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https://www.readbyqxmd.com/read/28336594/first-report-on-the-complete-genome-sequence-of-lactobacillus-crustorum-mn047-a-potent-probiotic-strain-isolated-from-koumiss-in-china
#1
Lanhua Yi, Xing Guo, Lian Liu, Chunge Shao, Xin Lü
The complete genome sequence of Lactobacillus crustorum deciphered by PacBio RS II and Illumina HiSeq 4000 sequencing was first reported with one chromosome and two plasmids. Sequence analysis of L. crustorum MN047 showed probiotic characteristics.
March 23, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28327967/genome-sequence-of-pacific-abalone-haliotis-discus-hannai-the-first-draft-genome-in-family-haliotidae
#2
Bo-Hye Nam, Woori Kwak, Young-Ok Kim, Dong-Gyun Kim, Hee Jeong Kong, Woo-Jin Kim, Jeong-Ha Kang, Jung Youn Park, Cheul Min An, Ji-Young Moon, Choul Ji Park, Jae Woong Yu, Joon Yoon, Minseok Seo, Kwondo Kim, Duk Kyung Kim, SaetByeol Lee, Samsun Sung, Chul Lee, Younhee Shin, Myunghee Jung, Byeong-Chul Kang, Shin Ga-Hee, Sojeong Ka, Kelsey Caetano-Anolles, Seoae Cho, Heebal Kim
Background: Abalones are large marine snails in the family Haliotidae and the genus Haliotis belonging to the class Gastropoda of the phylum Mollusca. The family Haliotidae contains only one genus, Haliotis, and this single genus is known to contain several species of abalone. With 18 additional subspecies, the most comprehensive treatment of Haliotidae considers 56 species valid [1]. Abalone is an economically important fishery and aquaculture animal which is considered a highly-prized seafood delicacy...
March 7, 2017: GigaScience
https://www.readbyqxmd.com/read/28316149/detecting-alternatively-spliced-transcript-isoforms-from-single-molecule-long-read-sequences-without-a-reference-genome
#3
Xiaoxian Liu, Wenbin Mei, Pamela S Soltis, Douglas E Soltis, W Brad Barbazuk
Alternative splicing (AS) is a major source of transcript and proteome diversity, but examining AS in species without well-annotated reference genomes remains difficult. Research on both human and mouse has demonstrated the advantages of using Iso-Seq(™) data for isoform-level transcriptome analysis, including the study of AS and gene fusion. We applied Iso-Seq(™) to investigate AS in Amborella trichopoda, a phylogenetically pivotal species that is sister to all other living angiosperms. Our data show that, compared with RNA-Seq data, the Iso-Seq(™) platform provides better recovery on large transcripts, new gene locus identification, and gene model correction...
March 18, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28314725/a-genome-survey-and-postharvest-transcriptome-analysis-in-lentinula-edodes
#4
Yuichi Sakamoto, Keiko Nakade, Shiho Sato, Kentaro Yoshida, Kazuhiro Miyazaki, Satoshi Natsume, Naotake Konno
Lentinula edodes is a popular cultivated edible and medicinal mushroom. Lentinula edodes is susceptible to postharvest problems such as gill browning, fruiting body softening, and lentinan degradation. We constructed a de novo assembly draft genome sequence and performed gene prediction of Lentinula edodesDe novo assembly was carried out using short reads from paired-end and mate-paired libraries and long reads by PacBio, resulting in a contig number of 1951 and an N50 of 1 Mb. Further, we predicted genes by Augustus using RNA-seq data from the whole life cycle of Lentinula edodes, resulting in 12,959 predicted genes...
March 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28298431/canu-scalable-and-accurate-long-read-assembly-via-adaptive-k-mer-weighting-and-repeat-separation
#5
Sergey Koren, Brian P Walenz, Konstantin Berlin, Jason R Miller, Nicholas H Bergman, Adam M Phillippy
Long-read single-molecule sequencing has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. However, given the relatively high error rates of such technologies, efficient and accurate assembly of large repeats and closely related haplotypes remains challenging. We address these issues with Canu, a successor of Celera Assembler that is specifically designed for noisy single-molecule sequences. Canu introduces support for nanopore sequencing, halves depth-of-coverage requirements, and improves assembly continuity while simultaneously reducing runtime by an order of magnitude on large genomes versus Celera Assembler 8...
