Advancements in Plant Genetics and Genome Characterization

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

Deadline for manuscript submissions: closed (20 July 2024) | Viewed by 2583

Special Issue Editors


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Guest Editor
Department of Life Sciences, Yeungnam University, Gyeongsan 705-717, Gyeongsangbuk-do, Republic of Korea
Interests: plant genetics; plant genome characterization; chloroplast genome; mitochondrial genome; phylogenomic analysis; next generation sequencing, transcriptomics
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Department of Life Sciences, Yeungnam University, Gyeongsan 705-717, Gyeongsangbuk-do, Republic of Korea
Interests: plant genetics; ecology and evolution; PCR; genotyping; DNA sequencing; biodiversity; systematics, next-generation sequencing
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Our planet, Earth, is intrinsically plant-oriented, and the significance of plants cannot be overstated. They enrich Earth's biodiversity and serve as the bedrock of all life forms. Within the realm of plant biology, the exploration of molecular diversity within plant groups is a vibrant area of research. Particularly, the intricate cellular processes occurring within plant organelles - chloroplasts, mitochondria, and the nucleus - are paramount to plant life. These organelles, believed to have originated from ancestral bacteria billions of years ago, operate as enigmatic cellular compartments, orchestrating complex biochemical and molecular functions vital for plant survival.

With the advent of next-generation sequencing technologies, thousands of organellar genomes have been meticulously characterized. This extensive analysis has unraveled the intricacies of plant genome structures, revealed structural variations, and shed light on the evolutionary forces at play, adapting plants to their ever-changing environments. Furthermore, it has raised compelling questions about the interplay between organellar and nuclear genomes when structural changes occur in the former.

In light of these developments, this special issue explores the multifaceted landscape of chloroplast and mitochondrial genome complexity. We invite contributions encompassing various topics, including genome rearrangements, comparative genome analysis, intracellular gene transfer, cytoplasmic male sterility, Phylogenomics, and molecular evolution. These studies promise to deepen our understanding of plant genetics and the intricate characterization of organellar genomes.

We welcome both experimental and bioinformatic analyses of plant organellar genomes. This research topic spans reviews and original research articles, delving into the structural intricacies, comparative and evolutionary facets, variations within and among populations, functional aspects, phylogenomic insights, and other relevant subjects related to plant organelles, utilizing next-generation sequencing data.

Join us in this exploration of plant genetics and the fascinating world of organellar genomes, as we embark on a journey to unravel the complexities that underpin Earth's green tapestry.

Prof. Dr. Gurusamy Raman
Prof. Dr. Seon-Joo Park
Guest Editors

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

  • plant phylogenomics
  • chloroplast genome
  • mitochondrial genome
  • nuclear genome
  • intracellular gene transfer
  • genome characterization
  • structural analysis
  • next-generation sequencing
  • multi-omics study
  • ecology and evolution
  • biodiversity
  • bioinformatic analysis

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Published Papers (1 paper)

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Research

25 pages, 12604 KiB  
Article
Decoding the Transcriptomics of Oil Palm Seed Germination
by Padungsak Suksa-Ard, Sunya Nuanlaong, Chettupon Pooljun, Azzreena Mohamad Azzeme and Potjamarn Suraninpong
Plants 2024, 13(19), 2680; https://doi.org/10.3390/plants13192680 - 24 Sep 2024
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Abstract
Seed dormancy and germination are critical factors affecting oil palm production efficiency. The typical dormancy-breaking process involves dry heat treatment (38–40 °C for 40–60 days) followed by germination at 30–32 °C. To understand the molecular mechanisms behind this process and improve germination rates [...] Read more.
Seed dormancy and germination are critical factors affecting oil palm production efficiency. The typical dormancy-breaking process involves dry heat treatment (38–40 °C for 40–60 days) followed by germination at 30–32 °C. To understand the molecular mechanisms behind this process and improve germination rates and speed, we conducted transcriptome analysis at three stages: pre-incubation, 45-day incubation at 40 °C, and 14-day germination at 32 °C. Our findings, supported by qRT–PCR and DEGs analysis, identified four key stages: ABA degradation, energy mobilization, starch mobilization, and cell elongation and division. ABA pathway genes (SnRK2, PYR/PYL) were active during dormancy release, while GAE and GPI were upregulated after heat treatment, indicating increased energy metabolism and structural changes. During germination, genes involved in starch/sucrose metabolism (SPS, TPP, SS, MGAM) and cell wall biosynthesis (GAUT1, PE, GAE) supported embryo expansion, with BAM, PGM, GlgB fueling early growth. Auxin (TIR1, AUX/IAA, ARF), brassinosteroid (BRI1, BSK, BIN2, CYCD3), ethylene (ETR, CTR1), and jasmonic acid (JAR1, COI1) pathway genes regulated cell growth and stress response, promoting seedling development. Though gibberellins were not crucial for this oil palm variety, gene expression varied between varieties. This study provides information on oil palm seed germination that could be applied to other oil palm species, particularly in terms of incubation times and chemical treatments. Full article
(This article belongs to the Special Issue Advancements in Plant Genetics and Genome Characterization)
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