A gap-free reference genome of Populus deltoides provides insights into karyotype evolution of Salicaceae by Changwei Bi, Ning Sun, Zhuangwei Hou, Xiaogang Dai, Huaitong Wu, Fuchuan Han, Zefu Wang, Tongming Yin

Get full text

A chromosome-level reference genome for the critically endangered Southern Corroboree frog (Pseudophryne corroboree) [version 1; peer review: 2 approved] by Lee Berger, Tiffany A. Kosch, Deon Gilbert, Andrew J. Crawford, David Hunter, Damian Goodall, Linelle Abueg, Michael McFadden, Giulio Formenti, Joanna Collins, Nivesh Jain, Tatiana Tilley, Conor Whelan, Brian O'Toole, Matthieu Muffato, Ira Cooke, Olivier Fedrigo, Bethan Yates, Erich D. Jarvis, Jennifer Balacco, Lee F. Skerratt

Subjects: Get full text

Description of bacterial RNA transcripts detected in Mycobacterium tuberculosis – infected cells from peripheral human granulomas by Philip J. Moos, Allison F. Carey, Jacklyn Joseph, Stephanie Kialo, Joe Norrie, Julie M. Moyareke, Anthony Amof, Hans Nogua, Albebson L. Lim, Louis R. Barrows

“…We included the H37Rv Mtb reference genome when assembling scRNA seq libraries from fine needle aspirate samples of peripheral nodal TB patients. …”
Get full text

Integrating parental genomes to reduce reference bias and identify intramuscular fat genes in Qinchuan Black pigs by Guangquan Lv, Peiyu Yang, Ao Guo, Minghao Cao, Dong Li, Zhe Liu, Mingyu Wang, Jingchun Sun, Rongrong Ding, Taiyong Yu

“…Abstract Background Traditional genomic analysis relies on a single reference genome, which struggles to effectively characterize the genetic diversity among populations. …”
Get full text

Telomere-to-telomere genome assembly of a male goat reveals variants associated with cashmere traits by Hui Wu, Ling-Yun Luo, Ya-Hui Zhang, Chong-Yan Zhang, Jia-Hui Huang, Dong-Xin Mo, Li-Ming Zhao, Zhi-Xin Wang, Yi-Chuan Wang, EEr He-Hua, Wen-Lin Bai, Di Han, Xing-Tang Dou, Yan-Ling Ren, Renqing Dingkao, Hai-Liang Chen, Yong Ye, Hai-Dong Du, Zhan-Qiang Zhao, Xi-Jun Wang, Shan-Gang Jia, Zhi-Hong Liu, Meng-Hua Li

“…Abstract A complete goat (Capra hircus) reference genome enhances analyses of genetic variation, thus providing insights into domestication and selection in goats and related species. …”
Get full text

High-quality chromosome-level genome of three Meretrix species using Nanopore and Hi-C technologies by Che-Chun Chen, Te-Hua Hsu, Hsin-Yun Lu, Sen-Lin Tang, Ying-Ning Ho

“…In this study, we present three reference genomes of Meretrix species: Meretrix sp. MF1, Meretrix sp. …”
Get full text

Sequence-based prioritization of i-Motif candidates in the human genome by Veronica Remori, Michela Prest, Mauro Fasano, Mauro Fasano

“…Despite their biological relevance, genome-wide prediction of iM-forming sequences remains limited by low specificity and high false-positive rates, leading to considerable experimental burden.MethodTo address this, we developed a refined computational approach that prioritizes high-confidence iM candidates using a Position-Specific Similarity Matrix (PSSM) derived from multiple sequence alignments. The human reference genome (hg38) was scanned using a custom regular expression targeting cytosine-rich motifs, followed by scoring each sequence with the PSSM. …”
Get full text

Whole-genome sequencing resources of 301 indigenous Tibetan sheep from the Himalayan region by Jipan Zhang, Yangshen Zhang, Mengying Wang, Gesang Luobu, Zhaxi Duoji, Ciren Pubu, Jikang Zheng, Hong Miao, Yongju Zhao