March 15, 2017: Genome Research
https://www.readbyqxmd.com/read/28293220/diversity-and-activity-of-alternative-nitrogenases-in-sequenced-genomes-and-coastal-environments
#6
Darcy L McRose, Xinning Zhang, Anne M L Kraepiel, François M M Morel
The nitrogenase enzyme, which catalyzes the reduction of N2 gas to NH4(+), occurs as three separate isozyme that use Mo, Fe-only, or V. The majority of global nitrogen fixation is attributed to the more efficient 'canonical' Mo-nitrogenase, whereas Fe-only and V-('alternative') nitrogenases are often considered 'backup' enzymes, used when Mo is limiting. Yet, the environmental distribution and diversity of alternative nitrogenases remains largely unknown. We searched for alternative nitrogenase genes in sequenced genomes and used PacBio sequencing to explore the diversity of canonical (nifD) and alternative (anfD and vnfD) nitrogenase amplicons in two coastal environments: the Florida Everglades and Sippewissett Marsh (MA)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28282934/alternative-splicing-profile-and-sex-preferential-gene-expression-in-the-female-and-male-pacific-abalone-haliotis-discus-hannai
#7
Mi Ae Kim, Jae-Sung Rhee, Tae Ha Kim, Jung Sick Lee, Ah-Young Choi, Beom-Soon Choi, Ik-Young Choi, Young Chang Sohn
In order to characterize the female or male transcriptome of the Pacific abalone and further increase genomic resources, we sequenced the mRNA of full-length complementary DNA (cDNA) libraries derived from pooled tissues of female and male Haliotis discus hannai by employing the Iso-Seq protocol of the PacBio RSII platform. We successfully assembled whole full-length cDNA sequences and constructed a transcriptome database that included isoform information. After clustering, a total of 15,110 and 12,145 genes that coded for proteins were identified in female and male abalones, respectively...
March 9, 2017: Genes
https://www.readbyqxmd.com/read/28272530/hybrid-sequencing-and-map-finding-hysemafi-optional-strategies-for-extensively-deciphering-gene-splicing-and-expression-in-organisms-without-reference-genome
#8
Guogui Ning, Xu Cheng, Ping Luo, Fan Liang, Zhen Wang, Guoliang Yu, Xin Li, Depeng Wang, Manzhu Bao
Using second-generation sequencing (SGS) RNA-Seq strategies, extensive alterative splicing prediction is impractical and high variability of isoforms expression quantification is inevitable in organisms without true reference dataset. we report the development of a novel analysis method, termed hybrid sequencing and map finding (HySeMaFi) which combines the specific strengths of third-generation sequencing (TGS) (PacBio SMRT sequencing) and SGS (Illumina Hi-Seq/MiSeq sequencing) to effectively decipher gene splicing and to reliably estimate the isoforms abundance...
March 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28265515/genomic-analysis-of-st88-community-acquired-methicillin-resistant-staphylococcus-aureus-in-ghana
#9
Grace Kpeli, Andrew H Buultjens, Stefano Giulieri, Evelyn Owusu-Mireku, Samuel Y Aboagye, Sarah L Baines, Torsten Seemann, Dieter Bulach, Anders Gonçalves da Silva, Ian R Monk, Benjamin P Howden, Gerd Pluschke, Dorothy Yeboah-Manu, Timothy Stinear
BACKGROUND: The emergence and evolution of community-acquired methicillin resistant Staphylococcus aureus (CA-MRSA) strains in Africa is poorly understood. However, one particular MRSA lineage called ST88, appears to be rapidly establishing itself as an "African" CA-MRSA clone. In this study, we employed whole genome sequencing to provide more information on the genetic background of ST88 CA-MRSA isolates from Ghana and to describe in detail ST88 CA-MRSA isolates in comparison with other MRSA lineages worldwide...
