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Sunday, July 7, 2019

Correction of persistent errors in arabidopsis reference mitochondrial genomes.

Arabidopsis thaliana remains the foremost model system for plant genetics and genomics, and researchers rely on the accuracy of its genomic resources. The first completely sequenced angiosperm mitochondrial genome was obtained from Arabidopsis C24 (Unseld et al., 1997), and more recent efforts have produced additional Arabidopsis reference genomes, including one for Col-0, the most widely used ecotype in plant genetic research (Davila et al., 2011). These studies were based on older DNA sequencing methods, making them subject to errors associated with lower levels of sequencing coverage or the extremely short read lengths produced by early-generation Illumina technologies. Indeed, although the…

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Sunday, July 7, 2019

Next-generation sequencing of Haematococcus lacustris reveals an extremely large 1.35-megabase chloroplast genome.

Haematococcus lacustris is an industrially relevant microalga that is used for the production of the carotenoid astaxanthin. Here, we report the use of PacBio long-read sequencing to assemble the chloroplast genome of H. lacustris strain UTEX:2505. At 1.35?Mb, this is the largest assembled chloroplast of any plant or alga known to date. Copyright © 2018 Bauman et al.

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Sunday, July 7, 2019

Identification of repetitive DNA sequences in the Chrysanthemum boreale genome

We previously revealed that the Chrysanthemum boreale genome is highly repetitive; however, the types and nucleotide sequences of repetitive DNA in this diploid wild chrysanthemum are not known. Here, we characterized repetitive DNA sequences in the C. boreale genome by analysing genomic sequences obtained by Illumina sequencing and confirmed their repetitive nature by conducting fluorescence in situ hybridization (FISH) analyses. Annotation of the obtained DNA sequences revealed that microsatellite-containing genomic sequences exhibited similarity with genomic sequences in Chrysanthemum morifolium, indicating sequence conservation of repetitive DNA sequences between the two Chrysanthemum species. Two superfamilies of repetitive DNA, Copia and Gypsy, belonging…

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Sunday, July 7, 2019

The case for not masking away repetitive DNA

In the course of analyzing whole-genome data, it is common practice to mask or filter out repetitive regions of a genome, such as transposable elements and endogenous retroviruses, in order to focus only on genes and thus simplify the results. This Commentary is a plea from one member of the Mobile DNA community to all gene-centric researchers: please do not ignore the repetitive fraction of the genome. Please stop narrowing your findings by only analyzing a minority of the genome, and instead broaden your analyses to include the rich biology of repetitive and mobile DNA. In this article, I present…

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Sunday, July 7, 2019

Optimise wheat A-genome.

The wild einkorn wheat Triticum urartu (Tu) is the A-genome progenitor of tetraploid (AABB) and hexaploid (AABBDD) wheat. A draft genome of Tu was published in 2013, but a better reference sequence is urgently needed by scientists and breeders. Hong-Qing Ling, from the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and colleagues have now completed a high-quality Tu genome using multiple methods.

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Sunday, July 7, 2019

TriPoly: haplotype estimation for polyploids using sequencing data of related individuals.

Knowledge of haplotypes, i.e. phased and ordered marker alleles on a chromosome, is essential to answer many questions in genetics and genomics. By generating short pieces of DNA sequence, high-throughput modern sequencing technologies make estimation of haplotypes possible for single individuals. In polyploids, however, haplotype estimation methods usually require deep coverage to achieve sufficient accuracy. This often renders sequencing-based approaches too costly to be applied to large populations needed in studies of Quantitative Trait Loci.We propose a novel haplotype estimation method for polyploids, TriPoly, that combines sequencing data with Mendelian inheritance rules to infer haplotypes in parent-offspring trios. Using realistic…

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Sunday, July 7, 2019

Fast-SG: an alignment-free algorithm for hybrid assembly.

Long-read sequencing technologies are the ultimate solution for genome repeats, allowing near reference-level reconstructions of large genomes. However, long-read de novo assembly pipelines are computationally intense and require a considerable amount of coverage, thereby hindering their broad application to the assembly of large genomes. Alternatively, hybrid assembly methods that combine short- and long-read sequencing technologies can reduce the time and cost required to produce de novo assemblies of large genomes.Here, we propose a new method, called Fast-SG, that uses a new ultrafast alignment-free algorithm specifically designed for constructing a scaffolding graph using light-weight data structures. Fast-SG can construct the graph…

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Sunday, July 7, 2019

Genome size estimation of Chinese cultured artemisia annua L.

Almost all of antimalarial artemisinin is extracted from the traditional Chinese medicinal plant Artemisia annua L. However, under the condition of insufficient genomic in- formation and unresolved genetic backgrounds, regulatory mechanism of artemisinin biosynthetic pathway has not yet been clear. The genome size of genuine A. annua plants is an especially important and fundamental parameter, which helpful for further insight into genomic studies of ar- temisinin biosynthesis and improvement. In current study, all those genome sizes of A. annua samples collected with Barcoding identification were evaluated to be 1.38-1.49 Gb by Flow Cytometry (FCM) with Nipponbare as the bench- mark…

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Sunday, July 7, 2019

Genome-wide analysis of the invertase gene family from maize.

