Technology-enabled great leap in deciphering plant genomes

Nature Plants, Journal Year: 2024, Volume and Issue: 10(4), P. 551 - 566

Published: March 20, 2024

Language: Английский

---

Phased telomere-to-telomere reference genome and pangenome reveal an expansion of resistance genes during apple domestication

PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 195(4), P. 2799 - 2814

Published: May 14, 2024

Abstract The cultivated apple (Malus domestica Borkh.) is a cross-pollinated perennial fruit tree of great economic importance. Earlier versions reference genomes were unphased, fragmented, and lacked comprehensive insights into the apple's highly heterozygous genome, which impeded advances in genetic studies breeding programs. In this study, we assembled haplotype-resolved telomere-to-telomere (T2T) genome for diploid cultivar Golden Delicious. Subsequently, constructed pangenome based on 12 assemblies from wild species to investigate dynamic changes functional genes. Our results revealed gene gain loss events during domestication. Compared with species, more families significantly enriched oxidative phosphorylation, pentose metabolic process, responses salt, abscisic acid biosynthesis process. analyses also demonstrated higher prevalence different types resistance analogs (RGAs) cultivars than their relatives, partially attributed segmental tandem duplication certain RGAs classes. Structural variations, mainly deletions insertions, have affected presence absence TIR-NB-ARC-LRR, NB-ARC-LRR, CC-NB-ARC-LRR Additionally, hybridization/introgression has contributed expansion genes domesticated apples. T2T provide important resources apples, emphasizing need study evolutionary mechanisms breeding.

Language: Английский

---

Telomere Length in Plants Estimated with Long Read Sequencing

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 27, 2024

Abstract Telomeres play an important role in chromosome stability and their length is thought to be related organism’s lifestyle lifespan. Telomere variable across plant species between cultivars of the same species, possibly conferring adaptive advantage. However, it not known whether telomere or life span a diverse array due lack information on plants. Here we leverage genomes assembled with long read sequencing data estimate by chromosome. We find that assemblies based Oxford Nanopore Technologies (ONT) accurately predict two model Arabidopsis thaliana Oryza sativa matching lab-based estimates. then different lifestyles lifespans general gymnosperms have shorter telomeres compared eudicots monocots. Crop frequently longer than wild relatives, been maintained clonally such as hemp reflecting this requires term chromosomal stability.

Language: Английский

---

Chromosome-level genome assemblies of Musa ornata and Musa velutina provide insights into pericarp dehiscence and anthocyanin biosynthesis in banana

Horticulture Research, Journal Year: 2024, Volume and Issue: 11(5)

Published: March 14, 2024

Abstract Musa ornata and velutina are members of the Musaceae family indigenous to South Southeast Asia. They very popular in horticultural market, but lack genomic sequencing data genetic studies has hampered efforts improve their ornamental value. In this study, we generated first chromosome-level genome assemblies for both species by utilizing Oxford Nanopore long reads Hi-C reads. The genomes M. were assembled into 11 pseudochromosomes with sizes 427.85 Mb 478.10 Mb, respectively. Repetitive sequences comprised 46.70% 50.91% total velutina, Differentially expressed gene (DEG) Gene Ontology (GO) enrichment analyses indicated that upregulated genes mature pericarps mainly associated saccharide metabolic processes, particularly at cell wall extracellular region. Furthermore, identified polygalacturonase (PG) exhibited higher expression level compared other tissues, potentially being accountable pericarp dehiscence. This study also anthocyanin biosynthesis pathway. Taken together, chromosomal-level provide valuable insights mechanism dehiscence banana, which will significantly contribute future molecular breeding efforts.

Language: Английский

---

The gap-free genome assemblies of two Pyrus bretschneideri cultivars and GWAS analyses identify a CCCH-type zinc finger protein as a key regulator of lignin biosynthesis and stone cell formation in pear fruit

Plant Communications, Journal Year: 2024, Volume and Issue: unknown, P. 101238 - 101238

Published: Dec. 1, 2024

Language: Английский

---

The Genetic Diversity, Population Structure, and Historical Dynamics of Wild Pyrus Species on the Yunnan–Kweichow Plateau

Horticulturae, Journal Year: 2025, Volume and Issue: 11(1), P. 106 - 106

Published: Jan. 20, 2025

Located in the southwestern region of China, Yunnan–Kweichow Plateau, is closely related to origins Pyrus L. Despite this important status, there has been relatively little population genetics research focused on wild species area. To address gap knowledge, present study was conducted investigating distributions Plateau region. These analyses entailed collection 80 accessions, whole-genome resequencing, and detection variants including SNPs, InDels, SVs, CNVs. Genetic structure revealed clear differences between P. pashia calleryana, where former additionally subdivided into five groups. The genetic these accessions aligned with their geographic distribution, highlighting fragmented nature populations Plateau. Analyses diversity suggested that central easter portions Yunnan Province are key centers whereas highest degree differentiation observed for southwest northwest regions. Demographic indicated currently a state contraction, evidence migration events populations.

