title: Genetic Adaptation of Giant Lobelias (Lobelia aberdarica and Lobelia telekii) to Different Altitudes in East African Mountains.
abstract: The giant lobelias in East African mountains are good models for studying molecular mechanisms of adaptation to different altitudes. In this study, we generated RNA-seq data of a middle-altitude species Lobelia aberdarica and a high-altitude species L. telekii, followed by selective pressure estimation of their orthologous genes. Our aim was to explore the important genes potentially involved in adaptation to different altitudes. About 9.3 Gb of clean nucleotides, 167,929-170,534 unigenes with total lengths of 159,762,099-171,138,936 bp for each of the two species were generated. OrthoMCL method identified 3,049 1:1 orthologous genes (each species was represented by one ortholog). Estimations of non-synonymous to synonymous rate were performed using an approximate method and a maximum likelihood method in PAML. Eighty-five orthologous genes were under positive selection. At least 8 of these genes are possibly involved in DNA repair, response to DNA damage and temperature stimulus, and regulation of gene expression, which hints on how giant lobelias adapt to high altitudinal environment that characterized by cold, low oxygen, and strong ultraviolet radiation. The negatively selected genes are over-represented in Gene Ontology terms of hydrolase, macromolecular complex assembly among others. This study sheds light on understanding the molecular mechanism of adaptation to different altitudes, and provides genomic resources for further studies of giant lobelias.
authors.affiliation: Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China; Sino-Africa Joint Research Centre, Chinese Academy of SciencesWuhan, China.
authors.forename: Shu-Ying
authors.initials: SY
authors.lastname: Zhao
authors.affiliation: Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China; Sino-Africa Joint Research Centre, Chinese Academy of SciencesWuhan, China.
authors.forename: Ling-Yun
authors.initials: LY
authors.lastname: Chen
authors.affiliation: Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China; Sino-Africa Joint Research Centre, Chinese Academy of SciencesWuhan, China.
authors.forename: John K
authors.initials: JK
authors.lastname: Muchuku
authors.affiliation: Sino-Africa Joint Research Centre, Chinese Academy of Sciences Wuhan, China.
authors.forename: Guang-Wan
authors.initials: GW
authors.lastname: Hu
authors.affiliation: Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China; Sino-Africa Joint Research Centre, Chinese Academy of SciencesWuhan, China.
authors.forename: Qing-Feng
authors.initials: QF
authors.lastname: Wang
keywords: RNA-Seq; dN/dS ratio (ω); giant lobelias; high altitude; natural selection