Precise Transcript Reconstruction with End-Guided Assembly

Accurate annotation of transcript isoforms is crucial for functional genomics research, but automated methods for reconstructing full-length transcripts from RNA sequencing (RNA-seq) data are imprecise. We developed a generalized transcript assembly framework called Bookend that incorporates data from multiple modes of RNA-seq, with a focus on identifying, labeling, and deconvoluting RNA 5′ and 3′ ends. Through end-guided assembly with Bookend we demonstrate that correctly modeling transcript start and end sites is essential for precise transcript assembly. Furthermore, we discover that reads from full-length single-cell RNA-seq (scRNA-seq) methods are sparsely end-labeled, and that these ends are sufficient to dramatically improve precision of assembly in single cells. Finally, we show that hybrid assembly across short-read, long-read, and end-capture RNA-seq in the model plant Arabidopsis and meta-assembly of single mouse embryonic stem cells (mESCs) are both capable of producing tissue-specific end-to-end transcript annotations of comparable or superior quality to existing reference isoforms.

Guideline for feedback of individual genetic research findings for genomics research in Africa

As human genomics research in Africa continues to generate large amounts of data, ethical issues arise regarding how actionable genetic information is shared with research participants. The Human Heredity and Health in Africa Consortium (H3Africa) Ethics and Community Engagement Working group acknowledged the need for such guidance, identified key issues and principles relevant to genomics research in Africa and developed a practical guideline for consideration of feeding back individual genetic results of health importance in African research projects. This included a decision flowchart, providing a logical framework to assist in decision-making and planning for human genomics research projects. Although presented in the context of the H3Africa Consortium, we believe the principles described, and the decision flowchart presented here is applicable more broadly in African genomics research.

Research challenges during the COVID-19 pandemic: The experience of a functional genomics laboratory

<p>Measures to mitigate and prevent COVID-19 infections included closing universities around the world for an indefinite time and transferring their educational activities to online platforms. Universities were not prepared for such a transition and the online teaching-learning process evolved gradually. Fortunately, there have been many advances in educational technology in recent decades which proved useful during this pandemic. I am proud that the National School of Higher Studies (Escuela Nacional de Estudios Superiores, ENES), Unidad León, of the National Autonomous University of Mexico (UNAM), was one of the institutions that was able to make this digital transition. Basic research has faced its own challenges during the current pandemic. My laboratory does functional genomics research in plants with undergraduate and master’s students. The experiments of the students were at different stages when the pandemic began and could not stop going to the laboratory due to the need to care for experimental plants and cell cultures. Different strategies were developed to maintain research activities, such as: 1) Scheduling research shifts to promote social distancing, 2) Postponing non-essential experiments, 3) Rationing research supplies that were in short supply during the pandemic. Personally, I consider that the use of digital platforms has also generated unexpected opportunities such as new types of scientific collaboration. I had enough free time to edit student theses, write and publish research articles. Interestingly, the students in my work team have participated in virtual international scientific conferences, the only format that evolved during this pandemic. Digital platforms allowed tutors to be in constant contact with students to advise and support them emotionally. The students in my laboratory have been through difficult times. I asked them to tell their story in their own words (These can be read in the student’s section. Editor’s Note).</p>

Populus trichocarpa (Black Cottonwood) As a Model for Plant Genomic Studies: A Review

Numerous plants have been the subject of recent research in the pharmacological, cosmetic, and agro-alimentary domains due to their chemical composition and multiple therapeutic capabilities. Populus trichocarpa is one of the most common trees found in deciduous forests (Salicaceae family). The current study examines Populus trichocarpa as a model plant for plant genomics research, as well as the most recent findings on phytochemical composition and medicinal potential. More than 45,000 potential protein-coding genes were discovered. In the Populus genome, a whole-genome duplication event was discovered, with approximately 8,000 pairs of duplicated genes surviving. Furthermore, the reproductive biology of Populus provides new opportunities and challenges in the study and analysis of natural genetic and phenotypic variation. In the present review, we endeavour to describe and compile the available knowledge on Populus trichocarpa as a model plant for genomic investigations and to bring that material up to date of Populus trichocarpa's phytochemical and medicinal properties.

