Variation and Evolution of Genome Size in Gymnosperms

Abstract

Gymnosperms show a significantly higher mean (1C=18.16, 1Cx=16.80) and a narrow range (16.89-fold) of genome sizes as compared with angiosperms. Among the 12 families the largest ranges of 1C values is shown by Ephedraceae (4.73-fold) and Cupressaceae (4.45-fold) which are partly due to polyploidy as 1Cx values vary 2.41 and 1.37-fold respectively. In rest of the families which have only diploid taxa the range of 1C values is from 1.18-fold (Cycadaeae) to 4.36-fold (Podocarpaceae). The question is how gymnosperms acquired such big genome sizes despite the rarity of recent instances of polyploidy. A general survey of different families and genera shows that gymnosperms have experienced both increase and decrease in their genome size during evolution. Various genomic components which have accounted for these large genomes have been discussed. The major contributors are the transposable elements particularly LTR-retrotransposons comprising of Ty3gypsy, Ty1copia and gymny superfamilies which are most widespread. The genomes of gymnosperms have been acquiring diverse LTR-RTs in their long evolution in the absence of any efficient mechanism of their elimination. The epigenetic machinery which silences these large tracts of repeat sequences into the stretches of heterochromatin and the adaptive value of these silenced repeat sequences need further investigation.

LocoGSE, a sequence-based genome size estimator for plants

“…Notably, in land plants, there is a, 2400-fold variation of genome size between different species ( Pellicer et al., 2018 ), which has been shown to be caused by lineage-specific insertion/excision dynamics of DNA elements such as retrotransposons ( Bennetzen et al., 2005 ; Grover et al., 2008 ; Pellicer et al., 2018 ; Chase et al., 2023 ). For example, genome size increases have been related to retrotransposon invasions in Poaceae ( Sanmiguel and Bennetzen, 1998 ; Hawkins et al., 2006 ; Piegu et al., 2006 ; Dai et al., 2022 ), Melanthiaceae ( Pellicer and Leitch, 2014 ; Pellicer et al., 2021 ) or Gymnosperms ( Morse et al., 2009 ; Ohri, 2021 ). In addition to retrotransposon invasions, giant genomes are thought to have arisen because of the lack of DNA removal ( Kelly et al., 2015 ).…”

Physicochemical determinants and mechanisms of the hard‐to‐cook problem of Senegalia seeds, overlooked wild legumes in the arid tropics

“…But still, the data obtained in the present study could contribute to the ongoing efforts to devise identification keys for Acacia s.l. seeds (Gunn, 1984; Bagchi et al ., 1990; Al‐Gohary & Mohammed, 2007). Also, the physical properties of Senegalia seeds investigated and presented in this study can help design equipment and techniques for post‐harvest handling and processing (Karababa & Cos, 2013; Kumar et al ., 2016; Mubaiwa et al ., 2017).…”

“…Still, although efforts are ongoing to devise identification keys for Acacia s.l. seeds (Gunn, 1984; Bagchi et al ., 1990; Al‐Gohary & Mohammed, 2007), very few seeds have been anatomically or morphologically examined for most species in Senegalia segregate (Maslin et al ., 2019), facilitating the frauds and posing an important knowledge gap that needs to be addressed.…”

Haplotype-resolvedde novogenome assemblies of four coniferous tree species

“…Owing to the recent advancements in long-read sequencing technologies, the genomes of gymnosperm species belonging to six families, including Cupressaceae, Cycadaceae, Ginkgoaceae, Pinaceae, Taxaceae, and Welwitschiaceae, have become available (Wan et al 2022). The giant genomes of gymnosperm species are rich in repetitive sequences such as transposable elements (Ohri 2021). The high-fidelity (HiFi) long-read sequencing technology generates reads spanning the repetitive sequences, resulting in an assembly that covers most of the gene spaces in the genome (Hon et al 2020).…”