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Hue T M Tran, Thiruvarangan Ramaraj, Agnelo Furtado, L Slade Lee, Robert J Henry
Arabica coffee (Coffea arabica) has a small gene pool limiting genetic improvement. Selection for caffeine content within this gene pool would be assisted by identification of the genes controlling this important trait. Sequencing of DNA bulks from 18 genotypes with extreme high or low caffeine content from a population of 232 genotypes was used to identify linked polymorphisms. To obtain a reference genome a whole genome assembly of arabica coffee (variety K7) was achieved by sequencing using short read (Illumina) and long read (PacBio) technology...
March 6, 2018: Plant Biotechnology Journal
Torunn Pedersen, John Osei Sekyere, Usha Govinden, Krishnee Moodley, Audun Sivertsen, Ørjan Samuelsen, Sabiha Yusuf Essack, Arnfinn Sundsfjord
Whole-genome sequence analyses revealed the presence of bla NDM-1 ( n =31), bla GES-5 ( n =8), bla OXA-232 ( n =1), or bla NDM-5 ( n =1) in extensively drug-resistant and pandrug-resistant Enterobacteriaceae isolated from in-patients in 10 private hospitals (2012-2013) in Durban, South Africa. Two novel NDM-1 encoding plasmids from Klebsiella pneumoniae were closed by PacBio sequencing. In p19-10_01 (IncFIB(K), 223.434 bp) bla NDM-1 was part of a Tn 1548 -like structure (16.276 bp) delineated by IS 26 The multireplicon plasmid p18-43_01 (IncR_1/IncFIB(pB171)/IncFII(Yp); 212...
March 5, 2018: Antimicrobial Agents and Chemotherapy
Renata de Castro Nunes, Simon Orozco-Arias, Dominique Crouzillat, Lukas A Mueller, Suzy R Strickler, Patrick Descombes, Coralie Fournier, Deborah Moine, Alexandre de Kochko, Priscila M Yuyama, André L L Vanzela, Romain Guyot
Centromeric regions of plants are generally composed of large array of satellites from a specific lineage of Gypsy LTR-retrotransposons, called Centromeric Retrotransposons. Repeated sequences interact with a specific H3 histone, playing a crucial function on kinetochore formation. To study the structure and composition of centromeric regions in the genus Coffea , we annotated and classified Centromeric Retrotransposons sequences from the allotetraploid C. arabica genome and its two diploid ancestors: Coffea canephora and C...
2018: Frontiers in Plant Science
Vincent Magrini, Xin Gao, Bruce A Rosa, Sean McGrath, Xu Zhang, Kymberlie Hallsworth-Pepin, John Martin, John Hawdon, Richard K Wilson, Makedonka Mitreva
BACKGROUND: The advantages of Pacific Biosciences (PacBio) single-molecule real-time (SMRT) technology include long reads, low systematic bias, and high consensus read accuracy. Here we use these attributes to improve on the genome annotation of the parasitic hookworm Ancylostoma ceylanicum using PacBio RNA-Seq. RESULTS: We sequenced 192,888 circular consensus sequences (CCS) derived from cDNAs generated using the CloneTech SMARTer system. These SMARTer-SMRT libraries were normalized and size-selected providing a robust population of expressed structural genes for subsequent genome annotation...
March 1, 2018: BMC Genomics
Junyan Liu, Lin Li, Brian M Peters, Bing Li, Dingqiang Chen, Zhenbo Xu, Mark E Shirtliff
OBJECTIVES: We previously described the novel qnrVC6 and blaIMP-45 carrying megaplasmid pBM413. This study aimed to investigate the complete genome of multidrug-resistance P. aeruginosa Guangzhou-Pae617, a clinical isolate from the sputum of a patient who was suffering from respiratory disease in Guangzhou, China. METHODS: The genome was sequenced using Illumina Hiseq 2500 and PacBio RS II sequencers and assembled de novo using HGAP. The genome was automatically and manually annotated...
February 24, 2018: Microbial Pathogenesis
Kazuma Nakano, Maiko Minami, Misuzu Shinzato, Makiko Shimoji, Noriko Ashimine, Akino Shiroma, Shun Ohki, Tetsuhiro Nakanishi, Hinako Tamotsu, Kuniko Teruya, Kazuhito Satou, Naoko Moriya, Hiromi Kimoto-Nira, Miho Kobayashi, Tatsuro Hagi, Masaru Nomura, Chise Suzuki, Takashi Hirano
Lactococcus lactis subsp. lactis G50 is a strain with immunostimulating activity, isolated from Napier grass ( Pennisetum purpureum ). We determined the complete genome sequence of this strain using the PacBio RS II platform. The single circular chromosome consists of 2,346,663 bp, with 35.03% G+C content and no plasmids.
