Use the keywords feature with a free QxMD account.
Use Read by QxMD to access full text via your institution or open access sources.
Read also provides personalized recommendations to keep you up to date in your field.
Existing User
Sign InNew to Read
Sign Up#21
JOURNAL ARTICLE
Si Yin, Yong Gao
Castanopsis orthacantha Franch. 1899 is one representative tree species distributed in the evergreen broad-leaved forests of southwestern China. This species is an important source of timber for manufacturing furniture, floors, and paper. It also plays a significant role in maintaining ecological balance and stability. To help with the genetic diversity assessment of C. orthacantha , we sequenced and assembled the first complete chloroplast genome. The length of the chloroplast genome was 160,588 bp, with a typical quadripartite structure (GenBank accession no...
2024: Mitochondrial DNA. Part B. Resources
#22
JOURNAL ARTICLE
Surmani Huidrom, Ng Ngashangva, Joshua Khumlianlal, Kongbrailatpam Chandradev Sharma, Pulok Kumar Mukherjee, Sarangthem Indira Devi
Lactiplantibacillus plantarum BRD3A was isolated from Atingba, a traditional fermented rice-based beverage of Manipur. Its genomic sequence has 13 contigs and its genome size is 3,320,817 bp with a guanine-cytosine (GC) ratio of 44.6%. It comprises 3185 genes including 3112 coding sequences (CDSs), 73 RNAs (including 66 tRNAs and others), and one clustered regularly interspaced short palindromic repeat (CRISPR) array. A comparative and phylogenetic analysis with the Lp. plantarum genome shows that this strain has close similarity with other Lp...
2024: Frontiers in Microbiology
#23
JOURNAL ARTICLE
Hyunok Doo, Jin Ho Cho, Minho Song, Eun Sol Kim, Sheena Kim, Gi Beom Keum, Jinok Kwak, Sriniwas Pandey, Sumin Ryu, Yejin Choi, Juyoun Kang, Hyeun Bum Kim, Ju-Hoon Lee
The Enterococcus faecium ( E. faecium ) strain AK_C_05 was isolated from cheonggukjang , the Korean traditional food, collected from a local market in South Korea. In this report, we presented the complete genome sequence of E. faecium strain AK_C_05. The genome of E. faecium strain AK_C_05 genome consisted of one circular chromosome (2,691,319 bp) with a guanine + cytosine (GC) content of 38.3% and one circular plasmid (177,732 bp) with a GC content of 35.48%. The Annotation results revealed 2,827 protein-coding sequences (CDSs), 18 rRNAs, and 68 tRNA genes...
March 2024: Journal of Animal Science and Technology
#24
JOURNAL ARTICLE
Sherman Lin, Christopher Tran, Ela Bandari, Tommaso Romagnoli, Yueyang Li, Michael Chu, Abinaya S Amirthakatesan, Adam Dallmann, Andrii Kostiukov, Angel Panizo, Anjelica Hodgson, Anna R Laury, Antonio Polonia, Ashley E Stueck, Aswathy A Menon, Aurélien Morini, Birsen Özamrak, Caroline Cooper, Celestine Marie G Trinidad, Christian Eisenlöffel, Dauda E Suleiman, David Suster, David A Dorward, Eman A Aljufairi, Fiona Maclean, Gulen Gul, Irene Sansano, Irma E Erana-Rojas, Isidro Machado, Ivana Kholova, Jayanthi Karunanithi, Jean-Baptiste Gibier, Jefree J Schulte, Joshua J X Li, Jyoti R Kini, Katrina Collins, Laurence A Galea, Louis Muller, Luca Cima, Luiz M Nova-Camacho, Marcus Dabner, Matthew J Muscara, Matthew G Hanna, Mehdi Agoumi, Nicholas J P Wiebe, Nicola K Oswald, Nusrat Zahra, Olaleke O Folaranmi, Oleksandr Kravtsov, Orhan Semerci, Namrata N Patil, Preethi Muthusamy Sundar, Prem Charles, Priyadarshini Kumaraswamy Rajeswaran, Qi Zhang, Rachael van der Griend, Raghavendra Pillappa, Raul Perret, Raul S Gonzalez, Robyn C Reed, Sachin Patil, Xiaoyin Sara Jiang, Sumaira Qayoom, Susan Prendeville, Swikrity U Baskota, Thanh-Truc Tran, Thar-Htet San, Tiia-Maria Kukkonen, Timothy J Kendall, Toros Taskin, Tristan Rutland, Varsha Manucha, Vincent Cockenpot, Yale Rosen, Yessica P Rodriguez-Velandia, Zehra Ordulu, Matthew J Cecchini
Introduction. The identification of mitotic figures is essential for the diagnosis, grading, and classification of various different tumors. Despite its importance, there is a paucity of literature reporting the consistency in interpreting mitotic figures among pathologists. This study leverages publicly accessible datasets and social media to recruit an international group of pathologists to score an image database of more than 1000 mitotic figures collectively. Materials and Methods. Pathologists were instructed to randomly select a digital slide from The Cancer Genome Atlas (TCGA) datasets and annotate 10-20 mitotic figures within a 2 mm2 area...
