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Genome - Europe PMC

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Last Updated: 03 September 2022

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A chromosome‐scale assembly of the bilberry genome identifies a complex locus controlling berry anthocyanin composition

Bilberry is a member of the Vaccinium genus, which includes blueberries and cranberry. Here's a look at the first bilberry genome assembly, which includes 12 pseudochromosomes assembled using Oxford Nanopore and Hi-u2010C Technologies. The pseudochromosomes display 96. 6% complete BUSCO genes with an assessed LAI score of 16. 3, indicating a high degree of synteny against the blueberry genome. To illustrate the genome quality, we discuss the intricate MYBA locus and identify the key controlling MYB genes that determine anthocyanin production. The new bilberry genome expands on the genetics and experience of Vaccinium species to help determine the genetics underpinning some of the breeding programs' desired quality attributes. Because the loci responsible for key characters are orthologous, high synteny between bilberry and blueberry genomes can be used to transfer information about marker-u2010trait association between these two species.

Source link: https://europepmc.org/article/MED/IND607601458


Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron

Standard plant DNA barcodes based on 2nd plastid regions and nrDNA ITS demonstrate variable levels of resolution and are difficult to distinguish among species in several plant groups. If adding substantially more plastid and nrDNA characters will result in an increase in discriminatory power, or whether standard plant barcode resolution limitations are largely due to plastid genomes and nrDNA not tracking species boundaries, there is a particular point of concern. These findings, despite previous reports showing an increase in discrimination success outside of 3u20134 plastid regions, indicate that with significant plastid genome data, a demonstrable increase in discrimination power is likely. Despite these advances, many species remain unsolved, and these findings also highlight the importance of finding transformative species discrimination in plants.

Source link: https://europepmc.org/article/MED/IND607601470


The chromosome‐scale assembly of the Canary Islands endemic spider Dysdera silvatica (Arachnida, Araneae) sheds light on the origin and genome structure of chemoreceptor gene families in chelicerates

We present the chromosome/u2010level genome assembly of Dysdera silvatica Schmidt, 1981, a nocturnal groundu2010dwelling spider endemic to the Canary Islands. The seven largest scaffolds or pseudochromosomes, which cover 87% of the total assembly size, are likely to correspond to the seven chromosomes of this species, which include a characteristic large X chromosome. We performed a comprehensive review of the two key arthropod chemoreceptor gene families in order to illustrate the value of this new resource. This chromosome-u2010scale assembly is the first high-quality genome sequence of the Synspermiata clade and only the third among spiders, presenting a new, useful resource for learning about chelicerate genome structure and organization, including the role that genetic variants, repetitive elements, and large gene families played in spiders' remarkable biology.

Source link: https://europepmc.org/article/MED/IND607601465


Good from far, but far from good: The impact of a reference genome on evolutionary inference

Inference studies on diversity and demographic history inference, we investigate how the consistency and phylogenetic divergence of reference genomes influences downstream analyses such as diversity and demographic history inference. In the same way, their findings indicate that heterozygosity estimates are dependent on phylogenetic distance and the procedure used to make the estimates, and ROHs are likely to be unconservable if a nonspecific reference is used. This review uncovers the role of divergence and quality of reference genomes in downstream studies, as well as a potential substitute for cross-u2010species scaffolding in instances where a conspecific reference genome is not available.

Source link: https://europepmc.org/article/MED/IND607601443


Chromosome‐level genome assembly of Scapharca kagoshimensis reveals the expanded molecular basis of heme biosynthesis in ark shells

Ark shells are a commercially important clam species that live in muddy sediments of shallow coasts in East Asia's muddy soils. Here, we report a high-quality chromosome assembly of Scapharca kagoshimensis, with the intention of finding the molecular basis of heme biosynthesis and genomic resources for genetic modification and population genetics in ark shells. In the genome of S. kagoshimensis, the enrichment experiments suggested that genes in heme biosynthesis pathways were expanded and positive selection of the haemoglobin genes was also found, providing further insight into the heme biosynthesis process in mollusca. The valuable genome assembly of S. kagoshimensis would provide a solid basis for investigating the cellular mechanisms that underlie the various biological functions and evolutionary adaptations of S. kagoshimensis.

