Insights into amphicarpy from the compact genome of the legume Amphicarpaea edgeworthii

Abstract

Amphicarpy (seed heteromorphy) is a unique and fascinating reproductive strategy wherein a single plant produces both aerial and subterranean fruits. This strategy is believed to be an adaptation to life under stressful or uncertain environments. Here, we sequenced and de novo assembled a chromosome-level genome assembly of the legume Amphicarpaea edgeworthii Benth. The 299-Mb A. edgeworthii genome encodes 27 899 protein-coding genes and is the most compact sequenced legume genome reported until date. Its reduced genome size may be attributed to the reduced long-terminal repeat retrotransposon content, which stems from the unequal homologous recombination. Gene families related to immunity and stress resistance have been contracted in A. edgeworthii, which is consistent with the notion that the amphicarpic reproductive strategy may be a complementary mechanism for its weak environmentaladaptation ability. We demonstrated the 'ABCE' model for the differentiation of chasmogamous and cleistogamous flowers. In addition, the characteristics of aerial and subterranean seeds in hard-seededness were explored. Thus, we suggest that the A. edgeworthii genome, which is the first of an amphicarpic plant, offers significant insights into its unusual reproductive strategy that is a key resource towards comprehending the evolution of angiosperms.

Multi-omics reveal differentiation and maintenance of dimorphic flowers in an alpine plant on the Qinghai-Tibet Plateau

“…Polyphenism is a unique type of phenotypic plasticity, in which the outputs are not continuous but relatively discrete, arising from the same genotype (Mayr, 1963;Moran, 1992;C.-H. Yang & Andrew Pospisilik, 2019). Its diverse traits and importance in conferring ecological fitness have been widely acknowledged (Darwin, 1897;Simpson, Sword, & Lo, 2011) in both animals and plants (Abouheif & Wray, 2002;Fawcett et al, 2018;Yiyang Liu et al, 2021;Zhang et al, 2021). As one of the most widespread polyphenisms (Joly & Schoen, 2021), dimorphic flowers evolved independently in roughly 700 species from 50 families of plants (Culley & Klooster, 2007).…”

“…In addition to ecological significance, it would be interesting to know what genes and their expressions have led to the differentiation and maintenance of such dimorphic flowers with the same genotype (Ansaldi et al, 2018;Morinaga et al, 2008). Two recent studies have investigated this genetic differentiation through sequencing the genome and examining gene expression of the dimorphic flowers (Yiyang Liu et al, 2021;Zhang et al, 2021). For Amphicarpaea edgeworthii (Fabaceae) with dimorphic flowers, the identified genes with contrasting expressions between aerial CH and subterranean CL flowers were mainly related to MADSbox genes (Yiyang Liu et al, 2021).…”

“…Two recent studies have investigated this genetic differentiation through sequencing the genome and examining gene expression of the dimorphic flowers (Yiyang Liu et al, 2021;Zhang et al, 2021). For Amphicarpaea edgeworthii (Fabaceae) with dimorphic flowers, the identified genes with contrasting expressions between aerial CH and subterranean CL flowers were mainly related to MADSbox genes (Yiyang Liu et al, 2021). Research on Cleistogenes songorica (Gramineae) with dimorphic flowers suggests miRNA, MYB transcription factors, and targeted genes are involved in the differential development of the highly reduced CH and CL flowers in this grass (Zhang et al, 2021).…”

Comparative cytogenomics reveals genome reshuffling and centromere repositioning in the legume tribe Phaseoleae

“…The centromeric regions were defined based on the centromeric data available in the genome assemblies (Schmutz et al, 2014;Pecrix et al, 2018;Lonardi et al, 2019;Liu et al, 2020;Garcia et al, 2021). Because the centromere positions for S. suberecuts were not indicated in the genome assembly, we hypothesized the centromere region according to the peaks of TE accumulations along the chromosomes (Qin et al, 2019).…”

Characterization of the complete plastome of Eleusine coracana (Gramineae), an annual crop

“…In areas with harsh natural conditions, E. coracana can be introduced for cultivation to meet the demand for grain (Hittalmani et al 2017). Therefore, obtaining genomic resources is of great significance for understanding and utilizing crops (Liu et al 2020). In this study, we determined the plastome of E. coracana, which would provide basic genetic resources for studying this important species and solving its phylogenetic placement.…”