Circadian rhythms driving a fast‐paced root clock implicate species‐specific regulation in Medicago truncatula

Abstract

Plants have a hierarchical circadian structure comprising multiple tissue-specific oscillators that operate at different speeds and regulate the expression of distinct sets of genes in different organs. However, the identity of the genes differentially regulated by the circadian clock in different organs, such as roots, and how their oscillations create functional specialization remain unclear. Here, we profiled the diurnal and circadian landscapes of the shoots and roots of Medicago truncatula and identified the conserved regulatory sequences contributing to transcriptome oscillations in each organ. We found that the light-dark cycles strongly affect the global transcriptome oscillation in roots, and many clock genes oscillate only in shoots. Moreover, many key genes involved in nitrogen fixation are regulated by circadian rhythms. Surprisingly, the root clock runs faster than the shoot clock, which is contrary to the hierarchical circadian structure showing a slow-paced root clock in both detached and intact Arabidopsis thaliana (L.) Heynh. roots. Our result provides important clues about the species-specific circadian regulatory mechanism, which is often overlooked, and possibly coordinates the timing between shoots and roots independent of the current prevailing model.

Identification of the global diurnal rhythmic transcripts, transcription factors and time-of-day specific cis elements in Chenopodium quinoa

“…Using HAYSTACK algorithm, We found as many as 44% of global transcripts in quinoa were diurnal rhythmic under at least one photoperiod (Fig. 1 ), larger than the proportion of periodic genes in Brachypodium distachyon (19.5%) [ 33 ], poplar (30.3%) and rice (40.8%) [ 24 ], while less than that in the shoots (76.54%) and roots (50.97%) of Medicago truncatula [ 34 ]. We found SD obviously rendered more genes rhythms than LD (Fig.…”

The plant circadian clock regulates autophagy rhythm through transcription factor LUX ARRHYTHMO

“…To investigate whether the autophagy rhythm is conserved across plant species, we analyzed the expression patterns of ATG s in other species, namely the C3 plants Medicago truncatula and Brassica rapa , and the C4 plants Setaria italica and Zea mays (Kim et al, 2019; Lai et al, 2020; Wang et al, 2021). Most ATG s were co‐expressed and oscillated under LD conditions in these plants (Figure S7).…”

“…The LDHH_ST and LL_LDHC data categories were used to represent the LD and LL conditions, respectively. RNA‐seq data of M. truncatula were acquired from the NCBI gene expression data repository (accession number: SRP299192) (Wang et al, 2021). The gene expression data of B. rapa , S. italic , and Z. mays were described previously (Kim et al, 2019; Lai et al, 2020).…”

Characterization of the REVEILLE family in Rosaceae and role of PbLHY in flowering time regulation

“…The function of RVE genes in roots has rarely been reported before. Recently, transcriptome analysis of Juglans regia and Medicago truncatula found that RVE genes may be involved in the nitrogen metabolic pathway [ 50 , 51 ]. Moreover, RVE genes had diverse expression patterns in different developmental stages of jujube fruit [ 52 ], and PbRVE1b promoted anthocyanin accumulation in P. bretschneideri peel [ 29 ].…”