Phylogenetics of Cucumis (Cucurbitaceae): Cucumber (C. sativus) belongs in an Asian/Australian clade far from melon (C. melo)

Abstract

BackgroundMelon, Cucumis melo, and cucumber, C. sativus, are among the most widely cultivated crops worldwide. Cucumis, as traditionally conceived, is geographically centered in Africa, with C. sativus and C. hystrix thought to be the only Cucumis species in Asia. This taxonomy forms the basis for all ongoing Cucumis breeding and genomics efforts. We tested relationships among Cucumis and related genera based on DNA sequences from chloroplast gene, intron, and spacer regions (rbcL, matK, rpl20-rps12, trnL, and trnL-F), adding nuclear internal transcribed spacer sequences to resolve relationships within Cucumis.ResultsAnalyses of combined chloroplast sequences (4,375 aligned nucleotides) for 123 of the 130 genera of Cucurbitaceae indicate that the genera Cucumella, Dicaelospermum, Mukia, Myrmecosicyos, and Oreosyce are embedded within Cucumis. Phylogenetic trees from nuclear sequences for these taxa are congruent, and the combined data yield a well-supported phylogeny. The nesting of the five genera in Cucumis greatly changes the natural geographic range of the genus, extending it throughout the Malesian region and into Australia. The closest relative of Cucumis is Muellerargia, with one species in Australia and Indonesia, the other in Madagascar. Cucumber and its sister species, C. hystrix, are nested among Australian, Malaysian, and Western Indian species placed in Mukia or Dicaelospermum and in one case not yet formally described. Cucumis melo is sister to this Australian/Asian clade, rather than being close to African species as previously thought. Molecular clocks indicate that the deepest divergences in Cucumis, including the split between C. melo and its Australian/Asian sister clade, go back to the mid-Eocene.ConclusionBased on congruent nuclear and chloroplast phylogenies we conclude that Cucumis comprises an old Australian/Asian component that was heretofore unsuspected. Cucumis sativus evolved within this Australian/Asian clade and is phylogenetically far more distant from C. melo than implied by the current morphological classification.

Genetic diversity among melon accessions from Iran and their relationships with melon germplasm of diverse origins using microsatellite markers

“…With regard to differences among reference accessions, which are from various cultivar groups and species of Cucumis, the genetic variability observed among Iranian accessions is significantly comparable with reference accessions. These results demonstrate that the Iranian melon is diversified and supports the idea of their origin in Asia (Renner et al 2007). In addition, it indicates the importance of Iranian inodorus and dudaim accessions for the study of origin and diversification of vars.…”

“…In fact, 'Musk' is a Persian word for a kind of perfume and 'melon' is derived from Greek words (Robinson and Decker-Walters 1997). The origin of diversity for melon was traditionally believed to be in Africa (Robinson and Decker-Walters 1997), although recent molecular systematic studies, suggested that it may be originated from Asia and then reached to Africa (Renner et al 2007). Central Asia, Iran, Afghanistan, India, Transcaucasia, Turkmenistan, Tajikistan, and Uzbekistan, as well as Afghanistan and China (Robinson and DeckerWalters 1997) are considered primary diversity centre for melon (Tzitzikas et al 2009).…”

An anionic class III peroxidase from zucchini may regulate hypocotyl elongation through its auxin oxidase activity

“…The protein sequence is largely conserved among cucurbital taxonomic group, but not in other Eudicotyledons, indicating that APRX might be a Cucurbitaceae speciWc peroxidase. Cucumis organellar genomes are unusually labile and numerous accumulations of repetitive sequences as well as major rearrangements are thought to have taken place during the evolution of Cucumis (Renner et al 2007). …”

A plastid tree can bring order to the chaotic generic taxonomy of Rytidosperma Steud. s.l. (Poaceae)

“…However, none of these studies test whether this holds true for their dataset although it is known that the outcome of bootstrap analyses may be highly dataset dependent (DeBry and Olmstead, 2000;Mort et al, 2000;Sanderson and Wojciechowski, 2000). Further, Müller's (2005b) conclusions have been extrapolated for use under RAS too (Renner et al, 2007;Komarova et al, 2008). To test the possible influence of RAS versus simple addition sequence and few versus many bootstrap iterations on the present dataset we ran four separate bootstrap analyses with full heuristic searches, holding one tree per taxon addition sequence, with TBR branch swapping: (1) RAS-500:500 bootstrap replicates, each of 50 replicates of RAS, saving no more than 10 trees in each replicate; (2) RAS-10,000:10,000 bootstrap replicates, each of 1 replicate of RAS, saving no more than one tree per replicate; (3) SIMPLE-500:500 bootstrap replicates, simple addition sequence, holding up to 50 trees during TBR branch swapping; (4) SIMPLE-10,000:10,000 bootstrap replicates, simple addition sequence, holding up to 50 trees during TBR branch swapping.…”