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July 7, 2019

Exploring structural variants in environmentally sensitive gene families.

Environmentally sensitive plant gene families like NBS-LRRs, receptor kinases, defensins and others, are known to be highly variable. However, most existing strategies for discovering and describing structural variation in complex gene families provide incomplete and imperfect results. The move to de novo genome assemblies for multiple accessions or individuals within a species is enabling more comprehensive and accurate insights about gene family variation. Earlier array-based genome hybridization and sequence-based read mapping methods were limited by their reliance on a reference genome and by misplacement of paralogous sequences. Variant discovery based on de novo genome assemblies overcome the problems arising from a reference genome and reduce sequence misplacement. As de novo genome sequencing moves to the use of longer reads, artifacts will be minimized, intact tandem gene clusters will be constructed accurately, and insights into rapid evolution will become feasible. Copyright © 2016 Elsevier Ltd. All rights reserved.

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July 7, 2019

Complete genome sequence of antibiotic and anticancer agent violacein producing Massilia sp. strain NR 4-1.

Massilia sp. NR 4-1 was a violacein producing strain newly isolated from topsoil under nutmeg tree, Torreya nucifera in Korean national monument Bijarim Forest. Violacein is a novel class of drug exhibiting anticancer and antibiotic activities originated from l-tryptophan. Here, we present the complete genome of Massilia sp. strain NR 4-1 of 6,361,416bp and total 5285 coding sequences (CDSs) including a complete violacein biosynthesis pathway, vioABCDE. The genome sequence of Massilia sp. NR 4-1 will provide stable and efficient biotechnological applications of violacein production. Copyright © 2016 Elsevier B.V. All rights reserved.

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July 7, 2019

Refined Pichia pastoris reference genome sequence.

Strains of the species Komagataella phaffii are the most frequently used “Pichia pastoris” strains employed for recombinant protein production as well as studies on peroxisome biogenesis, autophagy and secretory pathway analyses. Genome sequencing of several different P. pastoris strains has provided the foundation for understanding these cellular functions in recent genomics, transcriptomics and proteomics experiments. This experimentation has identified mistakes, gaps and incorrectly annotated open reading frames in the previously published draft genome sequences. Here, a refined reference genome is presented, generated with genome and transcriptome sequencing data from multiple P. pastoris strains. Twelve major sequence gaps from 20 to 6000 base pairs were closed and 5111 out of 5256 putative open reading frames were manually curated and confirmed by RNA-seq and published LC-MS/MS data, including the addition of new open reading frames (ORFs) and a reduction in the number of spliced genes from 797 to 571. One chromosomal fragment of 76kbp between two previous gaps on chromosome 1 and another 134kbp fragment at the end of chromosome 4, as well as several shorter fragments needed re-orientation. In total more than 500 positions in the genome have been corrected. This reference genome is presented with new chromosomal numbering, positioning ribosomal repeats at the distal ends of the four chromosomes, and includes predicted chromosomal centromeres as well as the sequence of two linear cytoplasmic plasmids of 13.1 and 9.5kbp found in some strains of P. pastoris. Copyright © 2016. Published by Elsevier B.V.

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July 7, 2019

Whole genome de novo sequencing and genome annotation of the world popular cultivated edible mushroom, Lentinula edodes.

Lentinula edodes, the popular shiitake mushroom, is one of the most important cultivated edible mushrooms. It is used as a food and for medicinal purposes. Here, we present the 46.1Mb draft genome of L. edodes, comprising 13,028 predicted gene models. The genome assembly consists of 31 scaffolds. Gene annotation provides key information about various signaling pathways and secondary metabolites. This genomic information should help establish the molecular genetic markers for MAS/MAB and increase our understanding of the genome structure and function. Copyright © 2016 Elsevier B.V. All rights reserved.

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July 7, 2019

Cloning of the ?-secalin gene family in a wheat 1BL/1RS translocation line using BAC clone sequencing

Wheat 1BL/1RS translocation lines are planted around the world for their disease resistance and high yield. Most of them are poor in bread making, which is partially caused by ?-secalins that are encoded by the ?-secalin gene family, which is located on the short arm of rye chromosome 1R (1RS). However, information on the structure and evolution of the ?-secalin gene family is still limited.

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July 7, 2019

Genome sequence of the nicotine-degrading Agrobacterium tumefaciens S33.

Agrobacterium tumefaciens S33 is capable of growing with nicotine as the sole source of carbon and nitrogen, and has the potential to dispose of tobacco wastes and transform nicotine into functionalized pyridines intermediates, which are important precursors for some valuable drugs and insecticides. Here we report the complete genome sequence of strain S33 and predict the gene cluster involved in nicotine catabolism according to the annotation. Copyright © 2016 Elsevier B.V. All rights reserved.

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July 7, 2019

Gene duplication confers enhanced expression of 27-kDa ?-zein for endosperm modification in quality protein maize.

The maizeopaque2(o2) mutant has a high nutritional value but it develops a chalky endosperm that limits its practical use. Genetic selection foro2modifiers can convert the normally chalky endosperm of the mutant into a hard, vitreous phenotype, yielding what is known as quality protein maize (QPM). Previous studies have shown that enhanced expression of 27-kDa ?-zein in QPM is essential for endosperm modification. Taking advantage of genome-wide association study analysis of a natural population, linkage mapping analysis of a recombinant inbred line population, and map-based cloning, we identified a quantitative trait locus (q?27) affecting expression of 27-kDa ?-zein.q?27was mapped to the same region as the majoro2 modifier(o2 modifier1) on chromosome 7 near the 27-kDa ?-zein locus.q?27resulted from a 15.26-kb duplication at the 27-kDa ?-zein locus, which increases the level of gene expression. This duplication occurred before maize domestication; however, the gene structure ofq?27appears to be unstable and the DNA rearrangement frequently occurs at this locus. Because enhanced expression of 27-kDa ?-zein is critical for endosperm modification in QPM,q?27is expected to be under artificial selection. This discovery provides a useful molecular marker that can be used to accelerate QPM breeding.

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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.

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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.

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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.

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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.

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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.

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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).

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July 7, 2019

Biosynthetic genes for the tetrodecamycin antibiotics.

We recently described 13-deoxytetrodecamycin, a new member of the tetrodecamycin family of antibiotics. A defining feature of these molecules is the presence of a five-membered lactone called a tetronate ring. By sequencing the genome of a producer strain, Streptomyces sp. strain WAC04657, and searching for a gene previously implicated in tetronate ring formation, we identified the biosynthetic genes responsible for producing 13-deoxytetrodecamycin (the ted genes). Using the ted cluster in WAC04657 as a reference, we found related clusters in three other organisms: Streptomyces atroolivaceus ATCC 19725, Streptomyces globisporus NRRL B-2293, and Streptomyces sp. strain LaPpAH-202. Comparing the four clusters allowed us to identify the cluster boundaries. Genetic manipulation of the cluster confirmed the involvement of the ted genes in 13-deoxytetrodecamycin biosynthesis and revealed several additional molecules produced through the ted biosynthetic pathway, including tetrodecamycin, dihydrotetrodecamycin, and another, W5.9, a novel molecule. Comparison of the bioactivities of these four molecules suggests that they may act through the covalent modification of their target(s).The tetrodecamycins are a distinct subgroup of the tetronate family of secondary metabolites. Little is known about their biosynthesis or mechanisms of action, making them an attractive subject for investigation. In this paper we present the biosynthetic gene cluster for 13-deoxytetrodecamycin in Streptomyces sp. strain WAC04657. We identify related clusters in several other organisms and show that they produce related molecules. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

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