The recent release of the maize genome (AGPv4) contains annotation errors of invertase genes and therefore the enzymes are bestly curated manually at the protein level in a comprehensible fashion The synthesis, transport and degradation of sucrose are determining factors for biomass allocation and yield of crop plants. Invertase (INV) is a key enzyme of carbon metabolism in both source and sink tissues. Current releases of the maize genome correctly annotates only two vacuolar invertases (ivr1 and ivr2) and four cell wall invertases (incw1, incw2 (mn1), incw3, and incw4). Our comprehensive survey identified 21 INV isogenes for which we propose…

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Sunday, July 7, 2019

Omics in weed science: A perspective from genomics, transcriptomics, and metabolomics approaches

Modern high-throughput molecular and analytical tools offer exciting opportunities to gain a mechanistic understanding of unique traits of weeds. During the past decade, tremendous progress has been made within the weed science discipline using genomic techniques to gain deeper insights into weedy traits such as invasiveness, hybridization, and herbicide resistance. Though the adoption of newer “omics” techniques such as proteomics, metabolomics, and physionomics has been slow, applications of these omics platforms to study plants, especially agriculturally important crops and weeds, have been increasing over the years. In weed science, these platforms are now used more frequently to understand mechanisms of…

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Sunday, July 7, 2019

Identification of woodland strawberry gene coexpression networks

What we think of as a strawberry is botanically not a berry or even a fruit, but rather multiple fruits (achenes that contain the seeds) on the outside of a swollen receptacle. This technicality aside, strawberries are both economically important and a useful system in which to study seed-fruit communication. While cultivated strawberries have a complex octoploid genome, one of their likely progenitors, the woodland strawberry (Fragaria vesca; Fig. 1), is a rapidly growing model system for the Rosaceae family due to its short generation time and capacity to be transformed. A draft of the woodland strawberry diploid genome sequence…

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Sunday, July 7, 2019

Genomic insights into date palm origins.

With the development of next-generation sequencing technology, the amount of date palm (Phoenix dactylifera L.) genomic data has grown rapidly and yielded new insights into this species and its origins. Here, we review advances in understanding of the evolutionary history of the date palm, with a particular emphasis on what has been learned from the analysis of genomic data. We first record current genomic resources available for date palm including genome assemblies and resequencing data. We discuss new insights into its domestication and diversification history based on these improved genomic resources. We further report recent discoveries such as the existence…

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Sunday, July 7, 2019

Genome-wide characterization and phylogenetic analysis of GSK gene family in three species of cotton: evidence for a role of some GSKs in fiber development and responses to stress

Background: The glycogen synthase kinase 3/shaggy kinase (GSK3) is a serine/threonine kinase with important roles in animals. Although GSK3 genes have been studied for more than 30years, plant GSK genes have been studied only since the last decade. Previous research has confirmed that plant GSK genes are involved in diverse processes, including floral development, brassinosteroid signaling, and responses to abiotic stresses. Result: In this study, 20, 15 (including 5 different transcripts) and 10 GSK genes were identified in G. hirsutum, G. raimondii and G. arboreum, respectively. A total of 65 genes from Arabidopsis, rice, and cotton were classified into 4…

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Sunday, July 7, 2019

Pilot satellitome analysis of the model plant, Physcomitrellapatens, revealed a transcribed and high-copy IGS related tandem repeat.

Satellite DNA (satDNA) constitutes a substantial part of eukaryotic genomes. In the last decade, it has been shown that satDNA is not an inert part of the genome and its function extends beyond the nuclear membrane. However, the number of model plant species suitable for studying the novel horizons of satDNA functionality is low. Here, we explored the satellitome of the model “basal” plant, Physcomitrellapatens (Hedwig, 1801) Bruch & Schimper, 1849 (moss), which has a number of advantages for deep functional and evolutionary research. Using a newly developed pyTanFinder pipeline (https://github.com/Kirovez/pyTanFinder) coupled with fluorescence in situ hybridization (FISH), we identified…

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Sunday, July 7, 2019

Alignment-free genome comparison enables accurate geographic sourcing of white oak DNA.

The application of genomic data and bioinformatics for the identification of restricted or illegally-sourced natural products is urgently needed. The taxonomic identity and geographic provenance of raw and processed materials have implications in sustainable-use commercial practices, and relevance to the enforcement of laws that regulate or restrict illegally harvested materials, such as timber. Improvements in genomics make it possible to capture and sequence partial-to-complete genomes from challenging tissues, such as wood and wood products.In this paper, we report the success of an alignment-free genome comparison method, [Formula: see text] that differentiates different geographic sources of white oak (Quercus) species with…

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