Ephedrae herba has been used for treating colds, relieving coughs and asthma from ancient times. We previously reported the distribution of
Ephedra sinica,
E. equisetina,
E. przewalskii,
E. regeliana,
E. monosperma and
Ephedra sp. in Mongolia, and among them
E. sinica and
E. equisetina were potential new resources of Ephedrae herba of Japanese pharmacopoeia grade, based on our field survey and subsequent molecular and chemical assessments. However, the
Ephedra population in southwestern areas showed a high possibility of having hybrid origins. Further field surveys in southwestern areas, and sequence analysis of the partial nuclear internal transcribed spacer 1 (ITS1) region, besides
trnK and 18S ribosomal RNA (rRNA) gene regions, were conducted in order to obtain detailed evidence of hybridization status. As a result, the distribution of
E. glauca in western area and
E. lomatolepis in western-most area was confirmed. The ITS sequences from all 8
Ephedra species collected in Mongolia were roughly divided into 5 types (types I—V). Type II sequence, having several additive nucleotides, was found in
Ephedra sp.,
E. glauca,
E. regeliana and
E. sinica, which provided useful information for tracing hybrid origins. Morphological, genetic and distribution evidence suggested that the hybridization of
Ephedra species occurred widely in southwestern Mongolia, and several
Ephedra species including
E. przewalkskii and
E. intermedia were involved in these events. Integrated with our previous report,
trnK-, 18S- and ITS-types from pure lines of each species are proposed. In addition, we propose a practicable method for detecting additive peaks on a direct sequencing electropherogram.
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