scholarly journals The haplotype-resolved reference genome of lemon (Citrus limon L. Burm f.)

2021 ◽  
Vol 17 (6) ◽  
Author(s):  
Di Guardo Mario ◽  
Moretto Marco ◽  
Moser Mirko ◽  
Catalano Chiara ◽  
Troggio Michela ◽  
...  
Keyword(s):  
Reference Genome ◽  
Citrus Limon

scholarly journals Correction to: The haplotype‑resolved reference genome of lemon (Citrus limon L. Burm f.)

2021 ◽  
Vol 17 (6) ◽  
Author(s):  
Mario Di Guardo ◽  
Marco Moretto ◽  
Mirko Moser ◽  
Chiara Catalano ◽  
Michela Troggio ◽  
...  
Keyword(s):  
Reference Genome ◽  
Citrus Limon

scholarly journals The haplotype-resolved reference genome of lemon (Citrus limon L. Burm f.)

2021 ◽  
Author(s):  
Mario Di Guardo ◽  
Marco Moretto ◽  
Mirko Moser ◽  
Chiara Catalano ◽  
Michela Troggio ◽  
...  
Keyword(s):  
Reference Genome ◽  
Perfect Match ◽  
In Silico Analysis ◽  
Mature Mirnas ◽  
Citrus Limon ◽  
Oxford Nanopore ◽  
A Genome ◽  
Set Up ◽  
Definition Of

Lemon (Citrus limon (L.) Burm. f.) is an evergreen tree belonging to the genus Citrus. The fruits are particularly prized for their organoleptic and nutraceutical properties of the juice. Herein we report, for the first time, the release of a high-quality reference genome of the two haplotypes of lemon. The sequencing has been carried out coupling Illumina short reads and Oxford Nanopore data leading to the definition of a primary and an alternative assembly characterized by a genome size of 312.8 Mb and 324.74 Mb respectively. The analysis of the long terminal repeat (LTR) allowed the identification of 1921 regions on the primary and 1911 on the alternative assembly distributed across the nine chromosomes. Furthermore, an in-silico analysis of the microRNA genes was carried out using 246 mature miRNA and the respective pre-miRNA hairpin sequences of C. sinensis. Such analysis highlighted a high conservation between the two species with 233 mature miRNAs and 51 pre-miRNA stem-loops aligning with perfect match on the lemon genome. In parallel, total RNA was extracted from fruit, flower, leaf and root enabling the detection of 38,205 and 37,753 predicted transcripts on primary and alternative assemblies respectively. Among those, the highest and lowest number of tissue-specific transcripts were detected in flower (2.73% and 2.71% in primary and alternative assemblies respectively) and leaf (0.7% and 0.68%) while gene ontology analysis enables a more precise characterization of the expressed genes based on their function. The availability of a reference genome is an important prerequisite both for the set-up of high-throughput genotyping analysis and for functional genomic approaches toward the characterization of the genetic determinism of traits of agronomic interest.

ANTIBACTERIAL, ANTIFUNGAL ACTIVITY OF COMPOSITE EDIBLE COATING INCORPORATED WITH CITRUS LIMON L. PEEL EXTRACT AND IT’S EFFECT ON FUJI APPLES.

2020 ◽  
Author(s):  
Renu Jaisinghani ◽  
Vishnu Vasant Dayare
Keyword(s):  
Shelf Life ◽  
Antimicrobial Properties ◽  
Edible Coating ◽  
Dilution Method ◽  
Citrus Limon ◽  
Edible Coatings ◽  
Lemon Peel ◽  
Fruit Shelf Life ◽  
Broth Dilution ◽  
Peel Extract

Edible film and coatings are been looked upon for preservation of fruits, vegetables and bakery products. Extended shelf life with preservation of natural properties of food is always been a challenge; by incorporation of bio-actives in edible coatings, the shelf life can be increased as they are known for their antioxidant and antimicrobial properties. With this view, present study was undertaken, where edible coatings were prepared from starch, gelatin and glycerol and incorporated with Lemon peel extracts and coated on apples for increased shelf life. Antimicrobial activity of Lemon peel extracts was studied on eight organisms by broth dilution method and were found to be effective at concentration 3mg/mL-9mg/mL for bacteria and 50mg/mL- 90mg/mL for fungi. Fuji apples coated with starch-gelatin based edible formulation containing lemon peel extracts were studied for the effect of coating on fruit shelf life during storage for 28 days. Incorporation of lemon peel extract into edible coating improved shelf life with reducing rate of browning of apples.

