Phylogeny and highland adaptation of Chinese species in Allium Section Daghestanica (Amaryllidaceae) revealed by transcriptome sequencing

Publication date: Available online 23 January 2020Source: Molecular Phylogenetics and EvolutionAuthor(s): Deng-Feng Xie, Yan Yu, Jun Wen, Jiao Huang, Jun-Pei Chen, Juan Li, Song-Dong Zhou, Xing-Jin HeAbstractAllium L. is one of the largest monocotyledonous genera with an extensive distribution in the Northern Hemisphere. The fundamental phylogenies of Allium have been investigated using many morphological and molecular characters. However, the morphological characters may not agree with the molecular results in some Allium groups or sections (such as the Chinese Allium section Daghestanica), which may result in ambiguous species relationships and hinder further evolutionary and adaptive researches. Here, transcriptome sequences of the six Chinese endemics from Allium section Daghestanica were collected, with their single-copy genes (SCGs) were extracted. The interspecies relationships were analyzed using concatenation and coalescent methods. Branch-site model (BSM) were conducted to detect the positively selected genes (PSGs) in five highland species of this section. Based on 1644, 1281 and 1580 SCGs in flowers, leaves, and flower-leaves combination respectively, a robust consistent and well-resolved phylogeny was generated from the concatenation method. Strong conflicts among individual gene trees were detected in the coalescent method, and morphological characters were incongruent with molecular relationships to some degree. Many PSGs were involved in responses of various s...
Source: Molecular Phylogenetics and Evolution - Category: Molecular Biology Source Type: research