In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Bison bonasus))—Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data

The European bison is a non-model organism; thus, most of its genetic and genomic analyses have been performed using cattle-specific resources, such as BovineSNP50 BeadChip or Illumina Bovine 800 K HD Bead Chip. The problem with non-specific tools is the potential loss of evolutionary diversified information (ascertainment bias) and species-specific markers. Here, we have used a genotyping-by-sequencing (GBS) approach for genotyping 256 samples from the European bison population in Bialowieza Forest (Poland) and performed an analysis using two integrated pipelines of the STACKS software: one is de novo (without reference genome) and the other is a reference pipeline (with reference genome). Moreover, we used a reference pipeline with two different genomes, i.e., Bos taurus and European bison. Genotyping by sequencing (GBS) is a useful tool for SNP genotyping in non-model organisms due to its cost effectiveness. Our results support GBS with a reference pipeline without PCR duplicates as a powerful approach for studying the population structure and genotyping data of non-model organisms. We found more polymorphic markers in the reference pipeline in comparison to the de novo pipeline. The decreased number of SNPs from the de novo pipeline could be due to the extremely low level of heterozygosity in European bison. It has been confirmed that all the de novo/Bos taurus and Bos taurus reference pipeline obtained SNPs were unique and not included in 800 K BovineHD BeadChip.

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AStrap: identification of alternative splicing from transcript sequences without a reference genome

Bioinformatics ◽

10.1093/bioinformatics/bty1008 ◽

2018 ◽

Vol 35 (15) ◽

pp. 2654-2656 ◽

Cited By ~ 5

Author(s):

Guoli Ji ◽

Wenbin Ye ◽

Yaru Su ◽

Moliang Chen ◽

Guangzao Huang ◽

...

Keyword(s):

Machine Learning ◽

Alternative Splicing ◽

Single Molecule ◽

Reference Genome ◽

De Novo ◽

Supplementary Information ◽

Model Organisms ◽

Sequencing Data ◽

Extensive Evaluation ◽

Reference Genomes

Abstract Summary Alternative splicing (AS) is a well-established mechanism for increasing transcriptome and proteome diversity, however, detecting AS events and distinguishing among AS types in organisms without available reference genomes remains challenging. We developed a de novo approach called AStrap for AS analysis without using a reference genome. AStrap identifies AS events by extensive pair-wise alignments of transcript sequences and predicts AS types by a machine-learning model integrating more than 500 assembled features. We evaluated AStrap using collected AS events from reference genomes of rice and human as well as single-molecule real-time sequencing data from Amborella trichopoda. Results show that AStrap can identify much more AS events with comparable or higher accuracy than the competing method. AStrap also possesses a unique feature of predicting AS types, which achieves an overall accuracy of ∼0.87 for different species. Extensive evaluation of AStrap using different parameters, sample sizes and machine-learning models on different species also demonstrates the robustness and flexibility of AStrap. AStrap could be a valuable addition to the community for the study of AS in non-model organisms with limited genetic resources. Availability and implementation AStrap is available for download at https://github.com/BMILAB/AStrap. Supplementary information Supplementary data are available at Bioinformatics online.

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De novo assembly of the cattle reference genome with single-molecule sequencing

GigaScience ◽

10.1093/gigascience/giaa021 ◽

2020 ◽

Vol 9 (3) ◽

Cited By ~ 35

Author(s):

Benjamin D Rosen ◽

Derek M Bickhart ◽

Robert D Schnabel ◽

Sergey Koren ◽

Christine G Elsik ◽

...

Keyword(s):

Single Molecule ◽

De Novo Assembly ◽

Reference Genome ◽

De Novo ◽

Bos Taurus ◽

Future Research ◽

Protein Coding ◽

Single Molecule Sequencing ◽

Assembly Accuracy ◽

Genomic Tools

Abstract Background Major advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10–12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies. Results We present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb and is >250× more continuous than the original assembly, with contig N50 >25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use. Conclusions We demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species.

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De novo genome assembly of the tobacco hornworm moth (Manduca sexta)

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkaa047 ◽

2021 ◽

Vol 11 (1) ◽

pp. 1-9

Author(s):

Ariel Gershman ◽

Tatiana G Romer ◽

Yunfan Fan ◽

Roham Razaghi ◽

Wendy A Smith ◽

...

