Improving helminth genome resources in the post-genomic era.

Rapid advancement in high-throughput sequencing and analytical approaches has seen a steady increase in the generation of genomic resources for helminth parasites. Now, helminth genomes and their annotations are a cornerstone of numerous efforts to compare genetic and transcriptomic variation, from single cells to populations of globally distributed parasites, to genome modifications to understand gene function. Our understanding of helminths is increasingly reliant on these genomic resources, which are primarily static once published and vary widely in quality and completeness between species. This article seeks to highlight the cause and effect of this variation and argues for the continued improvement of these genomic resources - even after their publication - which is necessary to provide a more accurate and complete understanding of the biology of these important pathogens.

Edición genómica heredable: un estudio exploratorio desde la perspectiva del principio bioético de la beneficencia / Heritable genome editing: an exploratory study from the bioethical principle of beneficence / Edição genômica herdável: um estudo exploratório a partir da perspectiva do princípio bioético da beneficência

Propósito/Contexto. Este artículo busca comprender el significado que tendría, para un grupo de personas residentes en Bogotá, la posibilidad de realizar variaciones genéticas, previas al nacimiento, en seres humanos. El estudio se centró en la aplicación de la técnica de alteración genómica CRISPR-Cas9, desde la perspectiva del principio bioético de la beneficencia, que está dirigido a realizar el mayor bien posible. Metodología/Enfoque. Primero, se efectuó una revisión teórica de la técnica CRISPR-Cas9 y del principio bioético de la beneficencia. Luego, se estudiaron documentos regulatorios internacionales acerca de la edición genómica. Con base en esto, se aplicó una encuesta, apoyada por un video, para conocer la decisión hipotética que tomaría un grupo de profesionales legos en temas bioéticos, frente a otro grupo de universitarios que recibieron formación bioética. Resultados. Los resultados mostraron que la modificación genómica destinada a la prevención o a la terapia fue aprobada por ambos grupos, aunque con diferencias. La mejora genómica fue rechazada, en general, por considerarse inmoral; en ambos grupos se abrió la posibilidad de admitirla, no obstante, pero solo como preparación genómica para las futuras generaciones, debido a los efectos del cambio climático. Discusión/Conclusiones/Contribuciones. El principio bioético de la beneficencia resulta esclarecedor porque sugiere el bien, no solo individual sino común. Igualmente, se corrobora que existe una reserva moral frente a la edición genómica heredable.

Purpose/Context. This article seeks to understand the meaning that the possibility of making genetic changes in human beings before birth would have for a group of individuals residing in Bogotá. The study focuses on the application of the CRISPR-Cas9 genome editing technique from the perspective of the bioethical principle of beneficence, i.e., to do the greatest good possible. Method/Approach. First, the CRISPR-Cas9 technique and the bioethical principle of beneficence are theoretically reviewed. Then, international regulatory documents on genome editing are examined. Based on this, a video-based survey is administered to find out the hypothetical decision that a group of lay professionals would make on bioethical issues compared to a group of university students who have received bioethical training. Results/Findings. Genome editing intended for prevention or therapy was approved by both groups, although with differences. Genome improvement was generally rejected for being immoral. However, both groups were open to accepting it but only as genome preparation for future generations due to the effects of climate change. Discussion/Conclusions/Contributions. The bioethical principle of beneficence is insightful as it suggests both the private and common good. Moral reservations over heritable genome editing are also corroborated.

Objetivo/Contexto. Este artigo procura compreender o significado que teria, para um grupo de pessoas residentes em Bogotá, a possibilidade de fazer variações genéticas, em seres humanos antes do nascimento. O estudo concentrou-se na aplicação da técnica de alteração genômica CRISPR-Cas9, a partir da perspectiva do princípio bioético da beneficência, que visa realizar ao máximo bem possível. Metodologia/Abordagem. Primeiramente, foi realizada uma revisão teórica da técnica CRISPR-Cas9 e do princípio bioético da beneficência. foram estudados documentos regulatórios internacionais sobre edição genômica. Logo após, baseado nisso, foi aplicada uma sondagem, apoiada em um vídeo, para descobrir a decisão hipotética que um grupo de profissionais leigos sobre questões bioéticas tomaria, em comparação com outro grupo de estudantes universitários que receberam treinamento bioético. Resultados/Descobertas. Os resultados mostraram que a modificação genômica destinada à prevenção ou à terapia foi aprovada pelos dois grupos, embora com diferenças. A melhoria genômica foi rejeitada, geralmente, por se achar imoral; nos dois grupos, foi aberta a possibilidade de admiti-la, não obstante, mas apenas como preparação genômica para as gerações futuras, devido aos efeitos das mudanças climáticas. Discussão/Conclusões/Contribuições. O princípio bioético da beneficência é esclarecedor porque sugere o bem, não apenas individual, mas sim comum. Da mesma forma, é corroborado que existe uma reserva moral perante a edição genômica herdável.

Genome Improvement and Genetic Map Construction for Aethionema arabicum, the First Divergent Branch in the Brassicaceae Family.

The genus Aethionema is a sister-group to the core-group of the Brassicaceae family that includes Arabidopsis thaliana and the Brassica crops. Thus, Aethionema is phylogenetically well-placed for the investigation and understanding of genome and trait evolution across the family. We aimed to improve the quality of the reference genome draft version of the annual species Aethionema arabicum Second, we constructed the first Ae. arabicum genetic map. The improved reference genome and genetic map enabled the development of each other. We started with the initially published genome (version 2.5). PacBio and MinION sequencing together with genetic map v2.5 were incorporated to produce the new reference genome v3.0. The improved genome contains 203 MB of sequence, with approximately 94% of the assembly made up of called (non-gap) bases, assembled into 2,883 scaffolds (with only 6% of the genome made up of non-called bases (Ns)). The N50 (10.3 MB) represents an 80-fold increase over the initial genome release. We generated a Recombinant Inbred Line (RIL) population that was derived from two ecotypes: Cyprus and Turkey (the reference genotype. Using a Genotyping by Sequencing (GBS) approach, we generated a high-density genetic map with 749 (v2.5) and then 632 SNPs (v3.0) was generated. The genetic map and reference genome were integrated, thus greatly improving the scaffolding of the reference genome into 11 linkage groups. We show that long-read sequencing data and genetics are complementary, resulting in an improved genome assembly in Ae. arabicum They will facilitate comparative genetic mapping work for the Brassicaceae family and are also valuable resources to investigate wide range of life history traits in Aethionema.

Single molecule sequencing-guided scaffolding and correction of draft assemblies.

BACKGROUND: Although single molecule sequencing is still improving, the lengths of the generated sequences are inevitably an advantage in genome assembly. Prior work that utilizes long reads to conduct genome assembly has mostly focused on correcting sequencing errors and improving contiguity of de novo assemblies. RESULTS: We propose a disassembling-reassembling approach for both correcting structural errors in the draft assembly and scaffolding a target assembly based on error-corrected single molecule sequences. To achieve this goal, we formulate a maximum alternating path cover problem. We prove that this problem is NP-hard, and solve it by a 2-approximation algorithm. CONCLUSIONS: Our experimental results show that our approach can improve the structural correctness of target assemblies in the cost of some contiguity, even with smaller amounts of long reads. In addition, our reassembling process can also serve as a competitive scaffolder relative to well-established assembly benchmarks.