Menu

Asset Tag: Plant and Animal Sciences,

July 7, 2019  |  

Genome sequencing and analysis of the first complete genome of Lactobacillus kunkeei strain MP2, an Apis mellifera gut isolate

Background. The honey bee (Apis mellifera) is the most important pollinator in agriculture worldwide. However, the number of honey bees has fallen significantly since 2006, becoming a huge ecological problem nowadays. The principal cause is CCD, or Colony Collapse Disorder, characterized by the seemingly spontaneous abandonment of hives by their workers. One of the characteristics of CCD in honey bees is the alteration of the bacterial communities in their gastrointestinal tract, mainly due to the decrease of Firmicutes populations, such as the Lactobacilli. At this time, the causes of these alterations remain unknown. We recently isolated a strain of Lactobacillus kunkeei (L. kunkeei strain MP2) from the gut of Chilean honey bees. L. kunkeei, is one of the most commonly isolated bacterium from the honey bee gut and is highly versatile in different ecological niches. In this study, we aimed to elucidate in detail, the L. kunkeei genetic background and perform a comparative genome analysis with other Lactobacillus species. Methods. L. kunkeei MP2 was originally isolated from the guts of Chilean A. mellifera individuals. Genome sequencing was done using Pacific Biosciences single-molecule real-time sequencing technology. De novo assembly was performed using Celera assembler. The genome was annotated using Prokka, and functional information was added using the EggNOG 3.1 database. In addition, genomic islands were predicted using IslandViewer, and pro-phage sequences using PHAST. Comparisons between L. kunkeei MP2 with other L. kunkeei, and Lactobacillus strains were done using Roary. Results. The complete genome of L. kunkeei MP2 comprises one circular chromosome of 1,614,522 nt. with a GC content of 36,9%. Pangenome analysis with 16 L. kunkeei strains, identified 113 unique genes, most of them related to phage insertions. A large and unique region of L. kunkeei MP2 genome contains several genes that encode for phage structural protein and replication components. Comparative analysis of MP2 with other Lactobacillus species, identified several unique genes of L. kunkeei MP2 related with metabolism, biofilm generation, survival under stress conditions, and mobile genetic elements (MGEs). Discussion. The presence of multiple mobile genetic elements, including phage sequences, suggest a high degree of genetic variability in L. kunkeei. Its versatility and ability to survive in different ecological niches (bee guts, flowers, fruits among others) could be given by its genetic capacity to change and adapt to different environments. L. kunkeei could be a new source of Lactobacillus with beneficial properties. Indeed, L. kunkeei MP2 could play an important role in honey bee nutrition through the synthesis of components as isoprenoids.

Read more
July 7, 2019  |  

Single-molecule sequencing assists genome assembly improvement and structural variation inference.

Dear editor, The single-molecule real-time (SMRT) sequencing platform presented by Pacific Biosciences (PacBio) is regarded as a third-generation sequencing technology (Eid et al., 2009, Roberts et al., 2013). PacBio delivers long reads from several to tens of kilobases (kbs), which are ideal for filling unsequenced gaps due to unusual sequence contexts, such as high-GC content or repeat-rich regions (Bashir et al., 2012, Berlin et al., 2015, Chaisson et al., 2015). PacBio long reads are also favorable for detecting large DNA fragments harboring structural variations (SVs), such as inversions, translocations, duplications, and large insertions/deletions (indels) (Ritz et al., 2010, English et al., 2014). However, one drawback of PacBio is the high error rate of base calling for single pass coverage of the genome (Au et al., 2012, Koren et al., 2012). This drawback can be mitigated by increasing sequencing coverage to achieve high consensus accuracy, but the requirements may be prohibitive for the de novo assembly of large- or medium-size genomes using only PacBio when considering both budgetary and computational costs. Alternatively, PacBio may be used for assembly improvement of near-finished reference genomes, especially for filling gaps in which unsequenced bases are represented by the letter N (English et al., 2012). Here, we combined PacBio (~15x) with Illumina reads (~40x) to improve the genome assemblies of African wild (Oryza barthii) and cultivated rice (O. glaberrima), and to infer large SVs between O. barthii and O. glaberrima.

Read more
July 7, 2019  |  

A pigeonpea gene confers resistance to Asian soybean rust in soybean.