Keyword(s):

Manduca Sexta ◽

Reference Genome ◽

De Novo ◽

Model Organism ◽

Tobacco Hornworm ◽

Model System ◽

Future Research ◽

De Novo Genome Assembly ◽

Lepidopteran Insect ◽

Modern Technologies

Abstract The tobacco hornworm, Manduca sexta, is a lepidopteran insect that is used extensively as a model system for studying insect biology, development, neuroscience, and immunity. However, current studies rely on the highly fragmented reference genome Msex_1.0, which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies. We present a new reference genome for M. sexta, JHU_Msex_v1.0, applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly is 470 Mb and is ∼20× more continuous than the original assembly, with scaffold N50 > 14 Mb. We annotated the assembly by lifting over existing annotations and supplementing with additional supporting RNA-based data for a total of 25,256 genes. The new reference assembly is accessible in annotated form for public use. We demonstrate that improved continuity of the M. sexta genome improves resequencing studies and benefits future research on M. sexta as a model organism.

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DiscoSnp++: de novo detection of small variants from raw unassembled read set(s)

10.1101/209965 ◽

2017 ◽

Cited By ~ 12

Author(s):

Pierre Peterlongo ◽

Chloé Riou ◽

Erwan Drezen ◽

Claire Lemaitre

Keyword(s):

Reference Genome ◽

De Novo ◽

Model Organisms ◽

Small Indels ◽

Desktop Computers ◽

Resource Requirements ◽

Computational Resources ◽

Next Generation Sequencing Ngs ◽

Ngs Data ◽

Source Of Information

AbstractMotivationNext Generation Sequencing (NGS) data provide an unprecedented access to life mechanisms. In particular, these data enable to detect polymorphisms such as SNPs and indels. As these polymorphisms represent a fundamental source of information in agronomy, environment or medicine, their detection in NGS data is now a routine task. The main methods for their prediction usually need a reference genome. However, non-model organisms and highly divergent genomes such as in cancer studies are extensively investigated.ResultsWe propose DiscoSnp++, in which we revisit the DiscoSnp algorithm. DiscoSnp++ is designed for detecting and ranking all kinds of SNPs and small indels from raw read set(s). It outputs files in fasta and VCF formats. In particular, predicted variants can be automatically localized afterwards on a reference genome if available. Its usage is extremely simple and its low resource requirements make it usable on common desktop computers. Results show that DiscoSnp++ performs better than state-of-the-art methods in terms of computational resources and in terms of results quality. An important novelty is the de novo detection of indels, for which we obtained 99% precision when calling indels on simulated human datasets and 90% recall on high confident indels from the Platinum dataset.LicenseGNU Affero general public licenseAvailabilityhttps://github.com/GATB/[email protected]

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Fruit Flies (Drosophila spp.) Collection, Handling, and Maintenance: Field to Laboratory

10.5772/intechopen.97014 ◽

2021 ◽

Author(s):

Pragya Topal ◽

Divita Garg ◽

Rajendra S. Fartyal

Keyword(s):

Developmental Biology ◽

Reproductive Biology ◽

Cancer Biology ◽

Life Sciences ◽

Model Organism ◽

Model Organisms ◽

Chemical Studies ◽

Males And Females ◽

Species Specific ◽

Food Media

As drosophilids are versatile, low maintenance and non-harming model organisms, they can be easily used in all fields of life sciences like Genetics, Biotechnology, Cancer biology, Genomics, Reproductive biology, Developmental biology, Micro chemical studies, ecology and much more. For using such a model organism, we need to learn capturing, rearing and culturing their progeny along with basic identification and differentiation between males and females. This chapter is being emphasized on techniques of capturing these flies with different and effective techniques. Along with it, most species-specific baits are discussed to catch more yield. Culture food media, a set measurement of different ingredients is used to rear the collected sample. The reasons for using each ingredient are also discussed in this chapter. At last, this chapter highlights the basic clues to identify different species in the field and lab along with learning distinguishing characteristics of males and females easily and effectively.

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Illumina TruSeq synthetic long-reads empowerde novoassembly and resolve complex, highly repetitive transposable elements

10.1101/001834 ◽

2014 ◽

Cited By ~ 1

Author(s):

Rajiv C McCoy ◽

Ryan W Taylor ◽

Timothy A Blauwkamp ◽

Joanna L Kelley ◽

Michael Kertesz ◽

...

