scholarly journals To Trim or Not to Trim: Effects of Read Trimming on the De Novo Genome Assembly of a Widespread East Asian Passerine, the Rufous-Capped Babbler (Cyanoderma ruficeps Blyth)

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 737 ◽  
Author(s):  
Shang-Fang Yang ◽  
Chia-Wei Lu ◽  
Cheng-Te Yao ◽  
Chih-Ming Hung
Keyword(s):  
Genome Assembly ◽  
Sex Chromosome ◽  
De Novo ◽  
Gene Annotation ◽  
East Asian ◽  
Computational Time ◽  
Nucleotide Polymorphisms ◽  
De Novo Genome Assembly ◽  
Single Nucleotide ◽  
Pros And Cons

Trimming low quality bases from sequencing reads is considered as routine procedure for genome assembly; however, we know little about its pros and cons. Here, we used empirical data to examine how read trimming affects assembled genome quality and computational time for a widespread East Asian passerine, the rufous-capped babbler (Cyanoderma ruficeps Blyth). We found that scaffolds assembled from raw reads were always longer than those from trimmed ones, whereas computational times for the former were sometimes much longer than the latter. Nevertheless, assembly completeness showed little difference among the trimming strategies. One should determine the optimal trimming strategy based on what the assembled genome will be used for. For example, to identify single nucleotide polymorphisms (SNPs) associated with phenotypic evolution, applying PLATANUS to gently trim reads would yield a reference genome with a slightly shorter scaffold length (N50 = 15.64 vs. 16.89 Mb) than the raw reads, but would save 75% of computational time. We also found that chromosomes Z, W, and 4A of the rufous-capped babbler were poorly assembled, likely due to a recently fused, neo-sex chromosome. The rufous-capped babbler genome with long scaffolds and quality gene annotation can provide a good system to study avian ecological adaptation in East Asia.

scholarly journals Gene Annotation and Transcriptome Delineation on a De Novo Genome Assembly for the Reference Leishmania major Friedlin Strain

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1359
Author(s):  
Esther Camacho ◽  
Sandra González-de la Fuente ◽  
Jose C. Solana ◽  
Alberto Rastrojo ◽  
Fernando Carrasco-Ramiro ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Leishmania Major ◽  
De Novo ◽  
Gene Annotation ◽  
Leishmania Species ◽  
De Novo Genome Assembly ◽  
Sequencing Platforms

Leishmania major is the main causative agent of cutaneous leishmaniasis in humans. The Friedlin strain of this species (LmjF) was chosen when a multi-laboratory consortium undertook the objective of deciphering the first genome sequence for a parasite of the genus Leishmania. The objective was successfully attained in 2005, and this represented a milestone for Leishmania molecular biology studies around the world. Although the LmjF genome sequence was done following a shotgun strategy and using classical Sanger sequencing, the results were excellent, and this genome assembly served as the reference for subsequent genome assemblies in other Leishmania species. Here, we present a new assembly for the genome of this strain (named LMJFC for clarity), generated by the combination of two high throughput sequencing platforms, Illumina short-read sequencing and PacBio Single Molecular Real-Time (SMRT) sequencing, which provides long-read sequences. Apart from resolving uncertain nucleotide positions, several genomic regions were reorganized and a more precise composition of tandemly repeated gene loci was attained. Additionally, the genome annotation was improved by adding 542 genes and more accurate coding-sequences defined for around two hundred genes, based on the transcriptome delimitation also carried out in this work. As a result, we are providing gene models (including untranslated regions and introns) for 11,238 genes. Genomic information ultimately determines the biology of every organism; therefore, our understanding of molecular mechanisms will depend on the availability of precise genome sequences and accurate gene annotations. In this regard, this work is providing an improved genome sequence and updated transcriptome annotations for the reference L. major Friedlin strain.

