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ABSTRACT: Genomes and demographic histories of the endangered Bretschneidera sinensis

PROVIDER: PRJNA779618 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR16917619.fastq.gz	Fastqsanger.gz
	SRR16917620_1.fastq.gz	Fastqsanger.gz
	SRR16917620_2.fastq.gz	Fastqsanger.gz
	SRR16917621_subreads.fastq.gz	Fastqsanger.gz

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Bretschneidera sinensis

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Genotyping of 327 individuals from 14 populations across the Sahel/Savannah belt that were genotyped on the Illumina H3Africa Consortium Array.

Project description:The Sahel/Savannah belt harbours diverse populations with different demographic histories and different subsistence patterns. However, populations from this large African region are notably under-represented in genomic research. To investigate the population structure and adaptation history of populations from the Sahel/Savannah space, we generated dense genome-wide genotype data of 327 individuals—comprising 14 ethnolinguistic groups, including ten previously unsampled populations. DNA samples were genotyped on the Illumina H3Africa Consortium Array (BeadChip type: H3Africa_2017_20021485_A2; designed for SNP-genotyping of 2,267,346 SNPs) at the SNP&SEQ Technology Platform, NGI/SciLifeLab Genomics (Sweden). Reference: Demographic and Selection Histories of Populations Across the Sahel/Savannah Belt. Fortes-Lima C, Tříska P, Čížková M, Podgorná E, Diallo MY, Schlebusch CM, Černý V. Molecular Biology and Evolution 2022 39(10):msac209. doi: 10.1093/molbev/msac209. PMID: 36173804 .

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Chromosome-level reference genome of tetraploid Isoetes sinensis provides insights into evolution and adaption of lycophytes

Project description:Background The Lycophyta species are the extant taxa most similar to early vascular plants that were once abundant on Earth. However, their distribution has greatly diminished. So far, the absence of chromosome level assembled lycophyte genomes, has hindered our understanding of evolution and environmental adaption of lycophytes. Findings We present the reference genome of the tetraploid aquatic quillwort, Isoetes sinensis, a lycophyte. This genome represents the first chromosome-level assembled genome of a tetraploid seed-free plant. Comparison of genomes between I. sinensis and the diploid I. taiwanensis revealed of genomic features and polyploid of lycophytes. Comparison of the I. sinensis genome with those of other species representing the evolutionary lineages of green plants revealed the inherited genetic tools for transcriptional regulation and most phytohormones in I. sinensis. The presence and absence of key genes related to development and stress responses provides insights into environmental adaption of lycophytes. Conclusions The high-quality reference genome and genomic analysis presented in this study are crucial for future genetic research and the conservation of not only I. sinensis but also other lycophytes.

2023-08-21 | GSE198194 | GEO

Chromosome-level reference genome of tetraploid Isoetes sinensis provides insights into evolution and adaption of lycophytes

2023-08-21 | GSE198196 | GEO