A CACTA-like transposon in the Anthocyanidin synthase 1 (Ans-1) gene is responsible for apricot fruit colour in the raspberry (Rubus idaeus) cultivar ‘Varnes’ DOI Creative Commons
Daniel James Sargent, Matteo Buti, Stefan Martens

et al.

PLoS ONE, Journal Year: 2025, Volume and Issue: 20(2), P. e0318692 - e0318692

Published: Feb. 3, 2025

Cultivated raspberries ( Rubus idaeus L.) most commonly bear small, red, highly aromatic fruits. Their colour is derived predominantly from anthocyanins, water soluble polyphenolic pigments, but as well red forms, there exist cultivars that display yellow- and apricot-coloured In this investigation, we used a multi-omics approach to elucidate the genetic basis of apricot fruit in raspberry. Using metabolomics, quantified anthocyanins raspberry fruits demonstrated that, contrast red-fruited raspberries, cultivar ‘Varnes’ contain low concentrations only small number anthocyanin compounds. By performing RNASeq, revealed differential expression patterns apricot-fruited for genes biosynthesis pathway following whole genome sequencing using long-read Oxford Nanopore Technologies sequencing, identified CACTA-like transposable element (TE) second exon Anthocyanidin synthase Ans ) gene caused truncated predicted ANS protein. PCR confirmed presence heterozygous form transposon an unrelated, ‘Veten’, indicating recessive it may be widespread germplasm, potentially explaining why forms appear at regular intervals modern breeding populations.

Language: Английский

Characterization and comparative analysis of the first mitochondrial genome of <i>Michelia</i> (Magnoliaceae) DOI
Suyan Wang, Jing Qiu, Ning Sun

et al.

Published: Jan. 1, 2025

Language: Английский

Citations

5
Pan-genome bridges wheat structural variations with habitat and breeding DOI
Chengzhi Jiao, Xiaoming Xie,

Chenyang Hao

et al.

Nature, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 27, 2024

Language: Английский

Citations

17
The Idesia polycarpa genome provides insights into its evolution and oil biosynthesis DOI Creative Commons

Yi Zuo,

Hongbing Liu, Bin Li

et al.

Cell Reports, Journal Year: 2024, Volume and Issue: 43(3), P. 113909 - 113909

Published: March 1, 2024

The deciduous tree Idesia polycarpa can provide premium edible oil with high polyunsaturated fatty acid contents. Here, we generate its high-quality reference genome, which is ∼1.21 Gb, comprising 21 pseudochromosomes and 42,086 protein-coding genes. Phylogenetic genomic synteny analyses show that it diverged Populus trichocarpa about 16.28 million years ago. Notably, most biosynthesis genes are not only increased in number genome but also highly expressed the fruits. Moreover, identify, through genome-wide association analysis RNA sequencing, I. SUGAR TRANSPORTER 5 (IpSTP5) gene as a positive regulator of accumulation Silencing IpSTP5 by virus-induced silencing causes significant reduction content fruits, suggesting has potential to be used molecular marker breed high-oil-content cultivars. Our results collectively lay foundation for breeding elite cultivars polycarpa.

Language: Английский

Citations

12
Chromosome-level genome assemblies reveal genome evolution of an invasive plant Phragmites australis DOI Creative Commons
Cui Wang, Lele Liu,

Meiqi Yin

et al.

Communications Biology, Journal Year: 2024, Volume and Issue: 7(1)

Published: Aug. 17, 2024

Biological invasions pose a significant threat to ecosystems, disrupting local biodiversity and ecosystem functions. The genomic underpinnings of invasiveness, however, are still largely unknown, making it difficult predict manage invasive species effectively. common reed (Phragmites australis) is dominant grass in wetland ecosystems has become particularly when transferred from Europe North America. Here, we present high-quality gap-free, telomere-to-telomere genome assembly Phragmites australis consisting 24 pseudochromosomes B chromosome. Fully phased subgenomes demonstrated considerable subgenome dominance revealed the divergence diploid progenitors approximately 30.9 million years ago. Comparative genomics using chromosome-level scaffolds for three other lineages previously published draft an lineage that gene family expansions form tandem duplications may have contributed invasiveness lineage. This study sheds light on evolution Arundinoideae grasses suggests genetic drivers, such as duplications, underly processes biological invasion plants. These findings provide crucial step toward understanding managing basis plant species.

Language: Английский

Citations

8
Comprehensive analysis of the Lycopodium japonicum mitogenome reveals abundant tRNA genes and cis-spliced introns in Lycopodiaceae species DOI Creative Commons
Ning Sun, Fuchuan Han, Suyan Wang

et al.

