Sciences in Cold and Arid Regions ›› 2018, Vol. 10 ›› Issue (5): 428-435.doi: 10.3724/SP.J.1226.2018.00428

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Transcriptomic comparison to identify rapidly evolving genes in Braya humilis

YuMing Wei1,XiaoFei Ma2,PengShan Zhao2,*()   

  1. 1 Animal Husbandry Pasture and Green Agriculture Institute of Gansu Academy of Agricultural Sciences, Lanzhou, Gansu 730070, China
    2 Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu 730000, China
  • Received:2018-04-16 Accepted:2018-08-15 Online:2018-11-19 Published:2018-11-21
  • Contact: PengShan Zhao
  • Supported by:
    This work was supported by National Natural Science Foundation of China (No. 41201048) and by the Youth Innovation Promotion Association of Chinese Academy of Sciences (2018463).


The Brassicaceae species Braya humilis shows broad adaptation to different climatic zones and latitudes. However, the molecular adaptation mechanism of B. humilis is poorly understood. In China, B. humilis is mainly distributed on the Qinghai-Tibetan Plateau (QTP) and in the adjacent arid region. Previous transcriptome analysis of B. humilis has revealed that 39 salt and osmotic stress response genes are subjected to purifying selection during its speciation. To further explore the adaptation mechanism of B. humilis to an arid environment, OrthoMCL program was employed in this study and 6,268 pairs of orthologous gene pairs with high confidence were obtained betweenB. humilis and Arabidopsis thaliana. A comparative evolutionary analysis based on nonsynonymous to synonymous substitution ratio (Ka/Ks) was then conducted. There were 64 pairs exhibiting a Ka/Ks ratio more than 0.5 and among which, three instrumental candidate genes, T2_20487, T2_22576, and T2_13757, were identified with strong selection signatures (Ka/Ks >1). The corresponding A. thaliana orthologs are double-stranded RNA-binding domain protein, MADS-box family protein, and NADH-dehydrogenase subunit 6, which is encoded by mitochondria genome. This report not only demonstrates the adaptation contribution of fast evolving nuclear genes, but also highlights the potential adaptive value of mitochondria gene to the speciation and adaptation of B. humilis toward the extreme environment in an arid region.

Key words: Braya humilis, positive selection, Ka/Ks, mitochondria gene variation, NADH-dehydrogenase subunit 6

Figure 1

Photographs of habitat and morphology of B. humilis. The habitat of B. humilis at the foot (a), middle (b), and top (c) of Baihushan Mountain, (d–f) Morphology of inflorescence, flower, and silique "

Figure 2

Ka/Ks distribution of 6,268 orthologous gene pairs of B. humilis and A. thaliana. (a) Scatter diagram of Ks and Ka value. The gene pairs with Ks >2 were filtered in this figure and the points with different Ka/Ks ratios are shown in different colour. (b) Histogram of Ka/Ks ratio "

Table 1

Positively selected genes in B. humilis "

