Recent structural variations in the Medicago chloroplast genomes and their horizontal transfer into nuclear chromosomes

Abstract

Medicago is a genus of legumes (Fabaceae) that resemble common clovers with pinnately trifoliate leaves and spirally coiled seed pods, and Medicago sativa is a famous forage crop throughout the world. In this study, we systematically assembled the complete plastid genomes of 18 Medicago species, representing 35 Medicago accessions, whose genome size ranged from ~119 to 125 kb, and identified one novel inverted repeat (IR) in two accessions of Medicago soleirolii (PI537242 and PI537243), albeit of no IRs in the most accessions. We built a phylogenetic tree based on common protein-coding sequences of 55 Medicago accessions in 38 species, which were placed into five clades with a divergence since 9.37 million years ago. Global alignment revealed independent genome evolution events, including eight inversions in nine species and four intron losses (ILs) in 10 species, among which four inversions and two ILs have not been reported previously. Within 109-111 unique genes, ndhA, rpl2, and ycf3 were under positive selection in 54 Medicago accessions. Finally, by aligning chloroplast genes against the nuclear genome assembly of M. sativa cultivar "Zhongmu No.1", we found that a large number of chloroplast gene fragments were horizontally transferred to nuclear chromosomes in alfalfa, especially on the chr3:47518422-48722257 coordinates of chromosome 3. Our comprehensive exploration of Medicago chloroplast genomes provided insights for the understanding of Medicago diversity and their genomic evolution events.

Plastid phylogenomics uncovers multiple species in Medicago truncatula (Fabaceae) germplasm accessions

“…The M . littoralis accession sampled in Jiao et al 37 lacks the 45-kb inversion 32 and was placed in a clade with M . truncatula accessions may also be a misidentification.…”

“…This suggests that the occurrence of two distinct plastome configurations in M. truncatula accessions is different from that of intraspecific inversion isomers, which share little or no DNA sequence divergence but mainly differ with regard to their gene order due to highly active genome rearrangements, such as found in Pinaceae 54 , Cupressaceae 55 , 56 , Taxus (Taxaceae) 57 , Eleocharis (Cyperaceae) 58 , Monsonia emarginata (L.f.) L'Hér. (Geraniaceae) 59 , and Medicago soleirolii (Fabaceae) 37 . The 45-kb inversion also differs from homoplastic plastome structural evolution found among various distinct taxonomic groups in Papilionoideae 33 , 34 , 60 – 62 .…”

“…the 45-kb inversion) and putative intraindividual structural (or assembly) variation from four Medicago species [ Medicago coronata (L.) Bartal., Medicago constricta Durieu , M. littoralis , and M. soleirolii Duby]. Jiao et al 37 verified intraindividual inversion variation of a 16-kb plastid region between a small IR (~ 300 bp) in M. soleirolii by polymerase chain reaction (PCR). However, the reasons why M. truncatula shows intraspecific plastome structural variation and how it is related to M. littoralis remain equivocal.…”

“…Recently, plastomes of dozens of Medicago species have been sequenced [33][34][35][36][37] and have shown multiple additional rearrangements across the genus. Medicago exhibits high plastid sequence variation at interspecific, intraspecific and intraindividual levels [32][33][34][35][36][37][38] . A recent plastome study of Jiao et al 37 found that two of three M. littoralis accessions had the same inversion as R108 (i.e.…”

“…Medicago exhibits high plastid sequence variation at interspecific, intraspecific and intraindividual levels [32][33][34][35][36][37][38] . A recent plastome study of Jiao et al 37 found that two of three M. littoralis accessions had the same inversion as R108 (i.e. the 45-kb inversion) and putative intraindividual structural (or assembly) variation from four Medicago species [Medicago coronata (L.) Bartal., Medicago constricta Durieu, M. littoralis, and M. soleirolii Duby].…”