A comparative analysis of methods for de novo assembly of hymenopteran genomes using either haploid or diploid samples

Abstract

Diverse invertebrate taxa including all 200,000 species of Hymenoptera (ants, bees, wasps and sawflies) have a haplodiploid sex determination system, where females are diploid and males are haploid. Thus, hymenopteran genome projects can make use of DNA from a single haploid male sample, which is assumed advantageous for genome assembly. For the purpose of gene annotation, transcriptome sequencing is usually conducted using RNA from a pool of individuals. We conducted a comparative analysis of genome and transcriptome assembly and annotation methods, using genetic sources of different ploidy: (1) DNA from a haploid male or a diploid female (2) RNA from the same haploid male or a pool of individuals. We predicted that the use of a haploid male as opposed to a diploid female will simplify the genome assembly and gene annotation thanks to the lack of heterozygosity. Using DNA and RNA from the same haploid individual is expected to provide better confidence in transcript-to-genome alignment, and improve the annotation of gene structure in terms of the exon/intron boundaries. The haploid genome assemblies proved to be more contiguous, with both contig and scaffold N50 size at least threefold greater than their diploid counterparts. Completeness evaluation showed mixed results. The SOAPdenovo2 diploid assembly was missing more genes than the haploid assembly. The SPAdes diploid assembly had more complete genes, but a higher level of duplicates, and a greatly overestimated genome size. When aligning the two transcriptomes against the male genome, the male transcriptome gave 2–3% more complete transcripts than the pool transcriptome for genes with comparable expression levels in both transcriptomes. However, this advantage disappears in the final results of the gene annotation pipeline that incorporates evidence from homologous proteins. The RNA pool is still required to obtain the full transcriptome with genes that are expressed in other life stages and castes. In conclusion, the use of a haploid source material for a de novo genome project provides a substantial advantage to the quality of the genome draft and the use of RNA from the same haploid individual for transcriptome to genome alignment provides a minor advantage for genes that are expressed in the adult male.

High quality 3C de novo assembly and annotation of a multidrug resistant ST-111 Pseudomonas aeruginosa genome: Benchmark of hybrid and non-hybrid assemblers

“…For short reads only or hybrid assemblies, SPAdes is still used to aseembly genomes 36,39,65 . In a recent study, SPAdes had better results when compared to others, where Unicycler was not included 3 .…”

“…This complicates selection of appropriate strategy. Thus, the need for more capable assemblers is still mandatory in terms of capabilities, accuracy and the way to deal with genomic features 3 .…”

“…On the other hand, notwithstanding all the three contiguity, completeness and correctness evaluation are frequently evaluated in genome assembly studies 3,8,12,[15][16][17] , no explicit conceptualization of "3C criterion" has been achieved. Here we emphasized its use to referrer to the classical metrics and comparisons.…”

CircParser: a novel streamlined pipeline for circular RNA structure and host gene prediction in non-model organisms

“…De novo genome sequencing has become a routine procedure, due to a decrease in sequencing costs, diversification of high-throughput sequencing platforms and improvement of bioinformatic tools (Ekblom & Wolf, 2014). However, the quality of non-model species genome assemblies and, as a result, their annotations are often of unsatisfactory quality, because of (1) repetitive sequences, including transposons, and short sequence repeats (SSRs); (2) gene and genome duplications; (3) single-nucleotide polymorphisms (SNPs) and genome rearrangements (Lien et al, 2016;Negrisolo et al, 2010;Rodriguez & Arkhipova, 2018;Yahav & Privman, 2019).…”

Peer Review #2 of "CircParser: a novel streamlined pipeline for circular RNA structure and host gene prediction in non-model organisms (v0.1)"

“…De novo genome sequencing has become a routine procedure, due to a decrease in sequencing costs, diversification of high-throughput sequencing platforms and improvement of bioinformatic tools (Ekblom & Wolf 2014). However, the quality of non-model species genome assemblies and, as a result, their annotations are often of unsatisfactory quality, because of (1) repetitive sequences, including transposons, and short sequence repeats (SSRs); (2) gene and genome duplications; (3) single-nucleotide polymorphisms (SNPs) and genome rearrangements (Lien et al 2016;Negrisolo et al 2010;Rodriguez & Arkhipova 2018;Yahav & Privman 2019).…”