Peter J. Maughan, Plant and Wildlife Sciences
Description of the results/finding of the project:
Amaranthus hypochondriacus is an emerging pseudo-cereal native to the New World which has garnered increased attention in recent years due to its nutritional quality, in particular its seed protein, and more specifically its high levels of the essential amino acid lysine. It belongs to the Amaranthaceae family, is an ancient paleopolyploid that shows disomic inheritance (2n=32), and has an estimated genome size of 466 Mb. Here we present a highquality draft genome sequence of the grain amaranth A. hypochondriacus. The genome assembly consisted of 377 Mb in 3,518 scaffolds with an N50 of 371 kb. Repetitive element analysis predicted that 48% of the genome is comprised of repeat sequences, of which Copia-like elements were the most commonly classified retrotransposon. A de novo transcriptome, consisting of 66,370 contigs, was assembled from eight different amaranth tissue and abiotic stress libraries. Annotation of the genome identified 23,059 proteincoding genes. Seven grain amaranths (A. hypochondriacus, A. caudatus, and A. cruentus) and their putative progenitor (A. hybridus) were re-sequenced. A SNP phylogeny supported the classification of A. hybridus as the progenitor species of the grain amaranths. Lastly, we generated a de novo physical map for A. hypochondriacus using the BioNano Genomics’ Genome Mapping platform. The physical map spanned 340 Mb and a hybrid assembly using the BioNano physical maps nearly doubled the N50 of the assembly to 697 kb. Moreover, we analyzed synteny between amaranth and Beta vulgaris (sugar beet) and estimated, using Ks analysis, the age of the most recent polyploidization event in amaranth.
Evaluation of how well the academic objectives were met:
The major objective of the research was to develop the first physical map in the amaranth. The BioNano Genomics (BNG) Irys system was used to generate a de novo physical map assembly of the A. hypochondriacus genome. A total of 169 Gb (363x coverage) of data were generated on the Irys instrument. After filtering out low-quality single molecules, a total of 80.7 Gb (~173x coverage) of data were included in the final de novo physical map assembly. This physical map assembly consisted of 619 individual maps that spanned 340 Mb (73.0% genome coverage). To make a hybrid assembly, all sequence scaffolds greater than 20 kb in length with a minimum of five label sites (1,419 scaffolds), as determined by an in silico digestion, were aligned to the physical map assembly. Of the 619 individual maps, 494 (80%) aligned to the 1,419 in silico digested sequence scaffolds with a unique alignment length of 222 Mb. The hybrid assembly collapsed 343 assembly scaffolds into 241 hybrid scaffolds, reducing the final number of scaffolds in the hybrid assembly to 3,416 (3,175 scaffolds and 241 hybrid scaffolds). The hybrid assembly nearly doubled the N50 of the assembly (696,622 bp), with the longest scaffold spanning 5,997,829 bp and a total length in the hybrid assembly of 429 Mb (92% of the predicted genome size). As expected, the %N in the hybrid assembly increased (15.08%), while the L50 was reduced to 147 (Table 2).
Evaluation of the mentoring environment:
Our research program has prospered greatly using the undergraduate mentoring philosophy. In plant genomic resources laboratory (shared by Drs. Maughan, Udall, Jellen, Stevens and Coleman) we mentor over 45 students each semester. The research focus of these students has led to the awarding of ORCA scholarships, peer-reviewed publications, and presentations at numerous scientific meetings. In addition to working with peerresearchers, our mentored students have continuous exposure to numerous BYU faculty within the Genetics and Biotechnology major (Drs. Maughan, Udall, Stevens, Jellen, Coleman), in addition to graduate students, technicians and several visiting scientists.
As a plant genetics resources group we held combined weekly mandatory laboratory meetings, where undergraduates, graduates and faculty report on their research. Each team was assigned a date and was responsible for developing a PowerPoint presentation and fielding questions regarding their progress and results. The combined meetings allowed for a sense of community among their peers as well as an opportunity to share data across several laboratories. New lab members, whose research may not be as advanced, have the opportunity to discuss recent research results published in plant genetics and molecular biology journals.
The following manuscripts and posters were supported in part from these MEG funds and represent the quality of mentored research expected in our laboratory in 2014-2015. Undergraduates supported in part by MEG funds are italicized. Graduate students are underlined.
- Clouse JW, Adhikary D, Page JT, Ramaraj T, Deyholos MK, Udall JA, Fairbanks DJ, Jellen EN, Maughan PJ (2016) The Amaranth (Amaranthus hypochondriacus) Genome: Genome, Transcriptome and Physical Map Assembly. Plant Genome 9(1)1:4.
- Jarvis DE, Shwen H, Lightfood D, Maughan PJ, Jellen EN, Tester M et al. (2016) The Genome of Chenopodium quinoa. Plant and Animal Genome XXV Conference, January 9-13, San Diego, CA (Oral presentation)
- Clouse J, Page JT, Ramaraj T, Udall JA, Jellen EN, Maughan PJ (2015) Genome Assembly of Amaranthus hypochondriacus: An Emerging C4 Pseudo – Cereal Grain Crop. Utah Plant Genetics Conference, Aspen Grove, Utah. Feb. 24, 2015 (Poster Abstract)
- Clouse J, Page JT, Ramaraj T, Udall JA, Jellen EN, Maughan PJ (2015) Genome Assembly of Amaranthus hypochondriacus. Plant and Animal Genome XXIII Conference, January 10- 14, San Diego, CA (Poster Abstract)
List of students who participated in this MEG:
- Jared Clouse – M.S. Thesis
- Dinesh Adhidary – M.S. Thesis
- Ryan Mangelson – Undergraduate
- Ryan Rupper – Undergraduate
- Warren Chatwin – Undergraduate
- David Elzinga – Undergraduate
Summary of how my 2013-2014 MEG funds were utilized:
Funds were used to support student wages (mentored research), student travel and for research supplies (consumables and plastics). Student travel and consumable were supplemented with departmental funds.