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Asset Tag: WGS

July 7, 2019

Identification and expression analysis of wheat TaGF14 genes.

The 14-3-3 gene family members play key roles in various cellular processes. However, little is known about the numbers and roles of 14-3-3 genes in wheat. The aims of this study were to identify TaGF14 numbers in wheat by searching its whole genome through blast, to study the phylogenetic relationships with other plant species and to discuss the functions of TaGF14s. The results showed that common wheat harbored 20 TaGF14 genes, located on wheat chromosome groups 2, 3, 4, and 7. Out of them, eighteen TaGF14s are non-e proteins, and two wheat TaGF14 genes, TaGF14i and TaGF14f, are e proteins. Phylogenetic analysis indicated that these genes were divided into six clusters: cluster 1 (TaGF14d, TaGF14g, TaGF14j, TaGF14h, TaGF14c, and TaGF14n); cluster 2 (TaGF14k); cluster 3 (TaGF14b, TaGF14l, TaGF14m, and TaGF14s); cluster 4 (TaGF14a, TaGF14e, and TaGF14r); cluster 5 (TaGF14i and TaGF14f); and cluster 6 (TaGF14o, TaGF14p, TaGF14q, and TaGF14t). Tissue-specific gene expressions suggested that all TaGF14s were likely constitutively expressed, except two genes, i.e., TaGF14p and TaGF14f. And the highest amount of TaGF14 transcripts were observed in developing grains at 20 days post anthesis (DPA), especially for TaGF14j and TaGF14l. After drought stress, five genes, i.e., TaGF14c, TaGF14d, TaGF14g, TaGF14h, and TaGF14j, were up-regulated expression under drought stress for both 1 and 6 h, suggesting these genes played vital role in combating against drought stress. However, all the TaGF14s were down-regulated expression under heat stress for both 1 and 6 h, indicating TaGF14s may be negatively associated with heat stress by reducing the expression to combat heat stress or through other pathways. These results suggested that cluster 1, e.g., TaGF14j, may participate in the whole wheat developing stages, e.g., grain-filling (starch biosynthesis) and may also participate in combating against drought stress. Subsequently, a homolog of TaGF14j, TaGF14-JM22, were cloned by RACE and used to validate its function. Immunoblotting results showed that TaGF14-JM22 protein, closely related to TaGF14d, TaGF14g, and TaGF14j, can interact with AGP-L, SSI, SSII, SBEIIa, and SBEIIb in developing grains, suggesting that TaGF14s located on group 4 may be involved in starch biosynthesis. Therefore, it is possible to develop starch-rich wheat cultivars by modifying TaGF14s.

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July 7, 2019

Complete genome sequence of uropathogenic Escherichia coli isolate UPEC 26-1.

Urinary tract infections (UTIs) are among the most common infections in humans, predominantly caused by uropathogenic Escherichia coli (UPEC). The diverse genomes of UPEC strains mostly impede disease prevention and control measures. In this study, we comparatively analyzed the whole genome sequence of a highly virulent UPEC strain, namely UPEC 26-1, which was isolated from urine sample of a patient suffering from UTI in Korea. Whole genome analysis showed that the genome consists of one circular chromosome of 5,329,753 bp, comprising 5064 protein-coding genes, 122 RNA genes (94 tRNA, 22 rRNA and 6 ncRNA genes), and 100 pseudogenes, with an average G+C content of 50.56%. In addition, we identified 8 prophage regions comprising 5 intact, 2 incomplete and 1 questionable ones and 63 genomic islands, suggesting the possibility of horizontal gene transfer in this strain. Comparative genome analysis of UPEC 26-1 with the UPEC strain CFT073 revealed an average nucleotide identity of 99.7%. The genome comparison with CFT073 provides major differences in the genome of UPEC 26-1 that would explain its increased virulence and biofilm formation. Nineteen of the total GIs were unique to UPEC 26-1 compared to CFT073 and nine of them harbored unique genes that are involved in virulence, multidrug resistance, biofilm formation and bacterial pathogenesis. The data from this study will assist in future studies of UPEC strains to develop effective control measures.

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July 7, 2019

Oryza rufipogon Griff.

Oryza rufipogon, the progenitor of present-day cultivated rice, O. sativa, is one of the most studied wild species of rice. It is a perennial plant commonly found in a marsh or aquatic habitats of eastern and southern Asia. It has partial outcrossing behavior and is photoperiod sensitive. The flowering time usually ranges between September and November. It has been and is being exploited as a source of valuable genes and QTLs for yield components as well as resistance against biotic and abiotic stresses. A number of populations like chromosome segment substitution lines, backcross inbred lines, near-isogenic lines, and recombinant inbred lines have been developed from crosses between O. rufipogon and O. sativa as a prebreeding resource. These are being employed for broadening the genetic base of cultivated rice and diversify the breeder’s pool. With the advent of sequencing technologies, a number of phylogenetic studies have been conducted to reveal the evolutionary relationship of O. rufipogon with cultivated rice O. sativa. Further, transcriptomic studies characterizing the effect of various abiotic stresses have been conducted on this wild species. Role of miRNA under stress reaction has also been studied. Though the genetic, genomic, and transcriptomic resources are abundant, the proteomic resources for O. rufipogon are limited.