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: Aug. 20, 2024

Lycophytes and ferns represent one of the earliest-diverging lineages vascular plants, with Lycopodiaceae family constituting basal clade among lycophytes. In this research, we successfully assembled annotated complete Lycopodium japonicum Thunb. ( L . ) mitochondrial genome (mitogenome) utilizing PacBio HiFi sequencing data, resulting in a single circular molecule size 454,458 bp. 64 unique genes were altogether, including 34 protein-coding genes, 27 tRNAs 3 rRNAs. It also contains 32 group II introns, all which undergo cis -splicing. We identified 195 simple sequence repeats, 1,948 dispersed 92 tandem repeats mitogenome. Collinear analysis indicated that mitogenomes are remarkably conserved compared to those other plants. totally 326 RNA editing sites 31 299 converting cytosine uracil reverse. Notably, L. mitogenome has small amounts foreign DNA from plastid or nuclear origin, accounting for only 2.81% The maximum likelihood phylogenetic based on 23 diverse land plant genomes supports position lycophytes within plants they form sister lineages, is consistent PPG I classification system. As first reported Lycopodioideae subfamily, study enriches our understanding mitogenomes, sets stage future research diversity evolution ferns.

Language: Английский

Citations

7
Pangeneric genome analyses reveal the evolution and diversity of the orchid genus Dendrobium DOI
Yan Li, Bin Zhang, Songyao Zhang

et al.

Nature Plants, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 10, 2025

Language: Английский

Citations

1
Remarkable mitochondrial genome heterogeneity in Meniocus linifolius (Brassicaceae) DOI
Jie Liu, Jin‐Yong Hu, Li D

et al.

Plant Cell Reports, Journal Year: 2024, Volume and Issue: 43(2)

Published: Jan. 11, 2024

Language: Английский

Citations

6
Natural variant of Rht27, a dwarfing gene, enhances yield potential in wheat DOI
X. Liu, Shusong Zheng, Shuiquan Tian

et al.

Theoretical and Applied Genetics, Journal Year: 2024, Volume and Issue: 137(6)

Published: May 11, 2024

Language: Английский

Citations

6
Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Ilex rotunda Thunb. DOI Open Access
Yuanjian Wang, Gang Cui,

Kaifeng He

et al.

Forests, Journal Year: 2024, Volume and Issue: 15(7), P. 1117 - 1117

Published: June 27, 2024

Ilex rotunda Thunb. stands as a representative tree species in subtropical evergreen broad-leaved forests, widely distributed across southeast Asia. This holds significant value forestry due to its ecological resilience and adaptability. Although researchers have conducted in-depth research on the plastid genome (plastome) of I. rotunda, mitochondrial (mitogenome) this has remained undocumented. In present study, we successfully sequenced assembled mitogenome. The mitogenome circular structure is 567,552 bp total length, with GC content 45.47%. composition encompasses 40 protein-coding genes, along 3 rRNA genes 19 tRNA genes. Notably, exhibits universal distribution repetitive sequences, but length repeats contributes relatively small proportion (4%) whole mitogenome, suggesting that do not serve primary cause amplification mitogenomes. Collinear analysis indicates very conservative within Aquifoliales species. Additionally, our identified 51 fragments genomic DNA, which migrated from plastome into five remaining intact. Eventually, phylogenetic analyses based plastomes mitogenomes 36 angiosperms determine be basal group campanulids. study establishes bedrock for prospective investigations molecular breeding research.

Language: Английский

Citations

6
The genome of Eleocharis vivipara elucidates the genetics of C3–C4 photosynthetic plasticity and karyotype evolution in the Cyperaceae DOI Creative Commons
Hongbing Liu, Hang Zhao,

Yanwen Zhang

et al.

Journal of Integrative Plant Biology, Journal Year: 2024, Volume and Issue: 66(11), P. 2505 - 2527

Published: Aug. 23, 2024

ABSTRACT Eleocharis vivipara , an amphibious sedge in the Cyperaceae family, has several remarkable properties, most notably its alternate use of C 3 photosynthesis underwater and 4 on land. However, absence genomic data hindered utility for evolutionary genetic research. Here, we present a high‐quality genome E. representing first chromosome‐level genus, with approximate size 965.22 Mb mainly distributed across 10 chromosomes. Its Hi–C pattern, chromosome clustering results, one‐to‐one synteny two subgroups indicates tetraploid structure count 2 n = x 20. Phylogenetic analysis suggests that diverged from Cyperus esculentus approximately 32.96 million years ago (Mya), underwent whole‐genome duplication (WGD) about 3.5 Mya. Numerous fusion fission events were identified between chromosomes close relatives. We demonstrate holocentromeres, chromosomal feature which can maintain stability such rearrangements. Experimental transplantation cross‐section studies showed terrestrial culms developed Kranz anatomy increased number chloroplasts bundle sheath (BS) cells. Gene expression weighted gene co‐expression network (WGCNA) overall elevated core genes associated pathway, significant enrichment related to modified culm efficiency. found evidence mixed nicotinamide adenine dinucleotide ‐ malic enzyme phosphoenolpyruvate carboxykinase type hypothesize evolution predates WGD event. The is dominated by subgenome A supplemented B. Collectively, our findings not only shed light karyotype within but also provide valuable insights into transition photosynthesis, offering promising avenues crop improvement breeding.

Language: Английский

Citations

6