Telomere-to-telomere genome assembly of Eleocharis dulcis and expression profiles during corm development DOI Creative Commons
Yang Chen, Xinyi Zhang, Lingling Wang

et al.

Scientific Data, Journal Year: 2024, Volume and Issue: 11(1)

Published: Aug. 10, 2024

Eleocharis dulcis (Burm. f.) Trin. ex Hensch., commonly known as Chinese water chestnut, is a traditional aquatic vegetable in China, and now widely cultivated throughout the world because of its high nutritional value unique tastes. Here, we report assembly 493.24 Mb telomere-to-telomere (T2T) genome E. accomplished by integrating ONT ultra-long reads, PacBio long reads Hi-C data. The reference was anchored onto 111 gap-free chromosomes, containing 48.31% repeat elements 33,493 predicted protein-coding genes. Whole duplication (WGD) inter-genomic synteny analyses indicated that chromosome breakage possibly occurred multiple times during evolution after divergence from common ancestor with Rhynchospora breviuscula at ca. 35.6 Mya. A comparative time-course transcriptome analysis corm development revealed different patterns gene expression between wild accessions highest number differentially expressed genes (DEGs, 15,870) middle swelling stage some DEGs were significantly enriched for starch metabolic process.

Language: Английский

Integrated analysis of metabolomics and transcriptomics reveals the metabolites responsible for the antioxidant activity of water caltrop hull DOI Creative Commons

Mingya Fang,

G Y Liu,

Wei Sheng

et al.

Plant Stress, Journal Year: 2025, Volume and Issue: unknown, P. 100746 - 100746

Published: Feb. 1, 2025

Language: Английский

Citations

0
Genomic research and genetic improvement of orphan crops: novel strategies for addressing global food security challenges DOI
Zijun Wang, Guisheng Xiang

Published: Jan. 1, 2025

Language: Английский

Citations

0
The Cissus quadrangularis genome reveals its adaptive features in an arid habitat DOI Creative Commons
Qingyun Li, Yi Wang, Huimin Zhou

et al.

Horticulture Research, Journal Year: 2024, Volume and Issue: 11(4)

Published: Feb. 2, 2024

Abstract Cissus quadrangularis is a tetraploid species belonging to the Vitaceae family and known for Crassulacean acid metabolism (CAM) pathway in succulent stem, while leaves perform C3 photosynthesis. Here, we report high-quality genome of C. comprising total size 679.2 Mb which was phased into two subgenomes. Genome annotation identified 51 857 protein-coding genes, approximately 47.75% composed repetitive sequences. Gene expression ratios subgenomes demonstrated that sub-A as dominant subgenome played vital role during drought tolerance. divergence analysis suggests tetraploidization event occurred around 8.9 million years ago. Transcriptome data revealed pathways related cutin, suberine, wax were enriched stem treatment, suggesting these genes contributed adaption. Additionally, subset CAM-related displayed diurnal patterns stems but not leaves, indicating stem-biased existing CAM evolution. Our findings provide insights mechanisms adaptation photosynthesis transition plants.

Language: Английский

Citations

1
Genome Variability in Artificial Allopolyploid Hybrids of Avena sativa L. and Avena macrostachya Balansa ex Coss. et Durieu Based on Marker Sequences of Satellite DNA and the ITS1–5.8S rDNA Region DOI Open Access
Аlexandra V. Amosova, А. А. Гнутиков, А. В. Родионов

et al.

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(10), P. 5534 - 5534

Published: May 19, 2024

Artificial hybrids between cultivated Avena species and wild macrostachya that possess genes for resistance to biotic abiotic stresses can be important oat breeding. For the first time, a comprehensive study of genomes artificial fertile sativa × their parental was carried out based on chromosome FISH mapping satellite DNA sequences (satDNAs) also analysis intragenomic polymorphism in 18S-ITS1-5.8S rDNA region, using NGS data. Chromosome distribution patterns marker satDNAs allowed us identify all chromosomes studied karyotypes, determine subgenomic affiliation, detect several rearrangements. Based obtained cytogenomic data, we revealed differences two A. subgenomes demonstrated only one them inherited octoploid hybrids. Ribotype analyses showed second major ribotype species-specific not represented pools octoploids, which could related allopolyploid origin this species. Our results indicate use studies provide data genomic relationships within hybrids, expand potential interspecific crosses

Language: Английский

Citations

1
Chromosome-level genome assembly of American sweetgum (Liquidambar styraciflua, Altingiaceae) DOI Creative Commons

Yazhen Ma,

Shi-Xiong Ding, Yingxiong Qiu

et al.

Scientific Data, Journal Year: 2024, Volume and Issue: 11(1)

Published: Oct. 3, 2024

The deciduous American sweetgum (Liquidambar styraciflua, Altingiaceae) is a popular ornamental and economically valuable tree renowned for its sweet-smelling bark resin, abundant volatile substances, spectacular fall leaf color. However, the absence of reference genome hinders thorough investigations into mechanisms underlying phenotypic variation, secondary metabolite synthesis adaptation, both in this species other Liquidambar members. In study, we sequenced constructed chromosome-level assembly L. styraciflua genome, covering 662.48 Mb with scaffold N50 39.54 Mb, by integrating PacBio, Illumina chromosome conformation capture data. We identified 58.83% sequences as repetitive elements 25,713 protein-coding genes, 97.28% which were functionally annotated. sequencing reads, annotation data have been deposited publicly available repositories. This high-quality provides resources further evolutionary functional genomic studies species.

Language: Английский

Citations

1
Telomere-to-telomere genome assembly of Eleocharis dulcis and expression profiles during corm development DOI Creative Commons
Yang Chen, Xinyi Zhang, Lingling Wang

et al.

Scientific Data, Journal Year: 2024, Volume and Issue: 11(1)

Published: Aug. 10, 2024

Eleocharis dulcis (Burm. f.) Trin. ex Hensch., commonly known as Chinese water chestnut, is a traditional aquatic vegetable in China, and now widely cultivated throughout the world because of its high nutritional value unique tastes. Here, we report assembly 493.24 Mb telomere-to-telomere (T2T) genome E. accomplished by integrating ONT ultra-long reads, PacBio long reads Hi-C data. The reference was anchored onto 111 gap-free chromosomes, containing 48.31% repeat elements 33,493 predicted protein-coding genes. Whole duplication (WGD) inter-genomic synteny analyses indicated that chromosome breakage possibly occurred multiple times during evolution after divergence from common ancestor with Rhynchospora breviuscula at ca. 35.6 Mya. A comparative time-course transcriptome analysis corm development revealed different patterns gene expression between wild accessions highest number differentially expressed genes (DEGs, 15,870) middle swelling stage some DEGs were significantly enriched for starch metabolic process.

Language: Английский

Citations

0