An enrichment method for mapping ambiguous reads to the reference genome for NGS analysis

2019 ◽  
Vol 17 (06) ◽  
pp. 1940012
Author(s):  
Yuan Liu ◽  
Yongchao Ma ◽  
Evan Salsman ◽  
Frank A. Manthey ◽  
Elias M. Elias ◽  
...  
Keyword(s):  
Reference Genome ◽  
Association Studies ◽  
Large Fraction ◽  
Snp Markers ◽  
Alternative Methods ◽  
Probability Method ◽  
Genome Wide Association Studies ◽  
Enrichment Method ◽  
Allele Distribution ◽  
Random Method

Mapping short reads to a reference genome is an essential step in many next-generation sequencing (NGS) analyses. In plants with large genomes, a large fraction of the reads can align to multiple locations of the genome with equally good alignment scores. How to map these ambiguous reads to the genome is a challenging problem with big impacts on the downstream analysis. Traditionally, the default method is to assign an ambiguous read randomly to one of the many potential locations. In this study, we explore two alternative methods that are based on the hypothesis that the possibility of an ambiguous read being generated by a location is proportional to the total number of reads produced by that location: (1) the enrichment method that assigns an ambiguous read to the location that has produced the most reads among all the potential locations, (2) the probability method that assigns an ambiguous read to a location based on a probability proportional to the number of reads the location produces. We systematically compared the performance of the proposed methods with that of the default random method. Our results showed that the enrichment method produced better results than the default random method and the probability method in the discovery of single nucleotide polymorphisms (SNPs). Not only did it produce more SNP markers, but it also produced SNP markers with better quality, which was demonstrated using multiple mainstay genomic analyses, including genome-wide association studies (GWAS), minor allele distribution, population structure, and genomic prediction.

Systematic benchmark of ancient DNA read mapping

2021 ◽  
Author(s):  
Adrien Oliva ◽  
Raymond Tobler ◽  
Alan Cooper ◽  
Bastien Llamas ◽  
Yassine Souilmi
Keyword(s):  
Ancient Dna ◽  
Dna Sequences ◽  
Population Genetic ◽  
Reference Genome ◽  
Population Data ◽  
Human Populations ◽  
Current Standard ◽  
Read Mapping ◽  
Reference Bias ◽  
The Impact

Abstract The current standard practice for assembling individual genomes involves mapping millions of short DNA sequences (also known as DNA ‘reads’) against a pre-constructed reference genome. Mapping vast amounts of short reads in a timely manner is a computationally challenging task that inevitably produces artefacts, including biases against alleles not found in the reference genome. This reference bias and other mapping artefacts are expected to be exacerbated in ancient DNA (aDNA) studies, which rely on the analysis of low quantities of damaged and very short DNA fragments (~30–80 bp). Nevertheless, the current gold-standard mapping strategies for aDNA studies have effectively remained unchanged for nearly a decade, during which time new software has emerged. In this study, we used simulated aDNA reads from three different human populations to benchmark the performance of 30 distinct mapping strategies implemented across four different read mapping software—BWA-aln, BWA-mem, NovoAlign and Bowtie2—and quantified the impact of reference bias in downstream population genetic analyses. We show that specific NovoAlign, BWA-aln and BWA-mem parameterizations achieve high mapping precision with low levels of reference bias, particularly after filtering out reads with low mapping qualities. However, unbiased NovoAlign results required the use of an IUPAC reference genome. While relevant only to aDNA projects where reference population data are available, the benefit of using an IUPAC reference demonstrates the value of incorporating population genetic information into the aDNA mapping process, echoing recent results based on graph genome representations.

scholarly journals Whole-Genome Sequencing and Characterization of Buffalo Genetic Resources: Recent Advances and Future Challenges

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 904
Author(s):  
Saif ur Rehman ◽  
Faiz-ul Hassan ◽  
Xier Luo ◽  
Zhipeng Li ◽  
Qingyou Liu
Keyword(s):  
Selective Breeding ◽  
Reference Genome ◽  
De Novo ◽  
Phenotypic Diversity ◽  
Molecular Data ◽  
Genomic Diversity ◽  
Production Performance ◽  
Phylogeographic Structure ◽  
Economic Significance ◽  
And Performance

The buffalo was domesticated around 3000–6000 years ago and has substantial economic significance as a meat, dairy, and draught animal. The buffalo has remained underutilized in terms of the development of a well-annotated and assembled reference genome de novo. It is mandatory to explore the genetic architecture of a species to understand the biology that helps to manage its genetic variability, which is ultimately used for selective breeding and genomic selection. Morphological and molecular data have revealed that the swamp buffalo population has strong geographical genomic diversity with low gene flow but strong phenotypic consistency, while the river buffalo population has higher phenotypic diversity with a weak phylogeographic structure. The availability of recent high-quality reference genome and genotyping marker panels has invigorated many genome-based studies on evolutionary history, genetic diversity, functional elements, and performance traits. The increasing molecular knowledge syndicate with selective breeding should pave the way for genetic improvement in the climatic resilience, disease resistance, and production performance of water buffalo populations globally.

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