Plant Communications, Год журнала: 2024, Номер 5(12), С. 101071 - 101071
Опубликована: Авг. 24, 2024
Язык: Английский
Aquatic Botany, Год журнала: 2025, Номер unknown, С. 103887 - 103887
Опубликована: Апрель 1, 2025
Язык: Английский
Процитировано
0
The Plant Journal, Год журнала: 2025, Номер 122(1)
Опубликована: Апрель 1, 2025
The pan-genome represents the complete genomic diversity of specific species, serving as a valuable resource for studying species evolution, crop domestication, and guiding breeding improvement. While there are several single-species-specific plant databases, availability multi-species databases is limited. Additionally, variations in methods data types used analysis across different hinder comparison integration information from various projects at or single-species levels. To tackle this challenge, we introduce PlantPan, comprehensive database housing results 195 genomes 11 species. PlantPan aims to provide extensive information, including gene-centric sequence-centric graph-based pan-genome, openness profiles, gene functions its variation characteristics, homologous genes, clusters Statistically, incorporates 9 163 011 694 191 clusters, 526 973 370 genome variations, 1 616 089 non-redundant groups level, 33 455,098 synteny, 177 827 synteny level. Regarding functional contains 5 222 720 genes related transcription factors, 395 247 literature-reported resistance 455 748 predicted microbial/disease 612 112 molecular pathways. In summary, vital platform advancing application pan-genomes crops evolutionary research plants.
Язык: Английский
Процитировано
0
Trends in Genetics, Год журнала: 2024, Номер unknown
Опубликована: Дек. 1, 2024
Язык: Английский
Процитировано
3
GigaScience, Год журнала: 2024, Номер 13
Опубликована: Янв. 1, 2024
Sweet orange (Citrus sinensis Osbeck) is a fruit crop of high nutritional value that widely consumed around the world. However, its susceptibility to low-temperature stress limits cultivation and production in regions prone frost damage, severely impacting sustainable development sweet industry. Therefore, developing cold-resistant varieties great necessity. Traditional hybrid breeding methods are not feasible due polyembryonic phenomenon oranges, necessitating enhancement germplasm through molecular breeding. High-quality reference genomes valuable for studying resistance biotic abiotic stresses. lack genomic resources has hindered progress such researching their mechanisms cold resistance.
Язык: Английский
Процитировано
2
Horticulture Research, Год журнала: 2024, Номер 11(12)
Опубликована: Дек. 1, 2024
Язык: Английский
Процитировано
2
bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown
Опубликована: Май 20, 2024
Abstract Technological advances have propelled DNA sequencing of non-model organisms, making more accessible and cost effective, which has also increased the availability raw data in public repositories. However, contamination is a significant concern, use reuse requires quality control curation. A reference genome for Australian native rainforest tree Rhodamnia argentea Benth. (malletwood) was assembled from Oxford Nanopore Technologies (ONT) long-reads, 10x Genomics Chromium linked-reads, Hi-C (N50 = 32.3 Mbp BUSCO completeness 98.0%) with 99.0% 347 assembly anchored to 11 chromosomes (2 n 22). The R . will inform conservation efforts Myrtaceae species threatened by global spread fungal disease myrtle rust. We observed further investigation revealed an arthropod source. Here, we demonstrate feasibility assembling high-quality gapless telomere-to-telomere mite using contaminated host plant data. exhibits streamlining 35 (68.6% completeness) on two chromosomes, capped novel TTTGG telomere sequence. Phylogenomic analysis suggests that it previously unsequenced eriophyoid mite. Despite its unknown identity, this complete nuclear provides valuable resource investigate invertebrate reduction. This study emphasises importance checking contamination, especially when working organisms. It enhances our understanding species, including faces substantial challenges, contributing broader biodiversity initiatives. Significance genomes associated mite, data, were first time. generated chromosome-level genomic resources rust impacted pest genomics, streamlining. research underscores growing prevalence experiments organisms while emphasising curation
Язык: Английский
