De novo Genome Sequencing and Gene Prediction in Lolium perenne, Perennial Ryegrass

2016 ◽  
pp. 127-131 ◽  
Author(s):  
E. M. B. Mollison ◽  
S. Barth ◽  
D. Milbourne ◽  
L. Milne ◽  
C. Halpin ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Lolium Perenne ◽  
Perennial Ryegrass ◽  
De Novo ◽  
Gene Prediction

scholarly journals First de novo whole genome sequencing and assembly of the bar-headed goose

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8914 ◽  
Author(s):  
Wen Wang ◽  
Fang Wang ◽  
Rongkai Hao ◽  
Aizhen Wang ◽  
Kirill Sharshov ◽  
...  
Keyword(s):  
High Altitude ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Assembly ◽  
De Novo ◽  
Gene Prediction ◽  
Repetitive Sequences ◽  
Gene Families ◽  
Whole Genome ◽  
Sequencing Data

Background The bar-headed goose (Anser indicus) mainly inhabits the plateau wetlands of Asia. As a specialized high-altitude species, bar-headed geese can migrate between South and Central Asia and annually fly twice over the Himalayan mountains along the central Asian flyway. The physiological, biochemical and behavioral adaptations of bar-headed geese to high-altitude living and flying have raised much interest. However, to date, there is still no genome assembly information publicly available for bar-headed geese. Methods In this study, we present the first de novo whole genome sequencing and assembly of the bar-headed goose, along with gene prediction and annotation. Results 10X Genomics sequencing produced a total of 124 Gb sequencing data, which can cover the estimated genome size of bar-headed goose for 103 times (average coverage). The genome assembly comprised 10,528 scaffolds, with a total length of 1.143 Gb and a scaffold N50 of 10.09 Mb. Annotation of the bar-headed goose genome assembly identified a total of 102 Mb (8.9%) of repetitive sequences, 16,428 protein-coding genes, and 282 tRNAs. In total, we determined that there were 63 expanded and 20 contracted gene families in the bar-headed goose compared with the other 15 vertebrates. We also performed a positive selection analysis between the bar-headed goose and the closely related low-altitude goose, swan goose (Anser cygnoides), to uncover its genetic adaptations to the Qinghai-Tibetan Plateau. Conclusion We reported the currently most complete genome sequence of the bar-headed goose. Our assembly will provide a valuable resource to enhance further studies of the gene functions of bar-headed goose. The data will also be valuable for facilitating studies of the evolution, population genetics and high-altitude adaptations of the bar-headed geese at the genomic level.

Effect of bacterial fertilizers on the properties of a pseudomyceliar chernozem soil and on the biomass of perennial ryegrass (Lolium perenne L.)

2011 ◽  
Vol 60 (1) ◽  
pp. 219-232 ◽  
Author(s):  
Anita Jakab ◽  
János Kátai ◽  
Magdolna Tállai ◽  
Andrea Balláné Kovács
Keyword(s):  
Lolium Perenne ◽  
Perennial Ryegrass ◽  
Chernozem Soil ◽  
Lolium Perenne L

A tenyészedényes kísérletünket a DE AGTC MÉK Agrokémiai és Talajtani Intézet tenyészházában állítottuk be 2010. május 27-én. A kísérletben Debrecen-Látókép környékéről származó mészlepedékes csernozjom vályogtalajt alkalmaztunk, amely az alábbi jellemzőkkel rendelkezett: KA: 37,5; leiszapolható rész: 51%; pH(KCl): 5,5; pH(H2O): 6,6; Hu%: 2,8; AL-P2O5: 140 mg·kg-1; AL-K2O: 316,3 mg·kg-1. Az adatok alapján a kísérleti talaj gyengén savanyú, vályog kötöttségű, közepes nitrogén- és foszfor-, valamint jó kálium-ellátottsággal rendelkezett. A kísérletben kontroll-, műtrágya-, valamint szalmakezelést alkalmaztunk, melyeket bizonyos kombinációkban három különböző baktériumkészítménnyel (Bactofil A, EM-1, Microbion UNC) egészítettünk ki. A kísérletet három ismétlésben véletlenblokk elrendezésben állítottuk be. A tesztnövény angolperje (Lolium perenneL.) volt. A kísérlet kezdetétől számított 8. héten a talaj-, valamint a növényminták begyűjtésére került sor. Meghatároztuk a növényminták száraztömegét, a növény foszfor- és káliumtartalmát, valamint a talajminták nitrát-, valamint AL-oldható foszfor- és káliumtartalmát. Eredményeink alapján főbb megállapításaink a következők: – Az angolperje száraztömegét a műtrágyakezelés szignifikánsan növelte. A hatás a tápelem-ellátottság javulásával magyarázható. – A növény foszforkoncentrációja a műtrágyázás következtében csökkent, amelyet a hígulási effektussal magyarázhatunk. – A növény káliumkoncentrációját a műtrágya-, valamint a műtrágya+baktériumtrágya kezelések szignifikánsan serkentették. – A talaj nitráttartalma szignifikánsan növekedett a műtrágyakezelés kivételével minden kezelésben. – A talaj AL-P2O5-tartalma az NPK-műtrágyázás és az EM-1 kezelés következtében statisztikailag igazolható mértékben megnövekedett, míg az AL-K2O-tartalom kizárólag a szalmakezelés hatására nőtt. A baktériumkészítmények önmagukban alkalmazva általában nem eredményeztek jelentős változást a vizsgált paraméterekben, azonban a készítmények szerves/ásványi anyagokkal kombinált adagolása esetében különböző mértékben befolyásolták a vizsgált mutatókat.