scholarly journals Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Yaoxi He ◽  
Xin Luo ◽  
Bin Zhou ◽  
Ting Hu ◽  
Xiaoyu Meng ◽  
...  
Keyword(s):  
Rhesus Macaque ◽  
Genome Assembly ◽  
De Novo ◽  
Gene Annotation ◽  
Large Body ◽  
Phenotypic Traits ◽  
Structural Variants ◽  
De Novo Genome Assembly ◽  
Chinese Rhesus Macaque ◽  
Long Read

Abstract We present a high-quality de novo genome assembly (rheMacS) of the Chinese rhesus macaque (Macaca mulatta) using long-read sequencing and multiplatform scaffolding approaches. Compared to the current Indian rhesus macaque reference genome (rheMac8), rheMacS increases sequence contiguity 75-fold, closing 21,940 of the remaining assembly gaps (60.8 Mbp). We improve gene annotation by generating more than two million full-length transcripts from ten different tissues by long-read RNA sequencing. We sequence resolve 53,916 structural variants (96% novel) and identify 17,000 ape-specific structural variants (ASSVs) based on comparison to ape genomes. Many ASSVs map within ChIP-seq predicted enhancer regions where apes and macaque show diverged enhancer activity and gene expression. We further characterize a subset that may contribute to ape- or great-ape-specific phenotypic traits, including taillessness, brain volume expansion, improved manual dexterity, and large body size. The rheMacS genome assembly serves as an ideal reference for future biomedical and evolutionary studies.

scholarly journals A De Novo Genome Assembly, Gene Annotation, And Expression Atlas For The Monarch Butterfly Danaus plexippus

2020 ◽  
Author(s):  
José M. Ranz ◽  
Pablo M. González ◽  
Bryan D. Clifton ◽  
Nestor O. Nazario ◽  
Pablo L. Hernández-Cervantes ◽  
...  
Keyword(s):  
Life Cycle ◽  
Genome Assembly ◽  
Noncoding Rna ◽  
De Novo ◽  
Gene Annotation ◽  
Life Stage ◽  
Monarch Butterfly ◽  
Major Advance ◽  
De Novo Genome Assembly ◽  
Expression Atlas

ABSTRACTThe monarch butterfly epitomizes insect biodiversity decline. Understanding the genetic basis of the adaptation of the monarch to a changing environment requires genomic and transcriptomic resources that better reflect its genetic diversity while being informative about gene functionality during life cycle. We report a reference-quality genome assembly from an individual resident at a nonmigratory colony in Mexico, and a new gene annotation and expression atlas for 14,865 genes, including 492 unreported long noncoding RNA (lncRNA) genes, based on RNA-seq data from 14 larval and pupal stages, plus adult morphological sections. Two thirds of the genes show significant expression changes associated with a life stage or section, with lncRNAs being more finely regulated during adulthood than protein-coding genes, and male-biased expression being four times more common than female-biased. The two portions of the heterochromosome Z display distinct patterns of differential expression between the sexes, reflecting that dosage compensation is either absent or incomplete –depending on the sample– in the ancestral but not in the novel portion of the Z. This study represents a major advance in the genomic and transcriptome resources available for D. plexippus while providing the first systematic analysis of its transcriptional program across most of its life cycle.

scholarly journals A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.)

2020 ◽  
Author(s):  
J. Mitchell (Mitch) McGrath ◽  
Andrew Funk ◽  
Paul Galewski ◽  
Shujun Ou ◽  
Belinda Townsend ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Beta Vulgaris ◽  
Genome Assembly ◽  
Copy Number ◽  
Large Scale ◽  
De Novo ◽  
Gene Annotation ◽  
Gene Copy ◽  
De Novo Genome Assembly ◽  
Short Read