2017: PeerJ
https://www.readbyqxmd.com/read/28261190/fungal-its1-deep-sequencing-strategies-to-reconstruct-the-composition-of-a-26-species-community-and-evaluation-of-the-gut-mycobiota-of-healthy-japanese-individuals
#10
Daisuke Motooka, Kosuke Fujimoto, Reiko Tanaka, Takashi Yaguchi, Kazuyoshi Gotoh, Yuichi Maeda, Yoki Furuta, Takashi Kurakawa, Naohisa Goto, Teruo Yasunaga, Masashi Narazaki, Atsushi Kumanogoh, Toshihiro Horii, Tetsuya Iida, Kiyoshi Takeda, Shota Nakamura
The study of mycobiota remains relatively unexplored due to the lack of sufficient available reference strains and databases compared to those of bacterial microbiome studies. Deep sequencing of Internal Transcribed Spacer (ITS) regions is the de facto standard for fungal diversity analysis. However, results are often biased because of the wide variety of sequence lengths in the ITS regions and the complexity of high-throughput sequencing (HTS) technologies. In this study, a curated ITS database, ntF-ITS1, was constructed...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28261177/the-histidine-decarboxylase-gene-cluster-of-lactobacillus-parabuchneri-was-gained-by-horizontal-gene-transfer-and-is-mobile-within-the-species
#11
Daniel Wüthrich, Hélène Berthoud, Daniel Wechsler, Elisabeth Eugster, Stefan Irmler, Rémy Bruggmann
Histamine in food can cause intolerance reactions in consumers. Lactobacillus parabuchneri (L. parabuchneri) is one of the major causes of elevated histamine levels in cheese. Despite its significant economic impact and negative influence on human health, no genomic study has been published so far. We sequenced and analyzed 18 L. parabuchneri strains of which 12 were histamine positive and 6 were histamine negative. We determined the complete genome of the histamine positive strain FAM21731 with PacBio as well as Illumina and the genomes of the remaining 17 strains using the Illumina technology...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28256586/characterization-of-the-dynamic-transcriptome-of-a-herpesvirus-with-long-read-single-molecule-real-time-sequencing
#12
Dóra Tombácz, Zsolt Balázs, Zsolt Csabai, Norbert Moldován, Attila Szűcs, Donald Sharon, Michael Snyder, Zsolt Boldogkői
Herpesvirus gene expression is co-ordinately regulated and sequentially ordered during productive infection. The viral genes can be classified into three distinct kinetic groups: immediate-early, early, and late classes. In this study, a massively parallel sequencing technique that is based on PacBio Single Molecule Real-time sequencing platform, was used for quantifying the poly(A) fraction of the lytic transcriptome of pseudorabies virus (PRV) throughout a 12-hour interval of productive infection on PK-15 cells...
March 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28245065/deletion-bias-in-dna-double-strand-break-repair-differentially-contributes-to-plant-genome-shrinkage
#13
Giang T H Vu, Hieu X Cao, Bernd Reiss, Ingo Schubert
In order to prevent genome instability, cells need to be protected by a number of repair mechanisms, including DNA double-strand break (DSB) repair. The extent to which DSB repair, biased towards deletions or insertions, contributes to evolutionary diversification of genome size is still under debate. We analyzed mutation spectra in Arabidopsis thaliana and in barley (Hordeum vulgare) by PacBio sequencing of three DSB-targeted loci each, uncovering repair via gene conversion, single strand annealing (SSA) or nonhomologous end-joining (NHEJ)...
February 28, 2017: New Phytologist
https://www.readbyqxmd.com/read/28229234/sequencing-the-genomic-regions-flanking-s-linked-pvglo-sequences-confirms-the-presence-of-two-glo-loci-one-of-which-lies-adjacent-to-the-style-length-determinant-gene-cyp734a50
#14
Benjamin A Burrows, Andrew G McCubbin
Primula vulgaris contains two GLOBOSA loci, one located adjacent to the style length determinant gene CYP734A50 which lies within the S -locus. Using a combination of BAC walking and PacBio sequencing, we have sequenced two substantial genomic contigs in and around the S-locus of Primula vulgaris. Using these data, we were able to demonstrate that two alleles of PvGlo (P) as well as PvGlo (T) can be present in the genome of a single plant, providing empirical evidence that these two forms of the MADS-box gene GLOBOSA are separate loci and not allelic as previously reported...
