Red Clover (Trifolium pratense) and Zigzag Clover (T. medium) – A Picture of Genomic Similarities and Differences

Abstract

The genus clover (Trifolium sp.) is one of the most economically important genera in the Fabaceae family. More than 10 species are grown as manure plants or forage legumes. Red clover’s (T. pratense) genome size is one of the smallest in the Trifolium genus, while many clovers with potential breeding value have much larger genomes. Zigzag clover (T. medium) is closely related to the sequenced red clover; however, its genome is approximately 7.5x larger. Currently, almost nothing is known about the architecture of this large genome and differences between these two clover species. We sequenced the T. medium genome (2n = 8x = 64) with ∼23× coverage and managed to partially assemble 492.7 Mbp of its genomic sequence. A thorough comparison between red clover and zigzag clover sequencing reads resulted in the successful validation of 7 T. pratense- and 45 T. medium-specific repetitive elements. The newly discovered repeats led to the set-up of the first partial T. medium karyotype. Newly discovered red clover and zigzag clover tandem repeats were summarized. The structure of centromere-specific satellite repeat resembling that of T. repens was inferred in T. pratense. Two repeats, TrM300 and TrM378, showed a specific localization into centromeres of a half of all zigzag clover chromosomes; TrM300 on eight chromosomes and TrM378 on 24 chromosomes. A comparison with the red clover draft sequence was also used to mine more than 105,000 simple sequence repeats (SSRs) and 1,170,000 single nucleotide variants (SNVs). The presented data obtained from the sequencing of zigzag clover represent the first glimpse on the genomic sequence of this species. Centromeric repeats indicated its allopolyploid origin and naturally occurring homogenization of the centromeric repeat motif was somehow prevented. Using various repeats, highly uniform 64 chromosomes were separated into eight types of chromosomes. Zigzag clover genome underwent substantial chromosome rearrangements and cannot be counted as a true octoploid. The resulting data, especially the large number of predicted SSRs and SNVs, may have great potential for further research of the legume family and for rapid advancements in clover breeding.

High-Density SNP-Based Association Mapping of Seed Traits in Fenugreek Reveals Homology with Clover

“…Our finding that two SNPs associated with seed size (length and width) and seed color are both localized in TE genes could be explained by the fact that other species from the Trifolieae tribe, in contrast to other legumes, have genomes that are rich in TEs. For example, Trifolium pretense and Trifolium medium genomes were reported to have more than 30 and 40%, respectively, of retrotransposable elements in their genome [ 24 , 52 ], and that our data show a similar trend for the fenugreek genome. Accordingly, this suggests an important role for TEs in shaping the fenugreek genome and thus in controlling important phenotypic and economic traits in addition to the ones studied here.…”

“…This is similar to previous studies that reported synteny between M. truncatula and legumes such as white clover [ 23 ], red clover [ 56 ], birdsfoot trefoil [ 57 , 58 ], common bean [ 58 ], chickpea and lentil [ 59 ], and faba bean [ 60 ]. Synteny was also reported between members of the Trifolieae tribe such as Red clover and zigzag clover [ 24 ].…”

“…Two very recent studies used comparative transcriptome analysis [ 21 ], and qRT-PCR [ 22 ]. Some gaps in our knowledge of fenugreek genome structure and function could potentially be filled by leveraging homology comparisons with known genomes, similar to the recent studies in the Trifolieae tribe of the Fabaceae family between Medicago truncatula (barrel clover) and Trifolium repens L. (white clover) [ 23 ], and between Trifolium pretense and Trifolium medium (zigzag clover) [ 24 ].…”

Extraordinary Sequence Diversity and Promiscuity of Centromeric Satellites in the Legume Tribe Fabeae

“…2015 ) but are comparably less abundant in the related legume taxa ( Macas et al. 2007 ; Dluhošová et al. 2018 ), potentially resulting in smaller numbers of Ogre-derived satellite repeats.…”

Transcriptional changes suggest a major involvement of Gibberellins in Trifolium pratense regrowth after mowing

“…Well-known disadvantages of red clover include poor persistence under several land use 31 scenarios, like grazing or cutting [1][2][3]. T. pratense is a member of the Fabaceae (or legumes), which 32 are, due to their economic value, among the most examined families in the plant kingdom with 33 genome sequences available for species like Medicago truncatula (barrel clover) [4], Lotus japonicus 34 (birdsfoot trefoil) [5], Glycine max (soy) [6], Phaseolus vulgaris (common bean) [7], Cicer arietinum 35 (chickpea) [8], Vigna unguiculata (cowpea) [9],Trifolium subterraneum (subterranean clover) [10] 36 Trifolium medium (zigzag clover) [11], and T. pratense (red clover) [12,13].…”