Exploring domestication pattern in lotus: insights from dispensable genome assembly

Area of Science:

• Genomics
• Plant Science
• Aquatic Botany

Background:

• Lotus (Nelumbo nucifera) is a significant aquatic plant with a 7000-year cultivation history.
• Domestication has resulted in distinct subgroups: flower, rhizome, and seed lotus.
• Understanding the genetic basis of these subgroups is crucial for further improvement.

Purpose of the Study:

• To explore the domesticated genomic regions of lotus subgroups.
• To assemble and annotate the dispensable genome of cultivated lotus varieties.
• To identify selective signals associated with lotus domestication.

Main Methods:

• Re-sequencing data from 371 lotus accessions were aligned to the 'China-Antique (CA)' genome.
• Metagenome-like assembly was used to construct the dispensable genome from unmapped reads.
• Selective sweep analysis was performed to detect domestication signals.

Main Results:

• Over 27 Mb of the dispensable genome was assembled, with 11,761 genes annotated.
• Dispensable genome contigs showed similarity to other lotus accessions.
• Subgroup-specific genes and pathways, like brassinosteroid metabolism in flower lotus, were identified.
• Selective signals were linked to specific genes and dispensable genome regions within each subgroup.

Conclusions:

• The study provides a valuable genomic resource for lotus research.
• Findings complement the reference genome and offer insights into domestication.
• The identified selective signals highlight key evolutionary events in lotus subgroups.