Genome Size Variation and Evolution Driven by Transposable Elements in the Genus Oryza

Area of Science:

• Plant genomics
• Evolutionary biology
• Comparative genomics

Background:

• Genome size variation is a key evolutionary factor in flowering plants.
• The genus Oryza comprises 25 wild and 2 cultivated rice species with 11 distinct genome types (6 diploid, 5 tetraploid).
• Understanding genome size dynamics in Oryza is crucial for evolutionary studies.

Purpose of the Study:

• To comprehensively analyze genome size variation across non-AA genome Oryza species.
• To investigate the evolutionary forces driving genome size differences.
• To identify the role of repetitive elements in genome size evolution.

Main Methods:

• Flow cytometry for genome size estimation in 166 accessions from 16 non-AA Oryza species.
• k-mer analyses to verify experimental genome size data.
• Comparative genomic analyses to assess repetitive element content and amplification histories.

Main Results:

• Genome sizes in Oryza varied fourfold, from 279 Mb (O. brachyantha, FF) to 1,203 Mb (O. ridleyi, HHJJ).
• Tetraploid species showed a 2-fold variation, while diploid species exhibited a 3-fold variation in genome size.
• Genome size correlated significantly with the content of transposable elements, particularly LTR/Gypsy retrotransposons.

Conclusions:

• LTR retrotransposons are a primary driver of genome size variation in the genus Oryza.
• Species within the same genome type exhibit similar genome sizes.
• Genome size shows a decreasing trend during evolution in the AA, BB, CC, and EE clades, linked to retrotransposon amplification history.