February 22, 2018: Genome Announcements
Euon Jung Tak, Hyun Sik Kim, June-Young Lee, Woorim Kang, Hojun Sung, Pil Soo Kim, Dong-Wook Hyun, Na-Ri Shin, Jeong Rae Roh, Sun Duk Park, Hyung Eun Shim, Jin-Woo Bae
A rod-shaped, Gram-stain-positive, motile and aerobic bacterium, designated LM2416T , was isolated from faeces of Lophuras winhoii living in Seoul Grand Park, Gyeonggi-do, Republic of Korea. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain LM2416T belonged to the genus Virgibacillus, sharing high 16S rRNA gene sequence similarities to Virgibacillus necropolis LMG 19488T (99.0 %), Virgibacillus carmonensis LMG 20964T (98.4 %), Virgibacillus arcticus Hal 1T (98.3 %) and Virgibacillus flavescens S1-20T (97...
February 21, 2018: International Journal of Systematic and Evolutionary Microbiology
Angeline Casale, Stephanie Clark, Melissa Grasso, Marta Kryschuk, Lukas Ritzer, Madyson Trudeau, Laura E Williams
We report here the complete genome sequence of Escherichia coli strain ML35. We assembled PacBio reads into a single closed contig with 169× mean coverage and then polished this contig using Illumina MiSeq reads, yielding a 4,918,774-bp sequence with 50.8% GC content.
February 15, 2018: Genome Announcements
Joseph Cerra, Hailey Donohue, Alexander Kral, Molly Oser, Laura Rostkowski, Luke Zappia, Laura E Williams
We report here the complete genome sequence of Pseudomonas sp. strain NC02, isolated from soil in eastern Massachusetts. We assembled PacBio reads into a single closed contig with 132× mean coverage and then polished this contig using Illumina MiSeq reads, yielding a 6,890,566-bp sequence with 61.1% GC content.
February 15, 2018: Genome Announcements
Rodrigo P Baptista, Joao Luis Reis-Cunha, Jeremy D DeBarry, Egler Chiari, Jessica C Kissinger, Daniella C Bartholomeu, Andrea M Macedo
Next-generation sequencing (NGS) methods are low-cost high-throughput technologies that produce thousands to millions of sequence reads. Despite the high number of raw sequence reads, their short length, relative to Sanger, PacBio or Nanopore reads, complicates the assembly of genomic repeats. Many genome tools are available, but the assembly of highly repetitive genome sequences using only NGS short reads remains challenging. Genome assembly of organisms responsible for important neglected diseases such as Trypanosoma cruzi, the aetiological agent of Chagas disease, is known to be challenging because of their repetitive nature...
February 14, 2018: Microbial Genomics
Manuel Tardaguila, Lorena de la Fuente, Cristina Marti, Cécile Pereira, Francisco Jose Pardo-Palacios, Hector Del Risco, Marc Ferrell, Maravillas Mellado, Marissa Macchietto, Kenneth Verheggen, Mariola Edelmann, Iakes Ezkurdia, Jesus Vazquez, Michael Tress, Ali Mortazavi, Lennart Martens, Susana Rodriguez-Navarro, Victoria Moreno-Manzano, Ana Conesa
High-throughput sequencing of full-length transcripts using long reads has paved the way for the discovery of thousands of novel transcripts, even in well-annotated mammalian species. The advances in sequencing technology have created a need for studies and tools that can characterize these novel variants. Here, we present SQANTI, an automated pipeline for the classification of long-read transcripts that can assess the quality of data and the preprocessing pipeline using 47 unique descriptors. We apply SQANTI to a neuronal mouse transcriptome using Pacific Biosciences (PacBio) long reads and illustrate how the tool is effective in characterizing and describing the composition of the full-length transcriptome...
February 9, 2018: Genome Research
Rubina Jibran, Helge Dzierzon, Nahla Bassil, Jill M Bushakra, Patrick P Edger, Shawn Sullivan, Chad E Finn, Michael Dossett, Kelly J Vining, Robert VanBuren, Todd C Mockler, Ivan Liachko, Kevin M Davies, Toshi M Foster, David Chagné
Black raspberry (Rubus occidentalis L.) is a niche fruit crop valued for its flavor and potential health benefits. The improvement of fruit and cane characteristics via molecular breeding technologies has been hindered by the lack of a high-quality reference genome. The recently released draft genome for black raspberry (ORUS 4115-3) lacks assembly of scaffolds to chromosome scale. We used high-throughput chromatin conformation capture (Hi-C) and Proximity-Guided Assembly (PGA) to cluster and order 9650 out of 11,936 contigs of this draft genome assembly into seven pseudo-chromosomes...
2018: Horticulture Research
Jixia Yang, Jialu Cao, Haiyan Xu, Qiangchuan Hou, Zhongjie Yu, Heping Zhang, Zhihong Sun
BACKGROUND: Traditional Chongqing radish paocai fermented with aged brine is considered to have the most intense flavor and authentic taste. Eight "Yanzhi" (red, RRPB group) and "Chunbulao" (white, WRPB) radish paocai brine samples were collected from Chongqing peasant households, and the diversity and community structures of bacteria present in these brines were determined using PacBio SMRT sequencing of their full-length 16S rRNA genes. RESULTS: In total, 30 phyla, 218 genera and 306 species were identified from the RRPB group, with 20 phyla, 261 genera and 420 species present in the WRPB group...