Keyword(s):

Transposable Elements ◽

Reference Genome ◽

De Novo ◽

Model Organism ◽

Genomic Analysis ◽

High Sequence Identity ◽

Current Reference ◽

Sequencing Technologies ◽

Long Reads ◽

Whole Genomes

High-throughput DNA sequencing technologies have revolutionized genomic analysis, including thede novoassembly of whole genomes. Nevertheless, assembly of complex genomes remains challenging, in part due to the presence of dispersed repeats which introduce ambiguity during genome reconstruction. Transposable elements (TEs) can be particularly problematic, especially for TE families exhibiting high sequence identity, high copy number, or present in complex genomic arrangements. While TEs strongly affect genome function and evolution, most currentde novoassembly approaches cannot resolve long, identical, and abundant families of TEs. Here, we applied a novel Illumina technology called TruSeq synthetic long-reads, which are generated through highly parallel library preparation and local assembly of short read data and achieve lengths of 1.5-18.5 Kbp with an extremely low error rate (∼0.03% per base). To test the utility of this technology, we sequenced and assembled the genome of the model organismDrosophila melanogaster(reference genome strainy;cn,bw,sp) achieving an N50 contig size of 69.7 Kbp and covering 96.9% of the euchromatic chromosome arms of the current reference genome. TruSeq synthetic long-read technology enables placement of individual TE copies in their proper genomic locations as well as accurate reconstruction of TE sequences. We entirely recovered and accurately placed 4,229 (77.8%) of the 5,434 of annotated transposable elements with perfect identity to the current reference genome. As TEs are ubiquitous features of genomes of many species, TruSeq synthetic long- reads, and likely other methods that generate long reads, offer a powerful approach to improvede novoassemblies of whole genomes.

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Draft genome of the Reindeer (Rangifer tarandus)

10.1101/154724 ◽

2017 ◽

Author(s):

Zhipeng Li ◽

Zeshan Lin ◽

Lei Chen ◽

Hengxing Ba ◽

Yongzhi Yang ◽

...

Keyword(s):

Rangifer Tarandus ◽

Reference Genome ◽

De Novo ◽

Bos Taurus ◽

Repetitive Sequences ◽

Draft Genome ◽

Divergence Time ◽

Capra Hircus ◽

High Quality ◽

Illumina Hiseq

AbstractBackgroundReindeer (Rangifer tarandus) is the only fully domesticated species in the Cervidae family, and is the only cervid with a circumpolar distribution. Unlike all other cervids, female reindeer regularly grow cranial appendages (antlers, the defining characteristics of cervids), as well as males. Moreover, reindeer milk contains more protein and less lactose than bovids’ milk. A high quality reference genome of this specie will assist efforts to elucidate these and other important features in the reindeer.FindingsWe obtained 723.2 Gb (Gigabase) of raw reads by an Illumina Hiseq 4000 platform, and a 2.64 Gb final assembly, representing 95.7% of the estimated genome (2.76 Gb according to k-mer analysis), including 92.6% of expected genes according to BUSCO analysis. The contig N50 and scaffold N50 sizes were 89.7 kilo base (kb) and 0.94 mega base (Mb), respectively. We annotated 21,555 protein-coding genes and 1.07 Gb of repetitive sequences by de novo and homology-based prediction. Homology-based searches detected 159 rRNA, 547 miRNA, 1,339 snRNA and 863 tRNA sequences in the genome of R. tarandus. The divergence time between R. tarandus, and ancestors of Bos taurus and Capra hircus, is estimated to be 29.55 million years ago (Mya).ConclusionsOur results provide the first high-quality reference genome for the reindeer, and a valuable resource for studying evolution, domestication and other unusual characteristics of the reindeer.

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Improved Apis mellifera reference genome based on the alternative long-read-based assemblies

10.1101/2021.04.30.442202 ◽

2021 ◽

Author(s):

Milyausha Kaskinova ◽

Bayazit Yunusbayev ◽

Radick Altinbaev ◽

Rika Raffiudin ◽

Madeline H. Carpenter ◽

...

Keyword(s):

Apis Mellifera ◽

Honey Bee ◽

Reference Genome ◽

De Novo ◽

Gene Annotation ◽

Model Organism ◽

Functional Genomic ◽

Long Read ◽

Chromosome Level

ABSTRACTApis mellifera L., the western honey bee is a major crop pollinator that plays a key role in beekeeping and serves as an important model organism in social behavior studies. Recent efforts have improved on the quality of the honey bee reference genome and developed a chromosome-level assembly of sixteen chromosomes, two of which are gapless. However, the rest suffer from 51 gaps, 160 unplaced/unlocalized scaffolds, and the lack of 2 distal telomeres. The gaps are located at the hard-to-assemble extended highly repetitive chromosomal regions that may contain functional genomic elements. Here, we use de-novo re-assemblies from the most recent reference genome Amel_HAv_3.1 raw reads and other long-read-based assemblies (INRA_AMelMel_1.0, ASM1384120v1, and ASM1384124v1) of the honey bee genome to resolve 13 gaps, five unplaced/unlocalized scaffolds and, the lacking telomeres of the Amel_HAv_3.1. The total length of the resolved gaps is 848,747 bp. The accuracy of the corrected assembly was validated by mapping PacBio reads and performing gene annotation assessment. Comparative analysis suggests that the PacBio-reads-based assemblies of the honey bee genomes failed in the same highly repetitive extended regions of the chromosomes, especially on chromosome 10. To fully resolve these extended repetitive regions, further work using ultra-long Nanopore sequencing would be needed. Our updated assembly facilitates more accurate reference-guided scaffolding and marker/sequence mapping in honey bee genomics studies.

