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Genome - Springer Nature

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Last Updated: 03 September 2022

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Consensus-Based Identification and Comparative Analysis of Structural Variants and Their Influence on 3D Genome Structure Using Long- and Short-Read Sequencing Technologies in Polish Families

Structural variants such as deletions, duplication, insertions, or inversions in the human genome that can be attributed to human disease pathology are common in human disease genetics. In this research, we carried out a comprehensive review of long-read sequencing of the human genome and compared it to short-read sequencing using Illumina technology in terms of the distribution of structural variants. The SVs were found in two families with three children each using fifteen independent SV callers. To find a comprehensive list of SVs for each of the families, we used the ConsensuSV algorithm to combine the results of these SV callers' callers to create the final list of SVs for each family member of the family. In addition, we investigated the effects of SVs on chromatin interaction-based paired-end tags. SVs discovered by our algorithm over sequencing data using ONT are superior to Illumina for various SV sizes and lengths, as well as the number of mapped to PETs. We conclude that SVs detected by our algorithm over sequencing results using ONT are superior to Illumina over all SV sizes and lengths, as well as the number of mapped to PETs.

Source link: https://doi.org/10.1007/978-981-19-0105-8_5


Genome-wide CRISPR screen identifies synthetic lethality between DOCK1 inhibition and metformin in liver cancer

It is also unknown which hepatocellular carcinoma patient subpopulations can profit from metformin therapy. TMOPP, a potentiative inhibitor, in vitro in liver cancer cell lines and patient-derived HCC organoids, and in vivo in xenografted liver cancer cells and immunocompetent mouse liver cancer models. Metformin enhances overall longevity of HCC patients with low DOCK1 levels but not among patients with elevated DOCK1 expression, according to the manufacturer. This review shows that metformin effectiveness is dependent on DOCK1 levels, and that combining metformin with DOCK1 inhibition may lead to a promising personalized therapeutic program for metformin-resistant HCC patients.

Source link: https://doi.org/10.1007/s13238-022-00906-6


Complete genome analysis of a novel iflavirus from the spotted lanternfly Lycorma delicatula

In a spotted lanternfly, we found a new iflavirus named "Lycorma delicatula iflavirus 1" here. The complete genome sequence of LDIV1 is 10,222 nt in length, and encodes a polyprotein that encodes a cricket paralysis virus capsid-domain, a cricket paralysis virus capsid superfamily domain, an RNA helicase domain, a peptidase C3 superfamily domain, and an RNA polymerase domain. LDIV1 is the first virus found in L. delicatula, according to the best of our knowledge, it was the first virus identified in the first viruses identified in L. delicatula.

Source link: https://doi.org/10.1007/s00705-022-05503-w


The full-length genome sequence of a novel amalgavirus in Lilium spp. in China

We present the complete genome sequence of a novel amalgavirus, tentatively identified as u2018lily amalgavirus 1u2019, which is isolated from Lilium spp. LAV-1's complete genome sequence matches 48. 23. 80% sequence identity with those of Amalgavirus members, with the highest nucleotide sequence similarity of 59. 8 percent with that of Allium cepa amalgavirus 1.

Source link: https://doi.org/10.1007/s00705-022-05523-6


Complete genome sequence and phylogenetic analysis of red seabream iridovirus isolated from a cage-cultured small yellow croaker (Larimichthys polyactis) in China

We present the complete genome sequence and phylogenetic analysis of iridovirus strain LPIV-ZS-2021, isolated from a small yellow croaker in China. The genome sequence sequence, which has a G+C content of 53. 2 percent, has 104 putative open reading frames, and has the highest sequence similarity with red seabream iridovirus isolated in Japan, with red seabream iridovirus isolated in Japan. The host range of members of the genus Megalocytivirus warrants more investigation to determine its potential economic and ecological impacts.

Source link: https://doi.org/10.1007/s00705-022-05508-5


Complete sequence and genome characterization of a new potexvirus isolated from Chaenostoma cordatum

Leaves from Chaenostoma cordatum Benth's ornamental plant Chaenostoma cordatum Benth's ornamental plant Chaenostoma cordatum Benth's ornamental plant Chaenostoma cordatum Benth's ornamental plant Chaenostoma cordatum Benth's ornamental plant Chaenostoma cordatum Benth's ornamental plant Chaenostoma cordat By high-throughput sequencing, a virus with characteristics similar to those of members of the genus Potexvirus was identified. The phylogenetic analysis of the RNA polymerase sequence from the viral genome revealed that the nearest cousin is Plantago asiatica mosaic virus, which is the plantago asiatica mosaic virus.

Source link: https://doi.org/10.1007/s00705-022-05520-9


Guar genes to genome and meta-analysis of SSR markers in sequencing studies

SSR markers in silico-based sequencing research discovered that guar transcriptome and genome were consistently devoid of di, tri, tetra, penta nucleotide SSRs, according to a meta-analysis of SSR results. The Guar transcriptome's majorly contains trinucleotide SSRs, although its genome contains many dinucleotide SSRs, which is present in abundance. Meta-analysis of guar transcriptomic studies was performed as a result of the increasing importance of transcriptomic SSR markers. Considering the total number of sequences reviewed and the number of sequences containing SSRs from the studies, significant heterogeneity was discovered among transcriptomic SSR designers. The effect size and Pearson correlation coefficient of the experiments was found to be 0. 28 u00b1 0. 09 and 0. 43 respectively, indicating that studies have a modest amount of practical relevance, according to their findings. According to the number of sequences reviewed by the researchers, the average ratio of SSR containing sequences in varying ratios is between 0. 01 and 0. 45.

Source link: https://doi.org/10.1007/s10722-022-01420-8


Genome-wide identification and expression analysis of the bZIP gene family in silver birch (Betula pendula Roth.)

However, information on the ancestors and patterns of gene expression of bZIP family members in woody plants has been limited. Here we found and characterized 47 BpbZIP genes from the silver birch genome. All BpbZIP proteins were clustered among ten groups in phylogeny, according to BZIP classifications for Arabidopsis thaliana, and BpbzIP proteins for Arabidopsis thaliana. Our findings in silver birch related to a comprehensive knowledge of bZIP transcription factors, evolutionary history, gene sequence, motif construction, and promoter element identification, which may lead to a deeper understanding of these transcription factors and potential biological functions.

Source link: https://doi.org/10.1007/s11676-022-01453-w


Genome survey and development of 13 SSR markers in Eucalyptus cloeziana by NGS

Eucalyptus cloeziana is a popular timber tree species due to its tenacity and excellent sawmilling characteristics. The E. cloeziana genome and its SSR markers development was surveyed by next-generation sequencing based on Illumina Hi-Seq X Ten platform, which was used to analyze the E. cloeziana genome and its SSR markers. The clean reads of E. cloeziana were converted into 995,093 scaffolds with a N50 value of 2297 bp. Polymorphism was detected in 13 of the 50 genome SSR primer pairs randomly selected for the screening test. All four E. cloeziana germplasms were tested, from 0. 317 to 0. 338, respectively, with the observed and predicted heterozygosity ranging from 0. 317 to 0. 376. Here, we provide the genome information of E. cloeziana and other eucalypts, as well as contributing to molecular breeding studies of E. cloeziana and other eucalypts.

Source link: https://doi.org/10.1007/s12041-022-01382-x

* 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