Language: Английский

---

Molecular Insights into the Functional Role of PbNRT2.4 in Potassium Homeostasis and Nutrient Transport in Pyrus ussuriensis

Plant Stress, Journal Year: 2025, Volume and Issue: unknown, P. 100752 - 100752

Published: Jan. 1, 2025

Language: Английский

---

Four glycosyltransferase genes are responsible for synthesis and accumulation of different flavonol glycosides in apple tissues

The Plant Journal, Journal Year: 2024, Volume and Issue: 119(4), P. 1937 - 1952

Published: June 25, 2024

SUMMARY Flavonols are widely synthesized throughout the plant kingdom, playing essential roles in physiology and providing unique health benefits for humans. Their glycosylation plays significant role improving their stability solubility, thus accumulation function. However, genes encoding enzymes catalyze this remain largely unknown apple. This study utilized a combination of methods to identify such enzymes. Initially, candidate were selected based on potential encode UDP‐dependent glycosyltransferases (UGTs) expression patterns response light induction. Subsequently, through testing vitro enzyme activity proteins produced Escherichia coli cells, four candidates confirmed flavonol 3‐ O ‐galactosyltransferase (UGT78T6), ‐glucosyltransferase (UGT78S1), ‐xylosyltransferase/arabinosyltransferase (UGT78T5), ‐rhamnosyltransferase (UGT76AE22), respectively. Further validation these genes' functions was conducted by modulating levels stably transformed apple plants. As anticipated, positive correlation observed between content specific glycosides corresponding each gene. Moreover, overexpression synthase gene, MdFLS , resulted increased glycoside roots leaves. These findings provide valuable insights breeding programs aimed at enriching flesh with flavonols identifying ‐glycosyltransferases other species.

Language: Английский

---

The complete reference genome of Tartary buckwheat and its mutation library provide important resources for genetic studies and breeding

Cell Reports, Journal Year: 2025, Volume and Issue: 44(5), P. 115621 - 115621

Published: May 1, 2025

Tartary buckwheat (TB), Fagopyrum tataricum, is an important medicinal and edible crop with a worldwide distribution. However, reference genomes gaps mutant population scarcity have hindered functional genomics genetic improvement of TB. Here, we present telomere-to-telomere (T2T) gap-free genome assembly the elite TB inbred line Guiku1 its ethyl-methyl-sulfonate (EMS)-induced phenotypically rich mutation library. The spans 453.83 Mb, containing 43,441 predicted protein-coding genes. library includes 751 mutants stably heritable phenotypes. Whole-genome resequencing 320 identified 105,682 single-nucleotide polymorphisms (SNPs) 21,461 insertions/deletions (indels), affecting sequences 25,986 Genes responsible for pink stem petiole trait flavonoid content variation were using forward- reverse-genetics approaches, respectively. Collectively, T2T EMS provide resources studies

Language: Английский

---

Advances in the omics research of Rosaceae

Ornamental Plant Research, Journal Year: 2024, Volume and Issue: 4(1), P. 0 - 0

Published: Jan. 1, 2024

Rosaceae plants are widely distributed worldwide. These plants, including well-known ornamental and those producing temperate fruits, have significant economic value. The utilization of omics technologies has significantly advanced the research progress on in various areas germplasm resources, molecular breeding, evolutionary domestication. Here, we provide an overview applications Rosaceae. It includes whole-genome sequencing assembly as well genome-wide association studies, transcriptome, proteomics, metabolomics, comparative genomics. techniques used to understand genetic regulatory mechanisms underlying important traits such flower color, fragrance, stress tolerance, fruit quality. We outline prospects genomics aiming establish a foundation for comprehending breeding traits. This could potentially theoretical support rapidly cultivating new varieties.

Language: Английский

---