February 8, 2018: Journal of the Science of Food and Agriculture
Weiping Zhang, Yudong Li, Yiwang Chen, Sha Xu, Guocheng Du, Huidong Shi, Jingwen Zhou, Jian Chen
Chinese rice wine is a popular traditional alcoholic beverage in China, while its brewing processes have rarely been explored. We herein report the first gapless, near-finished genome sequence of the yeast strain Saccharomyces cerevisiae N85 for Chinese rice wine production. Several assembly methods were used to integrate Pacific Bioscience (PacBio) and Illumina sequencing data to achieve high-quality genome sequencing of the strain. The genome encodes more than 6,000 predicted proteins, and 238 long non-coding RNAs, which are validated by RNA-sequencing data...
February 5, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
Simon Ardui, Adam Ameur, Joris R Vermeesch, Matthew S Hestand
Short read massive parallel sequencing has emerged as a standard diagnostic tool in the medical setting. However, short read technologies have inherent limitations such as GC bias, difficulties mapping to repetitive elements, trouble discriminating paralogous sequences, and difficulties in phasing alleles. Long read single molecule sequencers resolve these obstacles. Moreover, they offer higher consensus accuracies and can detect epigenetic modifications from native DNA. The first commercially available long read single molecule platform was the RS system based on PacBio's single molecule real-time (SMRT) sequencing technology, which has since evolved into their RSII and Sequel systems...
February 1, 2018: Nucleic Acids Research
Min-Lang Huang, Jing-Yao Huang, Cheng-Yen Kao, Tony J Fang
Background: Lactobacillus pentosus SLC13 is a high exopolysaccharide (EPS)-producing strain with broad-spectrum antimicrobial activity and the ability to grow in simulated gastrointestinal conditions. SLC13 was isolated from mustard pickles in Taiwan for potential probiotic applications. To better understand the molecular base for its antimicrobial activity and high EPS production, entire genome of SLC13 was determined by PacBio SMRT sequencing. Results: L. pentosus SLC13 contains a genome with a 3,520,510-bp chromosome and a 62,498-bp plasmid...
2018: Gut Pathogens
Slimane Khayi, Pauline Blin, Teik Min Chong, Kévin Robic, Kok-Gan Chan, Denis Faure
Dickeya spp. are bacterial pathogens causing soft-rot and blackleg diseases on a wide range of ornamental plants and crops. In this paper, we announce the PacBio complete genome sequences of the plant pathogens Dickeya solani RNS (PRI3337) and Dickeya dianthicola RNS04.9.
January 25, 2018: Genome Announcements
Peng Sun, Haifeng Luo, Xin Zhang, Jingyi Xu, Yanan Guo, Shenghu He
A genome sequence of the Mycoplasma bovis Ningxia-1 strain was tested by Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing technology. The strain was isolated from a lesioned calf lung in 2013 in Pengyang, Ningxia, China. The single circular chromosome of 1,033,629 bp shows differences between complete Mycoplasma bovis genome in insertion-like sequences (ISs), integrative conjugative elements (ICEs), lipoproteins (LPs), variable surface lipoproteins (VSPs), pathogenicity islands (PAIs), etc...
January 25, 2018: Genome Announcements
Yuko Makita, Mika Kawashima, Nyok Sean Lau, Ahmad Sofiman Othman, Minami Matsui
BACKGROUND: Natural rubber is an economically important material. Currently the Pará rubber tree, Hevea brasiliensis is the main commercial source. Little is known about rubber biosynthesis at the molecular level. Next-generation sequencing (NGS) technologies brought draft genomes of three rubber cultivars and a variety of RNA sequencing (RNA-seq) data. However, no current genome or transcriptome databases (DB) are organized by gene. RESULTS: A gene-oriented database is a valuable support for rubber research...
January 19, 2018: BMC Genomics
Fabrice Touzain, Laetitia Le Devendec, Claire de Boisséson, Sandrine Baron, Eric Jouy, Agnès Perrin-Guyomard, Yannick Blanchard, Isabelle Kempf
Resistance to extended-spectrum cephalosporins (ESC) is a global health issue. The aim of this study was to analyze and compare plasmids coding for resistance to ESC isolated from 16 avian commensal and 17 avian pathogenic Escherichia coli (APEC) strains obtained respectively at slaughterhouse or from diseased broilers in 2010-2012. Plasmid DNA was used to transform E. coli DH5alpha, and the resistances of the transformants were determined. The sequences of the ESC-resistance plasmids prepared from transformants were obtained by Illumina (33 plasmids) or PacBio (1 plasmid)...
2018: PloS One
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