“…By aligning the sequence data to the sheep reference genome ARS-UI_Ramb_v3.0 with variants filtration, 39,718,985 single nucleotide polymorphisms (SNPs) and 5,275,473 insertions-deletions (InDels) were obtained. …”
Get full text

Computational problems of analysis of short next generation sequencing reads by R. te Boekhorst, F. M. Naumenko, N. G. Orlova, E. R. Galieva, A. M. Spitsina, I. V. Chadaeva, Y. L. Orlov, I. I. Abnizova

“…We present here quality control of raw data, errors arising at the steps of alignment of sequencing reads to a reference genome and assembly. Finally this work presents identification of mutations (“Variant calling”) in sequencing data and its quality control.…”
Get full text

Modern Bioinformatics Solutions Used for Genetic Data Analysis by Ya. A. Kibirev, A. V. Kuznetsovskiy, S. G. Isupov, I. V. Darmov

“…Standard stages of primary genetic data analysis  are assessment of the quality control, data preprocessing, mapping to a reference genome or de novo genome assembly,  genome annotation, typing and identification of significant genetic determinants (resistance to antibacterial drugs,  pathogenicity factors, etc.), phylogenetic analysis. …”
Get full text

The chromosome-level genome assembly and annotation of the silver-lipped pearl oyster, Pinctada maxima by Qianqian Mu, Zijian Li, Mingyang Liu, Baojun Zhao, Zhihui Yang, Zhenmin Bao, Jingjie Hu, Pingping Liu

“…Here, annotated chromosome-level reference genome for P. maxima was generated by integrating PacBio long-read sequencing, Illumina short-read sequencing, and Hi-C sequencing data. …”
Get full text

Identification and Candidate Gene Analysis of qCTS11-TK9, a Novel Major Quantitative Trait Locus Associated with Chilling Tolerance in Rice Seedlings by Sheng-Shan Wang, Yu-Ting Liu, Pei-Hua Tsai, Shu-Fang Cheng, Kai-Yi Chen, Rong-Kuen Chen

“…High-resolution linkage analysis delimited qCTS11-TK9 to a 191-kb genomic region containing 16 annotated putative genes in the rice reference genome. Expression and sequence analyses revealed three candidate genes responsible for chilling tolerance in NSY1051070: LOC_Os11g42790, LOC_Os11g42800, and LOC_Os11g42850. …”
Get full text

Detection of viral contamination in cell lines using ViralCellDetector by Rama Shankar, Shreya Paithankar, Suchir Gupta, Bin Chen, Bin Chen, Bin Chen

“…To address this issue, we developed ViralCellDetector, a tool designed to detect viral contamination by mapping RNA-seq data to a comprehensive viral genome library.MethodsViralCellDetector processes RNA-seq data from any host species by first aligning reads to the host reference genome, followed by mapping the unmapped reads to the NCBI viral genome database. …”
Get full text

Ecological diversification of sea catfishes is accompanied by genome-wide signatures of positive selection by Melissa Rincon-Sandoval, Rishi De-Kayne, Stephen D. Shank, Stacy Pirro, Alfred Ko’ou, Linelle Abueg, Alan Tracey, Jackie Mountcastle, Brian O’Toole, Jennifer Balacco, Giulio Formenti, Erich D. Jarvis, Dahiana Arcila, Sergei L. Kosakovsky Pond, Aaron Davis, Devin D. Bloom, Ricardo Betancur-R

“…Here, we generate and analyze one long-read reference genome and 66 short-read whole genome assemblies, in conjunction with genomic data for 54 additional species. …”
Get full text

Transcriptome Profiling Reveals Genetic Basis of Muscle Development and Meat Quality Traits in Chinese Congjiang Xiang and Landrace Pigs by Jiada Yang, Qiaowen Tang, Chunying Sun, Qiuyue Li, Xiaoyu Li, Lu Hou, Yi Yang, Kang Yang