Source link: https://europepmc.org/article/MED/IND607601454


Improved genome assembly of Chinese shrimp (Fenneropenaeus chinensis) suggests adaptation to the environment during evolution and domestication

A chromosome-u2010level genome assembly of the Chinese shrimp Fenneropeneesis was carried out in the present research to determine the molecular mechanisms underlying important biological traits; in the current study, a high-quality reference genome was used to determine the molecular mechanisms that underlies key biological processes; as a result, a chromosome u2010level genome assembly of the Chinese shrimp Fenneropenaeus chinensis was conducted. In comparison to other penaeid species, F. chinensis' genome revealed significant decline in comparison to other penaeid species, which is likely due to migration observed in this species. However, the contracted gene families were identified with the virus infection process, and the F. chinensis genome contained several extended gene families related to cell biology and metabolic processes, as well as the virus infection process. The results indicate that F. chinensis' adaptation to migration and extreme environments has been adapted. The development of the genome of F. chinensis provided valuable insights for the further genetic mechanism analysis of key biological processes, as well as the analysis of genetic variations during evolution.

Source link: https://europepmc.org/article/MED/IND607601464


Chromosome‐level genome assembly of an agricultural pest, the rice leaffolder Cnaphalocrocis exigua (Crambidae, Lepidoptera)

Cnaphalocrocis exigua, a rice leaffolder, is a significant agricultural pest that attacks rice crops and other members of closely related grass families. C. medinalis, another species of rice leaffolder whose genome was recently discovered, has a very similar morphological pattern and feeding behavior to C. medinalis. However, genomic data for C. exigua is extremely limited. To obtain a high-quality chromosome assembly of C. exigua, we used a hybrid approach that combined various sequencing techniques, including Illumina, PacBio, 10u00d7 Genomics, and Hi2013C scaffolding. We started with a 798. 8 Mb assembly with a contig N50 size of 2. 9 Mb, and the N50 size was later increased to 25. 7 million b using Hi-u2013C technology to anchor 1413 scaffolds to 32 chromosomes. Our chromosome-u2010level genome assembly and comparative genomic analysis of C. exigua provide new insight into this rice insect pests' evolution and ecology, as well as useful pest control data.

Source link: https://europepmc.org/article/MED/IND607601453


Chromosome‐level genome assembly of Welwitschia mirabilis, a unique Namib Desert species

Welwitschia mirabilis, which is endemic to the Namib Desert, is the only living species of the family Welwitschiaceae. Here, we review a chromosome-level genome assembly for W. mirabilis with a 6. 30Mb genome sequence and contig N50 of 27. 50 Mb. In W. mirabilis, two brassinosteroidu2010related genes, the key regulators of cell division and elongation, were highly selected, and may play a role in the plant's long-growing leaves. Moreover, 29 gene families in the mitogen-activated protein kinase signalling pathway experienced significant growth, which may have contributed to the plant's desert adaptations. The divergence time of W. mirabilis and Gnetum montanum was estimated at 123. 5 million years ago, based on molecular clock measurements and fossil calibrations. The genome sequence in the current study provides insight into the evolution of W. mirabilis and may be a useful resource for future research into gnetophyte and gymnosperm evolution.

Source link: https://europepmc.org/article/MED/IND607601447


Evaluating the role of reference‐genome phylogenetic distance on evolutionary inference

A mappingu2010based assembly is a high-quality genome assembly of a target species when a target species's production process is ineffective, but a cheaper de novo assembly step is a mappingu2010based assembly. Here, we used short-u2010read results from a mammal and a bird species to see if reference genome phylogenetic distance can influence downstream demographic and genetic diversity analyses. Although reference genome phylogenetic distance has an effect on demographic analyses, we show that it is not pronounced until using a reference genome with > 3% divergence from the target species. We are unable to reproduce the original beluga demographic results when mapping to cross-u2010species scaffolded assemblies, but we are able to copy the rowi kiwi, possibly reflecting the more fragmented nature of the beluga assemblies. We find that increased phylogenetic distance has a dramatic effect on genetic diversity estimates; heterozygosity estimates deviate incrementally as increasing phylogenetic distance increases.

Source link: https://europepmc.org/article/MED/IND607601438


In silico analysis and a comparative genomics approach to predict pathogenic trehalase genes in the complete genome of Antarctica Shigella sp. PAMC28760.

Although four Shigella species have been identified, S. Shigella sp. is a species of Shigella species that lives in four Shigella species and our uncategorized Antarctica isolates. Our results revealed that only 56 out of 134 Shigella strains had two different trehalase genes. The treF gene is believed to be present in Shigella species, according to the author. In addition, both treA and treF genes were present in our strain S. In the complete genome of Shigella sp. , the primary aim of this study was to determine the presence of two specific trehalase genes. It is the first study to show that two types of trehalase genes are present in Shigella species of bacterial virulence, and the role of periplasmic trehalase genes in bacterial virulence.

Source link: https://europepmc.org/article/MED/36040103

* Please keep in mind that all text is summarized by machine, we do not bear any responsibility, and you should always check original source before taking any actions

* Please keep in mind that all text is summarized by machine, we do not bear any responsibility, and you should always check original source before taking any actions