The Amaranth Genome: Genome, Transcriptome, and Physical Map Assembly
The Plant Genome
|November 30, 2016
Summary
A high-quality draft genome sequence of grain amaranth was generated, revealing its genetic makeup and evolutionary history. This research provides a foundation for understanding amaranth
Area of Science:
- Genomics
- Plant Science
- Nutritional Science
Background:
- Amaranth ( L.) is a nutrient-rich pseudocereal gaining attention for its high lysine content.
- It is an ancient paleopolyploid with disomic inheritance (2n = 32) and a genome size of approximately 466 Mb.
Purpose of the Study:
- To present a high-quality draft genome sequence of grain amaranth.
- To analyze the genome's structure, repetitive elements, and gene content.
- To investigate the evolutionary relationships among grain amaranths and identify the progenitor species.
Main Methods:
- Genome sequencing and assembly (377 Mb in 3518 scaffolds).
- Repetitive element analysis and de novo transcriptome assembly (66,370 contigs).
- Protein-coding gene annotation (23,059 genes).
- Resequencing of seven grain amaranths and progenitor species for SNP phylogeny.
- De novo physical map generation using BioNano Genomics' Genome Mapping platform.
- Synteny analysis with sugar beet ( L.) and estimation of polyploidization event age.
Main Results:
- A draft genome assembly of 377 Mb with an N50 of 371 kb was produced.
- Approximately 48% of the genome consists of repeat sequences, with -like elements being the most common retrotransposon.
- A de novo transcriptome yielded 66,370 contigs.
- Annotation identified 23,059 protein-coding genes.
- SNP phylogeny identified as the progenitor of grain amaranths.
- A physical map spanning 340 Mb improved the hybrid assembly N50 to 697 kb.
- Synteny analysis provided insights into the timing of polyploidization.
Conclusions:
- The high-quality draft genome sequence provides a valuable resource for amaranth research.
- Understanding amaranth's genome structure and evolution can aid in crop improvement.
- This study clarifies the evolutionary history and progenitor of grain amaranths.
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