“…RNA sequencing was performed on muscle tissues from ten individuals of each breed, generating 874.5 million raw reads with an average mapping rate of 89.3% to the pig reference genome. (3) Results: Transcriptional profiling revealed distinct expression patterns with 785 genes exclusively expressed in CX pigs and 457 genes unique to LAN pigs, while 7099 co-expressed genes were shared by both breeds. …”
Get full text

Investigating the Blood Microbiome in Parkinson's Disease, Schizophrenia, and Posttraumatic Stress Disorder by C. Rust, D. Tonge, L. L. van denHeuvel, L. Asmal, J. Carr, E. Pretorius, S. Seedat, S. M. J. Hemmings

“…The RNA paired‐end sequence reads that did not map to the human reference genome (hg38/GRCH38) were isolated using the sequence alignment/map tools (SAMtools). …”
Get full text

Long read whole genome sequencing-based discovery of structural variants and their role in aetiology of non-syndromic autism spectrum disorder in India by Jhanvi Shah, Debasrija Mondal, Deepika Jain, Priti Mhatre, Ketan Patel, Anand Iyer, Manoj Pandya, Bhargavi Menghani, Gayatri Dave, Jayesh Sheth, Frenny Sheth, Shweta Ramdas, Harsh Sheth

“…Contigs generated from high accuracy base calling were aligned against GRCh38/hg38 human reference genome build. SVs were called using five variant callers- Sniffles2, cuteSV, NanoVar, SVIM, and npInv, and annotated using AnnotSV. …”
Get full text

Whole RNA-Seq Analysis Reveals Longitudinal Proteostasis Network Responses to Photoreceptor Outer Segment Trafficking and Degradation in RPE Cells by Rebecca D. Miller, Isaac Mondon, Charles Ellis, Anna-Marie Muir, Stephanie Turner, Eloise Keeling, Htoo A. Wai, David S. Chatelet, David A. Johnson, David A. Tumbarello, Andrew J. Lotery, Diana Baralle, J. Arjuna Ratnayaka

“…RNA-seq analysis of the highly differentiated human retinal pigment epithelial (RPE) cell-line ARPE-19, cultured on transwells for ≥4 months, yielded 44,909 genes showing 83.35% alignment with the human reference genome. These included mRNA transcripts of RPE-specific genes and those involved in retinopathies. …”
Get full text

Structural Variations Associated with Adaptation and Coat Color in Qinghai‐Tibetan Plateau Cattle by Xiaoting Xia, Fuwen Wang, Xiaoyu Luo, Shuang Li, Yang Lyu, Yining Zheng, Zhijie Ma, Kaixing Qu, Rende Song, Jianyong Liu, Jicai Zhang, Basang Wangdui, Basang Zhuzha, Suolang Quji, Li Zhao, Silang Wangmu, Ciren Luobu, Nima Cangjue, Danzeng Luosang, Suolang Sizhu, Haijian Cheng, Ruizhe Li, Zhipeng Wu, Ruihua Dang, Yongzhen Huang, Xianyong Lan, Luohao Xu, Haifei Hu, WaiYee Low, Zhuqing Zheng, Yu Wang, Yuanpeng Gao, Lu Deng, Johannes A. Lenstra, Jianlin Han, Xueyi Yang, Wenfa Lyu, Bizhi Huang, Chuzhao Lei, Ningbo Chen

“…It is found that using a lineage‐specific reference genome significantly increased variant detection accuracy and completeness. …”
Get full text

Use ATCCfinder to identify commercially available American Type Culture Collection strains based on sequence queries by Samuel I. Koehler, Earl A. Middlebrook, Blake T. Hovde, Erik R. Hanschen

“…Using ATCC-sourced reference genomes ensures consistent quality and analysis methodologies are implemented to accurately represent strain sequences. …”
Get full text