Asian soybean rust (ASR), caused by the fungus Phakopsora pachyrhizi, is one of the most economically important crop diseases, but is only treatable with fungicides, which are becoming less effective owing to the emergence of fungicide resistance. There are no commercial soybean cultivars with durable resistance to P. pachyrhizi, and although soybean resistance loci have been mapped, no resistance genes have been cloned. We report the cloning of a P. pachyrhizi resistance gene CcRpp1 (Cajanus cajan Resistance against Phakopsora pachyrhizi 1) from pigeonpea (Cajanus cajan) and show that CcRpp1 confers full resistance to P. pachyrhizi in soybean. Our findings show that legume species related to soybean such as pigeonpea, cowpea, common bean and others could provide a valuable and diverse pool of resistance traits for crop improvement.

Read more
July 7, 2019  |  

First complete genome sequence of the Dutch veterinary Coxiella burnetii strain NL3262, originating from the largest global Q fever outbreak, and draft genome sequence of its epidemiologically linked chronic human isolate NLhu3345937

The largest global Q fever outbreak occurred in The Netherlands during 2007 to 2010. Goats and sheep were identified as the major sources of disease. Here, we report the first complete genome sequence of Coxiella burnetiigoat outbreak strain NL3262 and that of an epidemiologically linked chronic human strain, both having the outbreak-related CbNL01multilocus variable-number tandem-repeat analysis (MLVA) genotype. Copyright © 2016 Kuley et al.

Read more
July 7, 2019  |  

De novo assembly of complete genome sequence of Planococcus kocurii ATCC 43650(T), a potential plant growth promoting bacterium.

Planococcus kocurii ATCC 43650(T) is a halotolerant and psychrotolerant bacterium isolated from the skin of a North sea cod. Here, we present the first complete genome and annotation of P. kocurii ATCC 43650(T), identifying its potential as a plant growth promoting bacterium and its capability in the biosynthesis of butanol. Copyright © 2016 Elsevier B.V. All rights reserved.

Read more
July 7, 2019  |  

Evolutionary redesign of the Atlantic cod (Gadus morhua L.) Toll-like receptor repertoire by gene losses and expansions.

Genome sequencing of the teleost Atlantic cod demonstrated loss of the Major Histocompatibility Complex (MHC) class II, an extreme gene expansion of MHC class I and gene expansions and losses in the innate pattern recognition receptor (PRR) family of Toll-like receptors (TLR). In a comparative genomic setting, using an improved version of the genome, we characterize PRRs in Atlantic cod with emphasis on TLRs demonstrating the loss of TLR1/6, TLR2 and TLR5 and expansion of TLR7, TLR8, TLR9, TLR22 and TLR25. We find that Atlantic cod TLR expansions are strongly influenced by diversifying selection likely to increase the detectable ligand repertoire through neo- and subfunctionalization. Using RNAseq we find that Atlantic cod TLRs display likely tissue or developmental stage-specific expression patterns. In a broader perspective, a comprehensive vertebrate TLR phylogeny reveals that the Atlantic cod TLR repertoire is extreme with regards to losses and expansions compared to other teleosts. In addition we identify a substantial shift in TLR repertoires following the evolutionary transition from an aquatic vertebrate (fish) to a terrestrial (tetrapod) life style. Collectively, our findings provide new insight into the function and evolution of TLRs in Atlantic cod as well as the evolutionary history of vertebrate innate immunity.

Read more
July 7, 2019  |  

Variable presence of the inverted repeat and plastome stability in Erodium.

Several unrelated lineages such as plastids, viruses and plasmids, have converged on quadripartite genomes of similar size with large and small single copy regions and a large inverted repeat (IR). Except for Erodium (Geraniaceae), saguaro cactus and some legumes, the plastomes of all photosynthetic angiosperms display this structure. The functional significance of the IR is not understood and Erodium provides a system to examine the role of the IR in the long-term stability of these genomes. We compared the degree of genomic rearrangement in plastomes of Erodium that differ in the presence and absence of the IR.We sequenced 17 new Erodium plastomes. Using 454, Illumina, PacBio and Sanger sequences, 16 genomes were assembled and categorized along with one incomplete and two previously published Erodium plastomes. We conducted phylogenetic analyses among these species using a dataset of 19 protein-coding genes and determined if significantly higher evolutionary rates had caused the long branch seen previously in phylogenetic reconstructions within the genus. Bioinformatic comparisons were also performed to evaluate plastome evolution across the genus.Erodium plastomes fell into four types (Type 1-4) that differ in their substitution rates, short dispersed repeat content and degree of genomic rearrangement, gene and intron content and GC content. Type 4 plastomes had significantly higher rates of synonymous substitutions (dS) for all genes and for 14 of the 19 genes non-synonymous substitutions (dN) were significantly accelerated. We evaluated the evidence for a single IR loss in Erodium and in doing so discovered that Type 4 plastomes contain a novel IR.The presence or absence of the IR does not affect plastome stability in Erodium. Rather, the overall repeat content shows a negative correlation with genome stability, a pattern in agreement with other angiosperm groups and recent findings on genome stability in bacterial endosymbionts.© The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Read more
July 7, 2019  |  

