Phylogeny and Species Delimitation of Chinese Medicago (Leguminosae) and Its Relatives Based on Molecular and Morphological Evidence

Phylogenetic and morphological analyses of Pilosocereus leucocephalus group s.s. (Cactaceae) reveal new taxonomical implications

Pilosocereus is one of the Cactaceae family's most relevant genera in terms of the number of species and its wide geographical range in the Americas. Within Pilosocereus, five informal taxonomic groups have been recognized, one of which is P. leucocephalus group s.s., whose phylogenetic relationships remain unresolved. Therefore, our objectives are to recognize the circumscriptions of the species in P. leucocephalus group s.s. and to corroborate the monophyly and phylogenetic relationships of this group through a set of morphological and molecular characters. This study is based on representative sampling along the broad distribution of this group in Mexico and Central America using multivariate and phylogenetic analyses. The morphological characters identified to contribute to species recognition and group formation are branch diameter, areole length, the areole length-width ratio, the distance between areoles, the length of the longest radial spine, and branch and spines colors. The chloroplast markers rpl16, trnL-trnF, and petL-psbE and the nuclear marker AT1G18270 support the monophyly of the P. leucocephalus group s.s., and two probable synapomorphies are suggested, including one transversion in rpl16 and another in petL-psbE. Together, our results demonstrate that sampled species of P. leucocephalus group s.s. encompass six species distributed in Mexico and Central America: P. alensis and P. purpusii in the western region, P. chrysacanthus and P. collinsii in the central region, and P. gaumeri and P. leucocephalus in the eastern region. A taxonomic key to recognized species is provided.

Extensive genomic rearrangements mediated by repetitive sequences in plastomes of Medicago and its relatives

BACKGROUND

Although plastomes are highly conserved with respect to gene content and order in most photosynthetic angiosperms, extensive genomic rearrangements have been reported in Fabaceae, particularly within the inverted repeat lacking clade (IRLC) of Papilionoideae. Two hypotheses, i.e., the absence of the IR and the increased repeat content, have been proposed to affect the stability of plastomes. However, this is still unclear for the IRLC species. Here, we aimed to investigate the relationships between repeat content and the degree of genomic rearrangements in plastomes of Medicago and its relatives Trigonella and Melilotus, which are nested firmly within the IRLC.

RESULTS

We detected abundant repetitive elements and extensive genomic rearrangements in the 75 newly assembled plastomes of 20 species, including gene loss, intron loss and gain, pseudogenization, tRNA duplication, inversion, and a second independent IR gain (IR ~ 15 kb in Melilotus dentata) in addition to the previous first reported cases in Medicago minima. We also conducted comparative genomic analysis to evaluate plastome evolution. Our results indicated that the overall repeat content is positively correlated with the degree of genomic rearrangements. Some of the genomic rearrangements were found to be directly linked with repetitive sequences. Tandem repeated sequences have been detected in the three genes with accelerated substitution rates (i.e., accD, clpP, and ycf1) and their length variation could be explained by the insertions of tandem repeats. The repeat contents of the three localized hypermutation regions around these three genes with accelerated substitution rates are also significantly higher than that of the remaining plastome sequences.

CONCLUSIONS

Our results suggest that IR reemergence in the IRLC species does not ensure their plastome stability. Instead, repeat-mediated illegitimate recombination is the major mechanism leading to genome instability, a pattern in agreement with recent findings in other angiosperm lineages. The plastome data generated herein provide valuable genomic resources for further investigating the plastome evolution in legumes.