AbstractA contiguous assembly of the inbred ‘EL10’ sugar beet (Beta vulgaris ssp. vulgaris) genome was constructed using PacBio long read sequencing, BioNano optical mapping, Hi-C scaffolding, and Illumina short read error correction. The EL10.1 assembly was 540 Mb, of which 96.7% was contained in nine chromosome-sized pseudomolecules with lengths from 52 to 65 Mb, and 31 contigs with a median size of 282 kb that remained unassembled. Gene annotation incorporating RNAseq data and curated sequences via the MAKER annotation pipeline generated 24,255 gene models. Results indicated that the EL10.1 genome assembly is a contiguous genome assembly highly congruent with the published sugar beet reference genome. Gross duplicate gene analyses of EL10.1 revealed little large-scale intra-genome duplication. Reduced gene copy number for well-annotated gene families relative to other core eudicots was observed, especially for transcription factors. Variation in genome size in B. vulgaris was investigated by flow cytometry among 50 individuals drawn from EL10 progeny and three unrelated germplasm accessions, producing estimates from 633 to 875 Mb/1C. Read depth mapping with short-read whole genome sequences from other sugar beet germplasm suggested that relatively few regions of the sugar beet genome appeared associated with high-copy number variation.

scholarly journals De Novo Genome Assembly of the Japanese Wheat Cultivar Norin 61 Highlights Functional Variation in Flowering Time and Fusarium Resistance Genes in East Asian Genotypes

2020 ◽  
Author(s):  
Kentaro K Shimizu ◽  
Dario Copetti ◽  
Moeko Okada ◽  
Thomas Wicker ◽  
Toshiaki Tameshige ◽  
...  
Keyword(s):  
Bread Wheat ◽  
Genome Assembly ◽  
De Novo ◽  
East Asian ◽  
Fusarium Head Blight Resistance ◽  
Copy Number Variations ◽  
Head Blight ◽  
Functional Variation ◽  
De Novo Genome Assembly ◽  
Functional Variants

Abstract Bread wheat is a major crop that has long been the focus of basic and breeding research. Assembly of its genome has been difficult because of its large size and allohexaploid nature (AABBDD genome). Following the first reported assembly of the genome of the experimental strain Chinese Spring (CS), the 10+ Wheat Genomes Project was launched to produce multiple assemblies of worldwide modern cultivars. The only Asian cultivar in the project is Norin 61, a representative Japanese cultivar adapted to grow across a broad latitudinal range, mostly characterized by a wet climate and a short growing season. Here, we characterize key aspects of its chromosome-scale genome assembly spanning 15 Gb with a raw scaffold N50 of 23 Mb. Analysis of the repetitive elements identified chromosomal regions unique to Norin 61 that encompass a tandem array of the pathogenesis-related-13 family. We report novel copy-number variations in the B homeolog of the florigen gene FT1/VRN3, pseudogenization of its D homeolog, and the association of its A homeologous alleles with the spring/winter growth habit. Further, the Norin 61 genome carries typical East Asian functional variants from CS ranging from a single nucleotide to multi-Mb scale. Examples of such variation are the Fhb1 locus, which confers Fusarium head-blight resistance, Ppd-D1a, which confers early flowering, Glu-D1f for Asian noodle quality, and Rht-D1b, which introduced semi-dwarfism during the green revolution. The adoption of Norin 61 as a reference assembly for functional and evolutionary studies will enable comprehensive characterization of the underexploited Asian bread wheat diversity.

scholarly journals Improved hybrid de novo genome assembly of domesticated apple (Malus x domestica)

GigaScience ◽  
2016 ◽  
Vol 5 (1) ◽  
Author(s):  
Xuewei Li ◽  
Ling Kui ◽  
Jing Zhang ◽  
Yinpeng Xie ◽  
Liping Wang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Malus X Domestica ◽  
De Novo Genome Assembly

scholarly journals Meraculous: De Novo Genome Assembly with Short Paired-End Reads

PLoS ONE ◽  
2011 ◽  
Vol 6 (8) ◽  
pp. e23501 ◽  
Author(s):  
Jarrod A. Chapman ◽  
Isaac Ho ◽  
Sirisha Sunkara ◽  
Shujun Luo ◽  
Gary P. Schroth ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
De Novo Genome Assembly

Ultra Efficient Acceleration for De Novo Genome Assembly via Near-Memory Computing

2021 ◽  
Author(s):  
Minxuan Zhou ◽  
Lingxi Wu ◽  
Muzhou Li ◽  
Niema Moshiri ◽  
Kevin Skadron ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
De Novo Genome Assembly
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