April 16, 2024: International Journal of Surgical Pathology
#25
JOURNAL ARTICLE
Anthony B Garza, Emmanuelle Lerat, Hani Z Girgis
Plant genomes include large numbers of transposable elements. One particular type of these elements is flanked by two Long Terminal Repeats (LTRs) and can translocate using RNA. Such elements are known as LTR-retrotransposons; they are the most abundant type of transposons in plant genomes. They have many important functions involving gene regulation and the rise of new genes and pseudo genes in response to severe stress. Additionally, LTR-retrotransposons have several applications in biotechnology. Due to the abundance and the importance of LTR-retrotransposons, multiple computational tools have been developed for their detection...
April 16, 2024: Mobile DNA
#26
JOURNAL ARTICLE
Kui Ding, Qinzeng Xu, Liyuan Zhao, Yixuan Li, Zhong Li, Wenge Shi, Qianhui Zeng, Xianyan Wang, Xuelei Zhang
The common dolphin (Delphinus delphis) is widely distributed worldwide and well adapted to various habitats. Animal genomes store clues about their pasts, and can reveal the genes underlying their evolutionary success. Here, we report the first high-quality chromosome-level genome of D. delphis. The assembled genome size was 2.56 Gb with a contig N50 of 63.85 Mb. Phylogenetically, D. delphis was close to Tursiops truncatus and T. aduncus. The genome of D. delphis exhibited 428 expanded and 1,885 contracted gene families, and 120 genes were identified as positively selected...
April 16, 2024: BMC Genomics
#27
JOURNAL ARTICLE
Nanbo Jiao, Jieru Xu, Yue Wang, Dunxi Li, Feifei Chen, Yu Chen, Jinhui Chen
BACKGROUND: Alternative polyadenylation (APA), alternative splicing (AS), and long non-coding RNAs (lncRNAs) play regulatory roles in post-transcriptional processes in plants. However, little is known about their involvement in xylem development in Dalbergia odorifera, a valuable rosewood species with medicinal and commercial significance. We addressed this by conducting Isoform Sequencing (Iso-Seq) using PacBio's SMRT technology and combined it with RNA-seq analysis (RNA sequencing on Illumina platform) after collecting xylem samples from the transition zone and the sapwood of D...
April 16, 2024: BMC Genomics
#28
JOURNAL ARTICLE
Hamid Beiki, Brenda M Murdoch, Carissa A Park, Chandlar Kern, Denise Kontechy, Gabrielle Becker, Gonzalo Rincon, Honglin Jiang, Huaijun Zhou, Jacob Thorne, James E Koltes, Jennifer J Michal, Kimberly Davenport, Monique Rijnkels, Pablo J Ross, Rui Hu, Sarah Corum, Stephanie McKay, Timothy P L Smith, Wansheng Liu, Wenzhi Ma, Xiaohui Zhang, Xiaoqing Xu, Xuelei Han, Zhihua Jiang, Zhi-Liang Hu, James M Reecy
BACKGROUND: The accurate identification of the functional elements in the bovine genome is a fundamental requirement for high-quality analysis of data informing both genome biology and genomic selection. Functional annotation of the bovine genome was performed to identify a more complete catalog of transcript isoforms across bovine tissues. RESULTS: A total of 160,820 unique transcripts (50% protein coding) representing 34,882 unique genes (60% protein coding) were identified across tissues...