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July 7, 2019

Oryza meridionalis NQ Ng

Oryza meridionalis is an AA genome species found in Northern Australia. Phylogenetic analysis places this as the most distant of the AA genome species from domesticated rice (Oryza sativa). This makes it a key genetic resource for rice improvement. A draft nuclear genome sequence is available, and also the chloroplast genome has been sequenced from many genotypes. The high amylose starch content in these taxa may be useful for developing new rice grain characteristics. Here we have reviewed the all the research advancements that are made till today on this species.

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July 7, 2019

Oryza glaberrima Steud.

Oryza glaberrima is the African cultivated rice species, domesticated from its wild ancestor by farmers living in Inland Delta of Niger River. Several studies indicated that it has extremely narrow genetic diversity compared to both its wild progenitor, Oryza barthii and the Asian rice, Oryza sativa which can mainly be attributed to a severe domestication bottleneck. Despite its scarcity in farmer’s field due to its low yield potential, high shattering and lodging susceptibility, O. glaberrima is of great value not only to Africa but also globally. Perhaps its greatest contribution to regional and global food security is as a source of genes, as it possesses resistance/tolerance to various biotic and abiotic stresses. It also has unique starch-related traits which give it good cooking and eating properties. Advances in DNA sequencing have provided useful genomic resources for African rice, key among them being whole genome sequences. Genomic tools are enabling greater understanding of the useful functional diversity found in this species. These advances have potential of addressing some of the undesirable attributes found in this species which have led to its continued replacement by Asian rice. Development of new generation of rice varieties for African farmers will therefore require the adoption of advanced molecular breeding tools as these will allow efficient utilization of the wealth and resilience found in African rice in rice improvement.

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July 7, 2019

Paucibacter aquatile sp. nov. isolated from freshwater of the Nakdong River, Republic of Korea.

A Gram-negative, aerobic, motile, and rod-shaped bacterial strain designated CR182T was isolated from freshwater of the Nakdong River, Republic of Korea. Optimal growth conditions for this novel strain were found to be: 25-30 °C, pH 6.5-8.5, and 3% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence indicates that the strain CR182T belongs to type strains of genus Paucibacter. Strain CR182T showed 98.0% 16S rRNA gene sequence similarity with Paucibacter oligotrophus CHU3T and formed a robust phylogenetic clade with this species. The average nucleotide identity value between strain CR182T and P. oligotrophus CHU3T was 78.4% and the genome-to-genome distance was 22.2% on average. The genomic DNA G+C content calculated from the genome sequence was 66.3 mol%. Predominant cellular fatty acids of strain CR182T were summed feature 3 (C16:1 ?7c and/or C16:1 ?6c) (31.2%) and C16:0 (16.0%). Its major respiratory quinine was ubiquinone Q-8. Its polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, and two unidentified phospholipids. Its genomic DNA G+C content was 66.3%. Based on data obtained from this polyphasic taxonomic study, strain CR182T represents a novel species belonging to genus Paucibacter, for which a name of P. aquatile sp. nov. is proposed. The type strain is CR182T (=?KCCM 90284T?=?NBRC 113032T).

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July 7, 2019

The ‘gifted’ actinomycete Streptomyces leeuwenhoekii.

Streptomyces leeuwenhoekii strains C34T, C38, C58 and C79 were isolated from a soil sample collected from the Chaxa Lagoon, located in the Salar de Atacama in northern Chile. These streptomycetes produce a variety of new specialised metabolites with antibiotic, anti-cancer and anti-inflammatory activities. Moreover, genome mining performed on two of these strains has revealed the presence of biosynthetic gene clusters with the potential to produce new specialised metabolites. This review focusses on this new clade of Streptomyces strains, summarises the literature and presents new information on strain C34T.

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July 7, 2019

Natural rubber and the Russian dandelion genome

The world needs rubber. Rubber is crucial for the tires on the cars, trucks and airplanes that propel modern transportation. It is equally important for daily tasks: latex gloves in the lab, balloons in angioplasty and wetsuits that warm a cold dip in the ocean. Rubber can be made synthetically from petroleum derivatives, but synthetic rubber is not as strong as rubber iso- lated from plants. The principal plant source for natural rubber (NR) is the sap of the Par´ a tree (Hevea brasiliensis), which is grown throughout Southeast Asia. Unfortunately, the produc- tion capacity of the Par´ a tree is limited by the availability of suitable land and by labor-intensive harvesting methods. The sustainability of the Par´ a crop is also constrained by its narrow genetic base, which may make the crop susceptible to disease.