Complete genome sequence of UV-resistant Campylobacter jejuni RM3194, including an 81.08-kilobase plasmid.

Campylobacter jejuni strain RM3194 was originally isolated from a human with enteritis and contains a novel 81,079-bp plasmid. RM3194 has exhibited superior survival compared to other Campylobacter jejuni strains when challenged with UV light. The chromosome of RM3194 was determined to be 1,651,183 bp, with a G+C content of 30.5%. Copyright © 2016 Gunther et al.

Read more
July 7, 2019  |  

Complete genome sequence of the larvicidal bacterium Lysinibacillus sphaericus strain OT4b.25.

Lysinibacillus sphaericus OT4b.25 is a native Colombian strain isolated from coleopteran larvae in an oak forest near Bogotá D.C.; this strain has shown high levels of pathogenic activity against Culex quinquefasciatus larvae in laboratory assays compared to that of other members of the same species. Using Pacific Biosciences sequencing technology, we propose a chromosomal contig of 4,665,775 bp that, according to comparative analysis, is highly similar to that of reference strain L. sphaericus C3-41. Copyright © 2016 Rey et al.

Read more
July 7, 2019  |  

Haemonchus contortus: genome structure, organization and comparative genomics

One of the first genome sequencing projects for a parasitic nematode was that for Haemonchus contortus. The open access data from the Wellcome Trust Sanger Institute provided a valuable early resource for the research community, particularly for the identification of specific genes and genetic markers. Later, a second sequencing project was initiated by the University of Melbourne, and the two draft genome sequences for H. contortus were published back-to-back in 2013. There is a pressing need for long-range genomic information for genetic mapping, population genetics and functional genomic studies, so we are continuing to improve the Wellcome Trust Sanger Institute assembly to provide a finished reference genome for H. contortus. This review describes this process, compares the H. contortus genome assemblies with draft genomes from other members of the strongylid group and discusses future directions for parasite genomics using the H. contortus model. Copyright © 2016 Elsevier Ltd. All rights reserved.

Read more
July 7, 2019  |  

Complete genome sequence of probiotic Lactobacillus reuteri ZLR003 isolated from healthy weaned pig.

Lactobacillus reuteri ZLR003 was isolated from the caecum mucosa of healthy weaned pigs with displaying probiotic properties in our laboratory. Here, we present the complete genome sequence of L. reuteri ZLR003, which consists of a circular 2, 234, 097bp chromosome (G+C content of 38.66%). Such information will provide insights into the molecular mechanism of its probiotic activity and facilitate its application in animal production. Copyright © 2016. Published by Elsevier B.V.

Read more
July 7, 2019  |  

Analysis of the genome sequence of the medicinal plant Salvia miltiorrhiza.

Salvia miltiorrhiza Bunge (Danshen) is a medicinal plant of the Lamiaceae family, and its dried roots have long been used in traditional Chinese medicine with hydrophilic phenolic acids and tanshinones as pharmaceutically active components (Zhang et al., 2014; Xu et al., 2016). The first step of tanshinone biosynthesis is bicyclization of the general diterpene precursor (E,E,E)-geranylgeranyl diphosphate (GGPP) to copalyl diphosphate (CPP) by CPP synthases (CPSs), which is followed by a cyclization or rearrangement reaction catalyzed by kaurene synthase-like enzymes (KSL).