January 2, 2024: GigaScience
#29
JOURNAL ARTICLE
Hengxin Pan, Zhenqi Wu, Wanting Liu, Gong Zhang
With the rapid expansion of sequencing of genomes, the functional annotation of proteins becomes a bottleneck in understanding proteomes. The Chromosome-centric Human Proteome Project (C-HPP) aims to identify all proteins encoded by the human genome and find functional annotations for them. However, until now there are still 1137 identified human proteins without functional annotation, called uPE1 proteins. Sequence alignment was insufficient to predict their functions, and the crystal structures of most proteins were unavailable...
April 16, 2024: Journal of Proteome Research
#30
JOURNAL ARTICLE
Tiffany Fang, Choukri Ben Mamoun
Pathogens such as Plasmodium, Babesia, and Theileria invade and multiply within host red blood cells, leading to the pathological consequences of malaria, babesiosis and theileriosis. Establishing continuous in vitro culture systems and suitable animal models is crucial for studying these pathogens. This review spotlights the B. duncani "in culture-in mouse (ICIM)" model as a promising resource for advancing research on the biology, pathogenicity, and virulence of intraerythrocytic parasites. The model offers practical benefits, encompassing well-defined culture conditions, ease of manipulation and a well-annotated genome...
April 16, 2024: Journal of Infectious Diseases
#31
JOURNAL ARTICLE
Sabyrkhan M Barmak, Ian H Mendenhall, Yuriy A Sinyavskiy, Aidar B Berdygaliev, Turegeldy Sh Sharmanov, Gulmira T Sultankulova, Dilyar N Tuigunov, Elena V Zholdybayeva
Here, we present the whole-genome sequence of Salmonella enterica subsp. enterica strain QazSL-4 isolated from a chicken fillet in 2018, Almaty, Kazakhstan. The genome obtained using Illumina MiSeq technology consists of 49 contigs with a total length of 4,711,816 bp with a GC content of 52.1%.
April 16, 2024: Microbiology Resource Announcements
#32
JOURNAL ARTICLE
Yui Murakami, Soichiro Ikuta, Wakao Fukuda, Naoki Akasaka, Jun-Ichi Maruyama, Shuichi Shinma, Eiichiro Fukusaki, Shinsuke Fujiwara
Aspergillus oryzae spores, when sprinkled onto steamed rice and allowed to propagate, are referred to as rice "koji ." Agmatine, a natural polyamine derived from arginine through the action of arginine decarboxylase (ADC), is abundantly produced by solid state-cultivated rice koji of A. oryzae RIB40 under low pH conditions, despite the apparent absence of ADC orthologs in its genome. Mass spectrometry imaging revealed that agmatine was accumulated inside rice koji at low pH conditions, where arginine was distributed...
April 16, 2024: Applied and Environmental Microbiology
#33
JOURNAL ARTICLE
Venkata Suresh Bonthala, Benjamin Stich
We constructed a gene expression atlas and co-expression network for potatoes and identified several novel genes associated with various agronomic traits. This resource will accelerate potato genetics and genomics research. Potato (Solanum tuberosum L.) is the world's most crucial non-cereal food crop and ranks third in food production after wheat and rice. Despite the availability of several potato transcriptome datasets at public databases like NCBI SRA, an effort has yet to be put into developing a global transcriptome atlas and a co-expression network for potatoes...
April 15, 2024: Plant Cell Reports
#34
JOURNAL ARTICLE
Aimei Bai, Tianzi Zhao, Yan Li, Feixue Zhang, Haibin Wang, Sayyed Hamad Ahmad Shah, Li Gong, Tongkun Liu, Yuhui Wang, Xilin Hou, Ying Li
Two major-effect QTL GlcA07.1 and GlcA09.1 for green leaf color were fine mapped into 170.25 kb and 191.41 kb intervals on chromosomes A07 and A09, respectively, and were validated by transcriptome analysis. Non-heading Chinese cabbage (NHCC) is a leafy vegetable with a wide range of green colors. Understanding the genetic mechanism behind broad spectrum of green may facilitate the breeding of high-quality NHCC. Here, we used F2 and F7:8 recombination inbred line (RIL) population from a cross between Wutacai (dark-green) and Erqing (lime-green) to undertake the genetic analysis and quantitative trait locus (QTL) mapping in NHCC...