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July 7, 2019

Rooting for new sources of natural rubber

Global production of natural rubber (NR) depends overwhelmingly on the Pará rubber tree (Hevea brasiliensis), a slow-growing tropical tree that is threatened by low genetic diversity and high susceptibility to fungal blight [1]. Alternative rubber sources have been sought for more than a century, but very few species have been found that produce rubber of comparable quality [2]. One of the brightest candidates, first noticed by breeders in Soviet-era Russia, is Taraxacum kok-saghyz (commonly called TKS). This close relative of the common weedy dandelion has a number of attractive features. As a native of central Asia, TKS can be cultivated as a hardy, annual field crop in temperate climates. Its natural latex, produced at highest levels in the roots, yields a high-molecular-weight NR that is chemically similar to the rubber tree and far superior to synthetic rubber. And, as an added bonus, TKS produces inulin, a dietary fiber and low-glycemic-index sweetener that can be fermented for industrial bioethanol production. What TKS has lacked—until now—is an assembled reference genome that could be used for genome-enabled crop improvement and elucidation of the pathways for rubber and inulin biosynthesis. In their paper published in this issue, Jiayang Li, Hong Yu and colleagues [3] have taken a major step in rectifying that problem.

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July 7, 2019

Supergene evolution triggered by the introgression of a chromosomal inversion.

Supergenes are groups of tightly linked loci whose variation is inherited as a single Mendelian locus and are a common genetic architecture for complex traits under balancing selection [1-8]. Supergene alleles are long-range haplotypes with numerous mutations underlying distinct adaptive strategies, often maintained in linkage disequilibrium through the suppression of recombination by chromosomal rearrangements [1, 5, 7-9]. However, the mechanism governing the formation of supergenes is not well understood and poses the paradox of establishing divergent functional haplotypes in the face of recombination. Here, we show that the formation of the supergene alleles encoding mimicry polymorphism in the butterfly Heliconius numata is associated with the introgression of a divergent, inverted chromosomal segment. Haplotype divergence and linkage disequilibrium indicate that supergene alleles, each allowing precise wing-pattern resemblance to distinct butterfly models, originate from over a million years of independent chromosomal evolution in separate lineages. These “superalleles” have evolved from a chromosomal inversion captured by introgression and maintained in balanced polymorphism, triggering supergene inheritance. This mode of evolution involving the introgression of a chromosomal rearrangement is likely to be a common feature of complex structural polymorphisms associated with the coexistence of distinct adaptive syndromes. This shows that the reticulation of genealogies may have a powerful influence on the evolution of genetic architectures in nature. Copyright © 2018 Elsevier Ltd. All rights reserved.

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July 7, 2019

Hercules: a profile HMM-based hybrid error correction algorithm for long reads.

Choosing whether to use second or third generation sequencing platforms can lead to trade-offs between accuracy and read length. Several types of studies require long and accurate reads. In such cases researchers often combine both technologies and the erroneous long reads are corrected using the short reads. Current approaches rely on various graph or alignment based techniques and do not take the error profile of the underlying technology into account. Efficient machine learning algorithms that address these shortcomings have the potential to achieve more accurate integration of these two technologies. We propose Hercules, the first machine learning-based long read error correction algorithm. Hercules models every long read as a profile Hidden Markov Model with respect to the underlying platform’s error profile. The algorithm learns a posterior transition/emission probability distribution for each long read to correct errors in these reads. We show on two DNA-seq BAC clones (CH17-157L1 and CH17-227A2) that Hercules-corrected reads have the highest mapping rate among all competing algorithms and have the highest accuracy when the breadth of coverage is high. On a large human CHM1 cell line WGS data set, Hercules is one of the few scalable algorithms; and among those, it achieves the highest accuracy.

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July 7, 2019

Smooth q-Gram, and its applications to detection of overlaps among long, error-prone sequencing reads

We propose smoothq-gram, the frst variant of q-gram that captures q-gram pair within a small edit distance. We apply smooth q-gram to the problem of detecting overlapping pairs of error-prone reads produced by single molecule real time sequencing (SMRT), which is the frst and most critical step of the de novo fragment assembly of SMRT reads. We have implemented and tested our algorithm on a set of real world benchmarks. Our empirical results demonstrated the signifcant superiority of our algorithm over the existing q-gram based algorithms in accuracy.

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