Ortholog ID Arabidopsis gene B. humilis gene Ka Ks Ka/Ks Annotation
OG10864 At|ATMG00270.1 Bh|T2_13757 0.021 0.017 1.216 NADH dehydrogenase subunit 6 (NAD6)
OG08423 At|AT4G00420.2 Bh|T2_20487 0.125 0.118 1.063 Double-stranded RNA-binding domain (DsRBD)-containing protein
OG07470 At|AT3G12510.1 Bh|T2_22576 0.157 0.153 1.023 MADS-box family protein
OG08984 At|AT4G28160.1 Bh|T2_14710 0.186 0.210 0.885 Hydroxyproline-rich glycoprotein family protein
OG10866 At|ATMG00830.1 Bh|T2_8533 0.024 0.028 0.867 Cytochrome c biogenesis biogenesis 382 (CCB382)
OG07331 At|AT3G07525.2 Bh|T2_11702 0.061 0.073 0.838 AUTOPHAGY 10 (ATG10)
OG07729 At|AT3G21000.1 Bh|T2_30213 0.142 0.185 0.769 Gag-Pol-related retrotransposon family protein
OG06437 At|AT2G20620.1 Bh|T2_29281 0.181 0.236 0.768 Hypothetical protein
OG05855 At|AT1G69588.1 Bh|T2_23885 0.096 0.131 0.737 CLAVATA3/ESR-Related 45 (CLE45)
OG10748 At|AT5G64680.3 Bh|T2_26444 0.222 0.304 0.730 Mediator-associated protein
OG05953 At|AT1G73490.2 Bh|T2_4714 0.248 0.342 0.726 RNA-binding (RRM/RBD/RNP motifs) family protein
OG10862 At|ATMG00070.1 Bh|T2_18626 0.010 0.014 0.704 NADH dehydrogenase subunit 9 (NAD9)
OG07972 At|AT3G46910.1 Bh|T2_11373 0.135 0.194 0.698 Cullin family protein
OG08608 At|AT4G12100.1 Bh|T2_25782 0.158 0.233 0.679 Cullin family protein
OG08323 At|AT3G59550.1 Bh|T2_1079 0.099 0.145 0.678 Sister Chromatid Cohesion1 1
OG05765 At|AT1G67025.1 Bh|T2_40572 0.258 0.382 0.674 Wall-associated receptor kinase carboxy-terminal protein
OG05646 At|AT1G60700.1 Bh|T2_10793 0.074 0.110 0.674 SMAD/FHA domain-containing protein
OG07674 At|AT3G19150.1 Bh|T2_37031 0.093 0.140 0.666 Kip-related protein 6 (KRP6)
OG07898 At|AT3G28230.2 Bh|T2_19666 0.113 0.174 0.649 Something about silencing protein
OG09161 At|AT4G34530.1 Bh|T2_30131 0.064 0.099 0.644 Cryptochrome-interacting basic-helix-loop-helix 1 (CIB1)
OG05689 At|AT1G63245.1 Bh|T2_15034 0.192 0.303 0.635 CLAVATA3/ESR-Related 14 (CLE14)
OG06478 At|AT2G22000.1 Bh|T2_17745 0.079 0.126 0.632 Elicitor peptide 6 precursor
OG09339 At|AT5G01940.1 Bh|T2_26401 0.067 0.106 0.628 EIF-2B family protein
OG08306 At|AT3G58850.1 Bh|T2_18718 0.048 0.077 0.618 Phytochrome Rapidly Regulated2 (PAR2)
OG06953 At|AT2G41360.1 Bh|T2_18958 0.114 0.187 0.611 Galactose oxidase/kelch repeat protein
OG07249 At|AT3G04800.1 Bh|T2_36362 0.089 0.145 0.609 Translocase inner membrane subunit 23-3 (TIM23-3)
OG06515 At|AT2G24350.1 Bh|T2_2266 0.079 0.131 0.604 RNA binding (RRM/RBD/RNP motifs) family protein
OG10863 At|ATMG00180.1 Bh|T2_15220 0.033 0.056 0.596 Cytochrome c biogenesis 452 (CCB452)
OG08477 At|AT4G02310.1 Bh|T2_23130 0.143 0.241 0.592 Galactose oxidase/kelch repeat superfamily protein
OG05580 At|AT1G55260.1 Bh|T2_24979 0.078 0.133 0.583 Lipid-transfer protein 6 (LTPG6)
OG06781 At|AT2G35140.1 Bh|T2_36395 0.112 0.193 0.581 Development and Cell Death protein (DCD)
OG07825 At|AT3G25080.1 Bh|T2_11865 0.102 0.176 0.580 Hypothetical protein
OG08827 At|AT4G21550.1 Bh|T2_27886 0.066 0.117 0.564 VP1/ABI3-like 3 (VAL3)
OG04784 At|AT1G08060.1 Bh|T2_38418 0.088 0.157 0.560 MORPHEUS MOLECULE 1 (MOM1)

Figure 3

GO enrichment analyses of 64 rapidly evolved genes in B. humilis. The enriched GO terms (p <0.05) were identified using the Classfication SuperViewer Tool and the normalized results are presented. BP, biological process; MF, molecular function; CC, cellular component "

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