April 15, 2024: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
#35
JOURNAL ARTICLE
Ya-Ting Ning, Rong-Chen Dai, Zheng-Yu Luo, Meng Xiao, Yingchun Xu, Qun Yan, Li Zhang
The rare fungus Candida saopaulonensis has never been reported to be associated with human infection. We report the draft genome sequence of the first clinical isolate of C. saopaulonensis, which was isolated from a very premature infant with sepsis. This is the first genome assembly reaching the near-complete chromosomal level with structural annotation for this species, opening up avenues for exploring evolutionary patterns and genetic mechanisms of pathogenesis.
April 15, 2024: Mycopathologia
#36
JOURNAL ARTICLE
Ji-Qing Zhou, Hua-Jian Li, Yu-Hao Zeng, Hua-Hua Chen, Wei-Yu Liang, Jin Zhang, Fu-Ping Ding
This study aims to investigate whether baicalin induces ferroptosis in HepG2 cells and decipher the underlying mechanisms based on network pharmacology and cell experiments. HepG2 cells were cultured in vitro and the cell viability was detected by the cell counting kit-8(CCK-8). The transcriptome data of hepatocellular carcinoma were obtained from the Cancer Genome Atlas(TCGA), and the ferroptosis gene data from FerrDb V2. The DEG2 package was used to screen the differentially expressed genes(DEGs), and the common genes between DEGs and ferroptosis genes were selected as the target genes that mediate ferroptosis to regulate hepatocellular carcinoma progression...
March 2024: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
#37
JOURNAL ARTICLE
Ping Qiao, Ming Qin, Wan-Heng Meng, Yi-Heng Wang, Bin-Bin Yan, Zi-Hua Zhang, Qing-Jun Yuan, Jia-Hui Sun, Sheng Wang
Rubus chingii and R. chingii var. suavissimus are unique dual-purpose plant resources, with significant nutraceutical, pharmaceutical, and economic value, as well as promising prospects for further development. To investigate the genetic structure and evolutionary characteristics of these two varieties, this study conducted plastome sequencing using the Illumina HiSeq XTen sequencing platform. Subsequently, the study performed assembly, annotation, and characterization of the genomes, followed by a comparative plastome and phylogenetic analysis using bioinformatics techniques...
March 2024: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
#38
JOURNAL ARTICLE
Xin Huang, Liyan Su, Baohang Xian, Qiyuan Yu, Miao Zhang, Jie Fan, Chenxi Zhang, Yiqi Liu, Houzheng He, Xin Zhong, Man Li, Shanchun Chen, Yongrui He, Qiang Li
Citrus bacterial canker (CBC) is a harmful bacterial disease caused by Xanthomonas citri subsp. citri (Xcc), negatively impacting citrus production worldwide. The basic helix-loop-helix (bHLH) transcription factor family plays crucial roles in plant development and stress responses. This study aimed to identify and annotate bHLH proteins encoded in the Citrus sinensis genome and explore their involvement and functional importance in regulating CBC resistance. A total of 135 putative CsbHLHs TFs were identified and categorized into 16 subfamilies...
April 13, 2024: International Journal of Biological Macromolecules
#39
REVIEW
Miguel Correa Marrero, Jürgen Jänes, Delora Baptista, Pedro Beltrao
The last five years have seen impressive progress in deep learning models applied to protein research. Most notably, sequence-based structure predictions have seen transformative gains in the form of AlphaFold2 and related approaches. Millions of missense protein variants in the human population lack annotations, and these computational methods are a valuable means to prioritize variants for further analysis. Here, we review the recent progress in deep learning models applied to the prediction of protein structure and protein variants, with particular emphasis on their implications for human genetics and health...
April 15, 2024: Annual Review of Genomics and Human Genetics
#40
JOURNAL ARTICLE
Gavrila Ang, Andrew Zhang, John Obrycki, Arun Sethuraman
Here we describe a high quality genome assembly and annotation of the convergent lady beetle, Hippodamia convergens (Coleoptera: Coccinellidae). The highest quality unmasked genome comprises 619 Megabases (Mb) of chromosomal DNA, organized into 899 contigs, with a contig N50 score of 89 Mbps. The genome was assessed to be 96% complete (BUSCO). Reconstruction of a whole genome phylogeny resolved H. convergens as sister to the Harlequin lady beetle, Harmonia axyridis, and nested within a clade of several known agricultural pests...
April 15, 2024: G3: Genes—Genomes—Genetics
Make the most of Read.
Download the mobile app.
Download the mobile app.
Fetching more papers... 