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Ion channel profiling of the Lymnaea stagnalis ganglia via transcriptome analysis

10.21203/rs.3.rs-31358/v1 ◽

2020 ◽

Author(s):

Nan Dong ◽

Julia Bandura ◽

Zhaolei Zhang ◽

Yan Wang ◽

Karine Labadie ◽

...

Keyword(s):

Ion Channels ◽

Reference Genome ◽

Lymnaea Stagnalis ◽

De Novo ◽

Model Organisms ◽

Sequence Length ◽

Pond Snail ◽

Sequence Information ◽

Functional Domain ◽

Rna Seq

Abstract Background. The pond snail Lymnaea stagnalis (L. stagnalis) has been widely used as a model organism in neurobiology, ecotoxicology, and parasitology due to the relative simplicity of its CNS. However, its usefulness is restricted by a limited availability of transcriptome data. While sequence information for the L. stagnalis CNS transcripts has been obtained from EST library and a de novo RNA-seq assembly, the quality of these assemblies is limited by a combination of low coverage of EST libraries, the fragmented nature of de novo assemblies, and lack of reference genome. Results. In this study, taking advantage of the recent availability of the L. stagnalis reference genome, we generated an RNA-seq library from the adult L. stagnalis CNS, using a combination of genome-guided and de novo assembly programs to identify 17,832 protein-coding L. stagnalis transcripts. We combined our library with existing resources to produce a transcript set with greater sequence length, completeness, and diversity than previously available ones. Using our assembly and functional domain analysis, we profiled L. stagnalis CNS transcripts encoding ion channels and ionotropic receptors, which are key proteins for CNS function, and compared their sequences to other vertebrate and invertebrate model organisms. Interestingly, L. stagnalis transcripts encoding numerous putative Ca2+ channels showed the most sequence similarity to those of mouse, zebrafish, Xenopus tropicalis, fruit fly, and C. elegans, suggesting that many calcium channel-related signaling pathways may be evolutionarily conserved. Conclusions. Our study provides the most thorough characterization to date of the L. stagnalis transcriptome and provides insights into differences between vertebrates and invertebrates in CNS transcript diversity, according to function and protein class. Furthermore, this study is, to the best of our knowledge, the first to provide a complete characterization of the ion channels of a single species, opening new avenues for future research on fundamental neurobiological processes.

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Glutton: large-scale integration of non-model organism transcriptome data for comparative analysis

10.1101/077511 ◽

2016 ◽

Cited By ~ 2

Author(s):

Alan Medlar ◽

Laura Laakso ◽

Andreia Miraldo ◽

Ari Löytynoja

Keyword(s):

Comparative Analysis ◽

Large Scale ◽

De Novo ◽

Sequence Data ◽

Model Organism ◽

Model Organisms ◽

Rna Seq ◽

Reference Species ◽

Wide Range ◽

The Impact

AbstractHigh-throughput RNA-seq data has become ubiquitous in the study of non-model organisms, but its use in comparative analysis remains a challenge. Without a reference genome for mapping, sequence data has to be de novo assembled, producing large numbers of short, highly redundant contigs. Preparing these assemblies for comparative analyses requires the removal of redundant isoforms, assignment of orthologs and converting fragmented transcripts into gene alignments. In this article we present Glutton, a novel tool to process transcriptome assemblies for downstream evolutionary analyses. Glutton takes as input a set of fragmented, possibly erroneous transcriptome assemblies. Utilising phylogeny-aware alignment and reference data from a closely related species, it reconstructs one transcript per gene, finds orthologous sequences and produces accurate multiple alignments of coding sequences. We present a comprehensive analysis of Glutton’s performance across a wide range of divergence times between study and reference species. We demonstrate the impact choice of assembler has on both the number of alignments and the correctness of ortholog assignment and show substantial improvements over heuristic methods, without sacrificing correctness. Finally, using inference of Darwinian selection as an example of downstream analysis, we show that Glutton-processed RNA-seq data give results comparable to those obtained from full length gene sequences even with distantly related reference species. Glutton is available from http://wasabiapp.org/software/glutton/ and is licensed under the GPLv3.

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