The effect of biological additives on the composition and nutritive value of silage

1990 ◽  
Vol 1990 ◽  
pp. 139-139
Author(s):  
M Gonzalez Yanez ◽  
R Mcginn ◽  
D H Anderson ◽  
A R Henderson ◽  
P Phillips
Keyword(s):  
Cell Wall ◽  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Lolium Perenne ◽  
Perennial Ryegrass ◽  
Nutritive Value ◽  
Enzyme System ◽  
Lolium Perenne L ◽  
Grass Silage ◽  
Forage Harvester

It Is claimed that the use of the correct enzyme system as an additive on grass silage will satisfactorily control the fermentation and reduce the cell-wall fibre content, thus preserving the nutrients In the silage and aiding their utilisation by the animal (Henderson and McDonald, 1977; Huhtanen et al, 1985; Raurama et al, 1987; Chamberlain and Robertson, 1989; Gordon, 1989;).The aim of the present experiment was to assess the effect of biological additives, enzymes or a combination of enzymes with an Inoculum of lactic acid bacteria, on the composition of silage and on its nutritive value when offered to store lambs as the sole constituent of their diet.On 1st June 1988, first cut perennial ryegrass (Lolium perenne L) at pre-ear emergence was ensiled direct cut untreated (U), treated with a commercial enzyme (E) or with a commercial inoculum of lactic acid bacteria with enzymes (I) in 6t capacity bunker silos. The grass was cut with a mower and lifted with a New Holland precision chop forage harvester. The additives were pumped onto the grass using a dribble bar sited over the pick-up drum.

scholarly journals Effective variant filtering and expected candidate variant yield in studies of rare human disease

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Brent S. Pedersen ◽  
Joe M. Brown ◽  
Harriet Dashnow ◽  
Amelia D. Wallace ◽  
Matt Velinder ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Rare Disease ◽  
Genome Sequencing ◽  
Autosomal Dominant ◽  
De Novo ◽  
Autosomal Dominant Inheritance ◽  
Compound Heterozygous ◽  
Whole Genome ◽  
Dominant Inheritance ◽  
Family Based

AbstractIn studies of families with rare disease, it is common to screen for de novo mutations, as well as recessive or dominant variants that explain the phenotype. However, the filtering strategies and software used to prioritize high-confidence variants vary from study to study. In an effort to establish recommendations for rare disease research, we explore effective guidelines for variant (SNP and INDEL) filtering and report the expected number of candidates for de novo dominant, recessive, and autosomal dominant modes of inheritance. We derived these guidelines using two large family-based cohorts that underwent whole-genome sequencing, as well as two family cohorts with whole-exome sequencing. The filters are applied to common attributes, including genotype-quality, sequencing depth, allele balance, and population allele frequency. The resulting guidelines yield ~10 candidate SNP and INDEL variants per exome, and 18 per genome for recessive and de novo dominant modes of inheritance, with substantially more candidates for autosomal dominant inheritance. For family-based, whole-genome sequencing studies, this number includes an average of three de novo, ten compound heterozygous, one autosomal recessive, four X-linked variants, and roughly 100 candidate variants following autosomal dominant inheritance. The slivar software we developed to establish and rapidly apply these filters to VCF files is available at https://github.com/brentp/slivar under an MIT license, and includes documentation and recommendations for best practices for rare disease analysis.

scholarly journals A study of transposable element-associated structural variations (TASVs) using a de novo-assembled Korean genome

2021 ◽  
Author(s):  
Seyoung Mun ◽  
Songmi Kim ◽  
Wooseok Lee ◽  
Keunsoo Kang ◽  
Thomas J. Meyer ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Genome Assembly ◽  
De Novo ◽  
Personal Genome ◽  
Human Populations ◽  
Whole Genome ◽  
Structural Variations ◽  
Insert Size ◽  
Human Genomes ◽  
Next Generation Sequencing Ngs

AbstractAdvances in next-generation sequencing (NGS) technology have made personal genome sequencing possible, and indeed, many individual human genomes have now been sequenced. Comparisons of these individual genomes have revealed substantial genomic differences between human populations as well as between individuals from closely related ethnic groups. Transposable elements (TEs) are known to be one of the major sources of these variations and act through various mechanisms, including de novo insertion, insertion-mediated deletion, and TE–TE recombination-mediated deletion. In this study, we carried out de novo whole-genome sequencing of one Korean individual (KPGP9) via multiple insert-size libraries. The de novo whole-genome assembly resulted in 31,305 scaffolds with a scaffold N50 size of 13.23 Mb. Furthermore, through computational data analysis and experimental verification, we revealed that 182 TE-associated structural variation (TASV) insertions and 89 TASV deletions contributed 64,232 bp in sequence gain and 82,772 bp in sequence loss, respectively, in the KPGP9 genome relative to the hg19 reference genome. We also verified structural differences associated with TASVs by comparative analysis with TASVs in recent genomes (AK1 and TCGA genomes) and reported their details. Here, we constructed a new Korean de novo whole-genome assembly and provide the first study, to our knowledge, focused on the identification of TASVs in an individual Korean genome. Our findings again highlight the role of TEs as a major driver of structural variations in human individual genomes.

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