Abstract
Amphicarpaea edgeworthii, an annual twining herb, is a widely distributed species and an attractive model for studying complex flowering types and evolutionary mechanisms of species. Herein, we have generated a high-quality assembly of A. edgeworthii by using a combination of PacBio, 10× Genomics libraries, and Hi-C mapping technologies. The final 11 chromosome-level scaffolds covered 90.61% of the estimated genome (343.78Mb), which is a chromosome-scale assembled genome of an amphicarpic plant. Subsequently, we characterized the genetic diversity and population structure of A. edgeworthii species by resequencing individuals collected from their natural area of distribution. Using transcriptome profiling, we observed that specific phenotypes are regulated by a complex network of light, hormones, and MADS-box gene families. These data are beneficial for the discovery of genes that control major agronomic traits and spur genetic improvement of and functional genetic studies in legumes, as well as supply comparative genetic resources for other amphicarpic plants.
Highlights
In nature, the distribution of key resources required for plant growth is often uneven
Thereafter, we sequenced the genome of A. edgeworthii by using a combination of PacBio, Illumina, and 10× Genomics libraries that resulted in the generation of a 343.78-Mbp genome
We used a total of 5.27 million reads from high-throughput chromosome conformation capture (Hi-C) libraries and mapped approximately 90.61% of the assembled sequences to 11 pseudochromosomes, with the longest scaffold length of 32.05 Mb (Table 1, Figure 2 and Supplementary Figure 3)
Summary
The distribution of key resources required for plant growth is often uneven. Amphicarpy is a phenomenon in which a plant produces both aerial and subterranean flowers and simultaneously bears both aerial and subterranean fruits on aerial and subterranean stems, respectively (Schnee and Waller, 1986; Cheplick, 1987; Koontz et al, 2017). This phenomenon is observed in at least 67 herbaceous species (31 in Fabaceae) in 39 genera and 13 families of angiosperms, as reported by Zhang et al (2020a). Amphicarpy is an important part of plant adaptive evolution, in which angiosperms generally display a special type of fruiting pattern and different fruit (seed) types
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