 during different developmental stages in first-year plants, while varying between 1000 and 2000 in second-year plants. Comparative analysis of DEGs between one- and two-year-old plants showed that they were primarily associated with sesquiterpene, triterpene, and terpene skeleton biosynthesis, as well as other metabolic pathways. Additionally, analysis of key genes involved in flavonoid biosynthesis—the major bioactive compounds in T. chinense—revealed their predominant accumulation during the first year of growth. This study provides valuable insights into the developmental biology of T. chinense and establishes a foundation for future research on flavonoid biosynthesis pathway genes and their therapeutic applications. Full article
(This article belongs to the Special Issue Crop Genome Sequencing and Analysis)
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25 pages, 6623 KB  
Article
Characterization of the Mitochondrial Genome of Hippophae rhamnoides subsp. sinensis Rousi Based on High-Throughput Sequencing and Elucidation of Its Evolutionary Mechanisms
by Mengjiao Lin, Na Hu, Jing Sun and Wu Zhou
Plants 2025, 14(16), 2547; https://doi.org/10.3390/plants14162547 - 15 Aug 2025
Viewed by 486
Abstract
Hippophae rhamnoides ssp. sinensis Rousi a species of significant ecological and economic value that is native to the Qinghai–Tibet Plateau and arid/semi-arid regions. Investigating the mitochondrial genome can elucidate stress adaptation mechanisms, population genetic structure, and hybrid evolutionary history, offering molecular insights for [...] Read more.
Hippophae rhamnoides ssp. sinensis Rousi a species of significant ecological and economic value that is native to the Qinghai–Tibet Plateau and arid/semi-arid regions. Investigating the mitochondrial genome can elucidate stress adaptation mechanisms, population genetic structure, and hybrid evolutionary history, offering molecular insights for ecological restoration and species conservation. However, the genetic information and evolutionary mechanisms of its mitochondrial genome remain poorly understood. This study aimed to assemble the complete mitochondrial genome of H. rhamnoides L. ssp. sinensis using Illumina sequencing, uncovering its structural features, evolutionary pressures, and environmental adaptability and addressing the research gap regarding mitochondrial genomes within the Hippophae genus. The study assembled a 454,444 bp circular mitochondrial genome of H. rhamnoides ssp. sinensis, with a GC content of 44.86%. A total of 73 genes and 3 pseudogenes were annotated, with the notable absence of the rps2 gene, which is present in related species. The genome exhibits significant codon usage bias, particularly with high-frequency use of the alanine codon GCU and the isoleucine codon AUU. Additionally, 449 repetitive sequences, potentially driving genome recombination, were identified. Our evolutionary pressure analysis revealed that most genes are under purifying selection, while genes such as atp4 and nad4 exhibit positive selection. A nucleotide diversity analysis revealed that the sdh4 gene exhibits the highest variation, whereas rrn5 is the most conserved. Meanwhile, phylogenetic analysis showed that H. rhamnoides ssp. sinensis from China is most closely related to Hippophae tibetana, with extensive homologous sequences (49.72% of the chloroplast genome) being identified between the chloroplast and mitochondrial genomes, indicating active inter-organellar gene transfer. Furthermore, 539 RNA editing sites, primarily involving hydrophilic-to-hydrophobic amino acid conversions, were predicted, potentially regulating mitochondrial protein function. Our findings establish a foundation for genetic improvement and research on adaptive evolutionary mechanisms in the Hippophae genus, offering a novel case study for plant mitochondrial genome evolution theory. Full article
(This article belongs to the Special Issue Crop Genome Sequencing and Analysis)
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