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ABSTRACT: The Chromosome level genome assembly of Lota lota provides insights into the evolutionary adaptions of freshwater

PROVIDER: PRJNA660279 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12549430_1.fastq.gz	Fastqsanger.gz
	SRR12549430_2.fastq.gz	Fastqsanger.gz
	SRR12550374_1.fastq.gz	Fastqsanger.gz
	SRR12550374_2.fastq.gz	Fastqsanger.gz
	SRR12577979_subreads.fastq.gz	Fastqsanger.gz

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Project description:Chromosome rearrangements in small apes are up to 20 times more frequent than in most mammals. Because of their complexity, the full extent of chromosome evolution in these hominoids is not yet fully documented. However, previous work with array painting, BAC-FISH and selective sequencing in two of the four karyomorphs, has shown that high resolution methods can precisely define chromosome breakpoints and map the complex flow of evolutionary chromosome rearrangements. Here we use these tools to precisely define the rearrangements that have occurred in the remaining two karyomorphs, genera Symphalangus (2n=50), and Hoolock (2n=38). This research provides the most comprehensive insight into the evolutionary origins of chromosome rearrangements involved in transforming small apes genome. Bioinformatics analyses of the human-gibbon synteny breakpoints revealed association with transposable elements and segmental duplications providing some insight into the mechanisms that might have promoted rearrangements in small apes. In the near future, the comparison of gibbon genome sequences will provide novel insights to test hypotheses concerning the mechanisms of chromosome evolution. The precise definition of synteny block boundaries and orientation, chromosomal fusions, and centromere repositioning event presented here will facilitate genome sequence assembly for these close relatives of humans.

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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.

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

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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 I. taiwanensis revealed conserved and different genomic features between diploid and polyploid 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 environmental studies of not only I. sinensis but also other lycophytes.

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