Процитировано
1
Forestry Research, Год журнала: 2024, Номер 4(1), С. 0 - 0
Опубликована: Янв. 1, 2024
Язык: Английский
Процитировано
1
International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(11), С. 5648 - 5648
Опубликована: Май 22, 2024
Two genes of nitrate transporters SaNRT2.1 and SaNRT2.5, putative orthologs high-affinity transporter AtNRT2.1 AtNRT2.5 from Arabidopsis thaliana, were cloned the euhalophyte Suaeda altissima. Phylogenetic bioinformatic analysis demonstrated that proteins SaNRT2.5 exhibited higher levels homology to corresponding plants family Amaranthaceae; similarity amino acid sequences between was lower (54%). Both are integral membrane forming 12 transmembrane helices as predicted by topological modeling. An attempt demonstrate transporting activity or heterologous expression in yeast Hansenula (Ogataea) polymorpha mutant strain Δynt1 lacking only not successful. The patterns studied S. altissima grown hydroponics under either low (0.5 mM) high (15 salinity 0 750 mM NaCl. growth strongly inhibited nitrogen supply while stimulated NaCl; it peaked at 250 NaCl for 500 nitrate. Under supply, contents roots, leaves stems reduced but increased medium increased. Potassium remained stable treatment Quantitative real-time PCR without salinity, expressed all organs, its influenced exclusively roots—its rose about 10-fold Salinity both roots with 15-fold increase; 150-fold increase. It is suggested ensures effective uptake functions an essential support adult deficiency.
Язык: Английский
Процитировано
1
bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown
Опубликована: Июль 29, 2024
Abstract Understanding the mechanisms driving centromere evolution is crucial for deciphering eukaryotic and speciation processes. Despite their widely recognized characteristics of conserved function in cell division, centromeres have showed high diversity composition structure between species. The mechanism underlying this paradox remain poorly understood. Here, we assembled 67 high-quality rice genomes from Oryza AA group, encompassing both Asian African species, conducted an extensive analysis over 800 nearly complete centromeres. Through de novo annotation satellite sequences employing a progressive compression strategy, quantified local homogenization multi-layer nested structures found that genetic innovations primarily arise internal structural variations retrotransposon insertions, along with certain number non-canonical repeats ( sati ). these rapid alterations, single-base substitution rate appears relatively lower compared to chromosome arms. Contrary KARMA model Arabidopsis evolution, our (RICE) suggests centrophilic LTRs contribute decline progenitor composed repeats, facilitate formation evolutionary neo-centromeres, which are enriched extended CENH3 binding regions beyond native arrays plant genomes. In summary, study provides novel insights into genomic divergence reproductive barriers among species subspecies, advances understanding evolution.
Язык: Английский
Процитировано
1
Plant Communications, Год журнала: 2024, Номер 5(11), С. 101064 - 101064
Опубликована: Авг. 18, 2024
The transcriptome serves as a bridge that links genomic variation to phenotypic diversity. A vast number of studies using next-generation RNA sequencing (RNA-seq) over the last 2 decades have emphasized essential roles plant in response developmental and environmental conditions, providing numerous insights into dynamic changes, evolutionary traces, elaborate regulation transcriptome. With substantial improvement accuracy throughput, direct (DRS) has emerged new powerful platform for precise detection native full-length transcripts, overcoming many limitations such read length PCR bias are inherent short-read RNA-seq. Here, we review recent advances dissecting complexity diversity transcriptomes DRS main technological approach, covering aspects metabolism, including novel isoforms, poly(A) tails, modification, propose comprehensive workflow processing data. Many challenges application plants, need machine learning tools tailored transcriptomes, remain be overcome, together outline future biological questions can addressed by DRS, allele-specific modification. This technology provides convenient support on which connection distinct features is tightly built, sustainably refining our understanding functions
Язык: Английский
Процитировано
1