March 2017: Plant Reproduction
https://www.readbyqxmd.com/read/28210248/coexistence-of-blaoxa-48-and-truncated-blandm-1-on-different-plasmids-in-a-klebsiella-pneumoniae-isolate-in-china
#15
Lianyan Xie, Yi Dou, Kaixin Zhou, Yue Chen, Lizhong Han, Xiaokui Guo, Jingyong Sun
Objectives: To describe the genetic environment, transferability, and antibiotic susceptibility of one clinical Klebsiella pneumoniae isolate harboring both blaOXA-48 and blaNDM-1 on different plasmids from a Chinese hospital. Methods: The isolate was subjected to antimicrobial susceptibility testing and multilocus sequence typing using Etest and PCR. The plasmids harboring blaOXA-48 and blaNDM-1 were analyzed through conjugation experiments, S1-nuclease pulsed-field gel electrophoresis, and hybridization with specific probes...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28209832/complete-genome-sequences-of-three-multidrug-resistant-clinical-isolates-of-streptococcus-pneumoniae-serotype-19a-with-different-susceptibilities-to-the-myxobacterial-metabolite-carolacton
#16
Jannik Donner, Boyke Bunk, Isabel Schober, Cathrin Spröer, Simone Bergmann, Michael Jarek, Jörg Overmann, Irene Wagner-Döbler
The full-genome sequences of three drug- and multidrug-resistant Streptococcus pneumoniae clinical isolates of serotype 19A were determined by PacBio single-molecule real-time sequencing, in combination with Illumina MiSeq sequencing. A comparison to the genomes of other pneumococci indicates a high nucleotide sequence identity to strains Hungary19A-6 and TCH8431/19A.
February 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28209827/first-complete-genome-sequence-of-marinilactibacilluspiezotolerans-strain-15r-a-marine-lactobacillus-isolated-from-coal-bearing-sediment-2-0-kilometers-below-the-seafloor-determined-by-pacbio-single-molecule-real-time-technology
#17
Yuli Wei, Junwei Cao, Jiasong Fang, Chiaki Kato, Weicheng Cui
Marinilactibacillus piezotolerans strain 15R is a facultatively anaerobic heterotrophic lactobacillus isolated from deep marine subsurface sediment nearly 2 km below the seafloor in the northwestern Pacific. We report here the first whole-genome sequence of strain 15R. The identified genome sequence has 2,767,908 bp, 35.4% G+C content, and predicted 2,552 candidate protein-coding sequences, with no identified plasmids.
February 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28209817/genome-sequence-of-a-unique-magnaporthe-oryzae-rmg-dl-isolate-from-india-that-causes-blast-disease-in-diverse-cereal-crops-obtained-using-pacbio-single-molecule-and-illumina-hiseq2500-sequencing
#18
Aundy Kumar, Neelam Sheoran, Ganesan Prakash, Arpita Ghosh, Surendra K Chikara, Hosahatti Rajashekara, Uday Dhari Singh, Rashmi Aggarwal, Rakesh Kumar Jain
The whole-genome assembly of a unique rice isolate from India, Magnaporthe oryzae RMg-Dl that causes blast disease in diverse cereal crops is presented. Analysis of the 34.82 Mb genome sequence will aid in better understanding the genetic determinants of host range, host jump, survival, pathogenicity, and virulence factors of M. oryzae.
February 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28201990/a-vast-genomic-deletion-in-the-c56bl-6-genome-affects-different-genes-within-the-ifi200-cluster-on-chromosome-1-and-mediates-obesity-and-insulin-resistance
#19
Heike Vogel, Markus Jähnert, Mandy Stadion, Daniela Matzke, Stephan Scherneck, Annette Schürmann
BACKGROUND: Obesity, the excessive accumulation of body fat, is a highly heritable and genetically heterogeneous disorder. The complex, polygenic basis for the disease consisting of a network of different gene variants is still not completely known. RESULTS: In the current study we generated a BAC library of the obese-prone NZO strain to clarify the genomic alteration within the gene cluster Ifi200 on chr.1 including Ifi202b, an obesity gene that is in contrast to NZO not expressed in the lean B6 mouse...
February 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28181326/single-molecule-rna-sequencing-uncovers-trans-splicing-and-improves-annotations-in-anopheles-stephensi
#20
X Jiang, A B Hall, J K Biedler, Z Tu
Single molecule real-time (SMRT) sequencing has recently been used to obtain full-length cDNA sequences that improve genome annotation and reveal RNA isoforms. Here, we used one such method called isoform sequencing from Pacific Biosciences (PacBio) to sequence a cDNA library from the Asian malaria mosquito Anopheles stephensi. More than 600 000 full-length cDNAs, referred to as reads of insert, were identified. Owing to the inherently high error rate of PacBio sequencing, we tested different approaches for error correction...
February 9, 2017: Insect Molecular Biology
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