Plant Genomes and Polyploidy

What is a whole genome duplication (WGD), and why does a polyploid genome often look diploid again after a long time?

A whole genome duplication is a polyploidisation event in which the entire chromosome set is duplicated, initially doubling genome size and chromosome number.

Over hundreds of millions of years, processes such as chromosome fusions and fissions, gene loss, and silencing of duplicates lead to diploidisation, so the karyotype and segregation patterns look diploid again, even though the genome still carries signatures of ancient WGD.

How do LTR retrotransposons influence plant genome size in monocots and conifers, and what key differences exist between these groups?

LTR‑RTs are the most abundant TEs in most plants and a major determinant of genome size.

In monocots (cereals, grasses) they usually account for 30–70% of the genome (around 65% in maize), often forming nested arrays that complicate assembly.

In conifers, 60–85% of the genome can be LTR‑RT, but large genome sizes there are driven mainly by inefficient removal and repair rather than unusually high transposition rates, leading to accumulation of many old elements.

How can the two LTRs of an LTR‑RT insertion be used as a molecular clock, and what does this show about LTR‑RT turnover in different plant lineages?

When an LTR‑RT inserts, its two terminal LTRs are initially identical.

Over time, random mutations accumulate independently in each LTR, so the sequence divergence between them can be used as a molecular clock to estimate insertion age.

Applying this shows that monocot genomes often contain many young LTR‑RT insertions, whereas conifer genomes are enriched for older insertions, consistent with slow removal and long‑term accumulation.

Distinguish autopolyploidy from allopolyploidy, and explain how bread wheat (Triticum aestivum) illustrates one of these processes.

In autopolyploidy, all chromosome sets come from a single species, typically via meiotic non‑disjunction producing unreduced gametes or somatic chromosome doubling.

In allopolyploidy, chromosome sets come from two or more diverged species, formed by hybridisation followed by genome doubling.

Bread wheat is an allohexaploid (AABBDD) that arose via multiple interspecific hybridisations among ancestral Triticum and Aegilops species, bringing together three homeologous genomes with relatively little chromosome reshaping.

What are the main evolutionary fates of duplicated genes after a WGD, and how can these processes promote plant adaptation?

After WGD, duplicated genes may undergo non‑functionalisation (one copy becomes a pseudogene), subfunctionalisation (ancestral roles are partitioned between copies), or neofunctionalisation (one copy acquires a novel function).

Selection can favour retained duplicates when they increase gene dosage, diversify regulation, or provide new biochemical or developmental functions. These processes give plants additional genetic material for innovation and adaptive diversification.