Read more
July 7, 2019  |  

Genome sequence and analysis of a stress-tolerant, wild-derived strain of Saccharomyces cerevisiae used in biofuels research

The genome sequences of more than 100 strains of the yeast Saccharomyces cerevisiae have been published. Unfortunately, most of these genome assemblies contain dozens to hundreds of gaps at repetitive sequences, including transposable elements, tRNAs, and subtelomeric regions, which is where novel genes generally reside. Relatively few strains have been chosen for genome sequencing based on their biofuel production potential, leaving an additional knowledge gap. Here, we describe the nearly complete genome sequence of GLBRCY22-3 (Y22-3), a strain of S. cerevisiae derived from the stress-tolerant wild strain NRRL YB-210 and subsequently engineered for xylose metabolism. After benchmarking several genome assembly approaches, we developed a pipeline to integrate Pacific Biosciences (PacBio) and Illumina sequencing data and achieved one of the highest quality genome assemblies for any S. cerevisiae strain. Specifically, the contig N50 is 693 kbp, and the sequences of most chromosomes, the mitochondrial genome, and the 2-micron plasmid are complete. Our annotation predicts 92 genes that are not present in the reference genome of the laboratory strain S288c, over 70% of which were expressed. We predicted functions for 43 of these genes, 28 of which were previously uncharacterized and unnamed. Remarkably, many of these genes are predicted to be involved in stress tolerance and carbon metabolism and are shared with a Brazilian bioethanol production strain, even though the strains differ dramatically at most genetic loci. The Y22-3 genome sequence provides an exceptionally high-quality resource for basic and applied research in bioenergy and genetics. Copyright © 2016 McIlwain et al.

Read more
July 7, 2019  |  

An improved genome assembly of Azadirachta indica A. Juss.

Neem (Azadirachta indica A. Juss.), an evergreen tree of the Meliaceae family, is known for its medicinal, cosmetic, pesticidal and insecticidal properties. We had previously sequenced and published the draft genome of the plant, using mainly short read sequencing data. In this report, we present an improved genome assembly generated using additional short reads from Illumina and long reads from Pacific Biosciences SMRT sequencer. We assembled short reads and error corrected long reads using Platanus, an assembler designed to perform well for heterozygous genomes. The updated genome assembly (v2.0) yielded 3- and 3.5-fold increase in N50 and N75, respectively; 2.6-fold decrease in the total number of scaffolds; 1.25-fold increase in the number of valid transcriptome alignments; 13.4-fold less mis-assembly and 1.85-fold increase in the percentage repeat, over the earlier assembly (v1.0). The current assembly also maps better to the genes known to be involved in the terpenoid biosynthesis pathway. Together, the data represents an improved assembly of the A. indica genome. The raw data described in this manuscript are submitted to the NCBI Short Read Archive under the accession numbers SRX1074131, SRX1074132, SRX1074133, and SRX1074134 (SRP013453). Copyright © 2016 Author et al.

Read more
July 7, 2019  |  

Complete chloroplast genome sequences of Eucommia ulmoides: genome structure and evolution.

Eucommia ulmoides is an important traditional medicinal plant that is used for the production of locative Eucommia rubber. In this study, the complete chloroplast (cp) genome sequence of E. ulmoides was obtained by total DNA sequencing; this is the first cp genome sequence of the order Garryales. The cp genome of E. ulmoides was 163,341 bp long and included a pair of inverted repeat (IR) regions (31,300 bp), one large single copy (LSC) region (86,592 bp), and one small single copy (SSC) region (14,149 bp). The genome structure and GC content were similar to those of typical angiosperm cp genomes and contained 115 unique genes, including 80 protein-coding genes, 31 transfer RNA (tRNAs), and four ribosomal RNA (rRNAs). Compared with the entire cp genome sequence, three unique genome rearrangements were observed in the LSC region. Moreover, compared with the Sesamum and Nicotiana cp genomes, E. ulmoides contained no indels in the IR regions, and variable regions were identified in noncoding regions. The E. ulmoides cp genome showed extreme expansion at the IR/SSC boundary owing to the integration of an additional complete gene, ycf1. Twenty-nine simple sequence repeats (SSRs) were identified in the E. ulmoides cp genome. In addition, 36 protein-coding genes were used for phylogenetic inference, supporting a sister relationship between E. ulmoides and Aucuba, which belongs to Euasterids I. In summary, we described the complete cp genome sequence of E. ulmoides; this information will be useful for phylogenetic and evolutionary studies.

Read more

Subscribe for blog updates:

Talk with an expert

If you have a question, need to check the status of an order, or are interested in purchasing an instrument, we're here to help.