Sequencing the ‘Dairy Mind’ Using Mind Genomics to Create an “MRI of Consumer Decisions”

We present the research methodology that generates an integrated database of the mind of a dairy consumer, regarding nine different dairy products. The set of studies deals with a variety of end products, presenting alternative messages about each product. Respondents rate combinations of messages, that is, vignettes, which are created using an advanced form of conjoint analysis. OLS (ordinary least-squares) regression is used to deconstruct the ratings at the level of the individual respondents, producing a coefficient value for each message that was tested. Cluster analyses revealed three distinct mind-sets around dairy products: a strong focus on flavor, a strong focus on health, and a strong focus on price. This chapter demonstrates how the science of Mind Genomics is further applied through a typing tool, known as PVI (personal viewpoint identifier). The PVI is able to identify the mind-set of any individual that provides a binary response to six short questions. The chapter concludes with a vision for the future of the Mind Genomics research methodology in the fields of science and business.

The Multipartite Mitochondrial Genome of Marama (Tylosema esculentum)

Tylosema esculentum (marama bean), a wild legume from tropical Africa, has long been considered as a potential crop for local farmers due to its rich nutritional value. Genomics research of marama is indispensable for the domestication and varietal improvement of the bean. The chloroplast genome of marama has been sequenced and assembled previously using a hybrid approach based on both Illumina and PacBio data. In this study, a similar method was used to assemble the mitochondrial genome of marama. The mitochondrial genome of the experimental individual has been confirmed to have two large circles OK638188 and OK638189, which do not recombine according to the data. However, they may be able to restructure into five smaller circles through recombination on the 4 pairs of long repeats (&gt;1 kb). The total length of marama mitogenome is 399,572 bp. A 9,798 bp DNA fragment has been found that is homologous to the chloroplast genome of marama, accounting for 2.5% of the mitogenome. In the Fabaceae family, the mitogenome of Millettia pinnata is highly similar to marama, including for both the genes present and the total size. Some genes including cox2, rpl10, rps1, and sdh4 have been lost during the evolution of angiosperms and are absent in the mitogenomes of some legumes. However, these remain intact and functional in marama. Another set of genes, rpl2, rps2, rps7, rps11, rps13, and rps19 are either absent, or present as pseudogenes, in the mitogenome of marama.

Co-designing genomics research with a large group of donor-conceived siblings

Background Human genomics research is growing rapidly. More effective methods are required for co-design and involving people, especially those sub-populations which are inherently high interest to medical research and thus at greater risk of being exploited. This case study documents how we worked with a large group of donor-conceived siblings who share the same sperm donor father, to explore how they might want to engage with and influence any future genomic research. Method A participatory action research process was used to explore the views of a group of 18 people who knew they are donor-conceived siblings. They are part of a larger group of up to 1000 people who share the same sperm donor father but the only ones in contact with each other; it is likely that many of the uncontacted siblings are unaware of their biological father, have been unable to trace others or have died. The discussion explored views about how the group would like to be involved in future research. Five members participated in co-design; 12 completed a pre-discussion online survey; and six participated in an online discussion forum and evaluation survey. The online discussion was led by one facilitator, supported by the study team. Results Of the 18 siblings approached in 2018, 14 participated in the co-design stages or the surveys and online discussion. Co-design informed the research process. Participants reported enjoying the overall experience of the surveys and discussion forum, which were perceived as inclusive and flexible. Most participants’ views regarding the value of involvement in research changed during the process, and ‘widened’ about who should be involved. Participants were supportive of future research being done with the siblings group. All who completed the final survey requested to remain part of the co-design process. Other themes in the online discussion included concerns about conflicting interests and a desire for research participation to improve the situation for people affected by assisted conception. The process informed later discussions in the sibling group about participating in a self-managed biobank and informed decision making about participating in genomics research. Conclusion Findings from this study help inform ways in which people from certain sub-populations can be involved in planning and defining their participation in genomic research, particularly those that are inherently high interest to medical research and thus at greater risk of exploitation. This process provides a replicable method of involving potential participants in co-designing genomics research using online discussions, with positive outcomes. Reporting this study using ‘Standardised data on initiatives (STARDIT)’ to report the process allows comparison with other studies.