title: Different Sets of Post-Embryonic Development Genes Are Conserved or Lost in Two Caryophyllales Species (Reaumuria soongorica and Agriophyllum squarrosum).
abstract: Reaumuria soongorica and sand rice (Agriophyllum squarrosum) belong to the clade of Caryophyllales and are widely distributed in the desert regions of north China. Both plants have evolved many specific traits and adaptation strategies to cope with recurring environmental threats. However, the genetic basis that underpins their unique traits and adaptation remains unknown. In this study, the transcriptome data of R. soongorica and sand rice were compared with three other species with previously sequenced genomes (Arabidopsis thaliana, Oryza sativa, and Beta vulgaris). Four different gene sets were identified, namely, the genes conserved in both species, those lost in both species, those conserved in R. soongorica only, and those conserved in sand rice only. Gene ontology showed that post-embryonic development genes (PEDGs) were enriched in all gene sets, and different sets of PEDGs were conserved or lost in both the R. soongorica and sand rice genomes. Expression profiles of Arabidopsis orthologs further provided some clues to the function of the species-specific conserved PEDGs. Such orthologs included LEAFY PETIOLE, which could be a candidate gene involved in the development of branch priority in sand rice.
authors.affiliation: Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, P.R. China.|Shapotou Desert Research & Experiment Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, P.R. China.
authors.forename: Pengshan
authors.initials: P
authors.lastname: Zhao
authors.affiliation: Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, P.R. China.|Shapotou Desert Research & Experiment Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, P.R. China.
authors.forename: Jiwei
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, P.R. China.|Shapotou Desert Research & Experiment Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, P.R. China.
authors.forename: Xin
authors.initials: X
authors.lastname: Zhao
authors.affiliation: Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, P.R. China.|Shapotou Desert Research & Experiment Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, P.R. China.
authors.forename: Guoxiong
authors.initials: G
authors.lastname: Chen
authors.affiliation: Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, P.R. China.|Shapotou Desert Research & Experiment Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, P.R. China.
authors.forename: Xiao-Fei
authors.initials: XF
authors.lastname: Ma
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000254:growth & development; D019143:Evolution, Molecular; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D017343:Genes, Plant; D019684:Magnoliopsida / Q000235:genetics* / Q000254:growth & development; D005810:Multigene Family; D059467:Transcriptome
references.citation: Science. 2013 Dec 20;342(6165):1241089
references.pmid: 24357323
references.citation: Genome Biol Evol. 2015 Jan 09;7(2):444-56
references.pmid: 25577200
references.citation: Development. 2000 Nov;127(22):4971-80
references.pmid: 11044410
references.citation: Plant Cell. 2011 Apr;23(4):1231-48
references.pmid: 21467579
references.citation: PLoS One. 2011;6(12):e29123
references.pmid: 22195004
references.citation: Nat Commun. 2013;4:2797
references.pmid: 24256998
references.citation: Plant J. 2010 Jul;63(2):212-228
references.pmid: 20444235
references.citation: Plant J. 2008 Aug;55(4):568-79
references.pmid: 18433436
references.citation: Plant Cell. 2002 Aug;14(8):1919-35
references.pmid: 12172031
references.citation: Plant Physiol. 2008 Dec;148(4):2121-33
references.pmid: 18835996
references.citation: BMC Genomics. 2004 Nov 16;5:89
references.pmid: 15546486
references.citation: Proc Natl Acad Sci U S A. 2009 Mar 31;106(13):5418-23
references.pmid: 19276109
references.citation: Proc Natl Acad Sci U S A. 2005 May 24;102(21):7760-5
references.pmid: 15894620
references.citation: Plant Cell Rep. 2011 Jun;30(6):955-64
references.pmid: 21327391
references.citation: Science. 2002 Mar 15;295(5562):2073-6
references.pmid: 11847307
references.citation: BMC Genomics. 2014 Oct 07;15:872
references.pmid: 25287394
references.citation: Plant J. 2012 Aug;71(3):492-502
references.pmid: 22443345
references.citation: J Exp Bot. 2015 Mar;66(5):1489-98
references.pmid: 25563969
references.citation: Plant Cell. 2009 Jan;21(1):72-89
references.pmid: 19136646
references.citation: Funct Plant Biol. 2013 May;40(4):315-328
references.pmid: 32481110
references.citation: Plant Physiol. 2007 Feb;143(2):684-96
references.pmid: 17158585
references.citation: New Phytol. 2013 Sep;199(4):1060-1068
references.pmid: 23701123
references.citation: Nature. 2014 Jan 23;505(7484):546-9
references.pmid: 24352233
references.citation: PLoS One. 2013 May 23;8(5):e63993
references.pmid: 23717523
references.citation: Plant Cell. 2004 Jul;16(7):1925-37
references.pmid: 15208394
references.citation: Proc Natl Acad Sci U S A. 2015 May 5;112(18):5833-7
references.pmid: 25902549
references.citation: Mol Biol Evol. 2015 Aug;32(8):2001-14
references.pmid: 25837578
references.citation: Genes Dev. 1999 Jul 1;13(13):1678-91
references.pmid: 10398681
references.citation: Front Plant Sci. 2013 Nov 28;4:482
references.pmid: 24348488
references.citation: Sci Rep. 2015 Oct 29;5:15823
references.pmid: 26510579
references.citation: PLoS One. 2014 Apr 15;9(4):e94277
references.pmid: 24736242
references.citation: BMC Evol Biol. 2015 Apr 18;15:66
references.pmid: 25927997
references.citation: Curr Opin Plant Biol. 2000 Apr;3(2):117-24
references.pmid: 10712956
references.citation: Biochem J. 2012 Mar 15;442(3):573-81
references.pmid: 22150398
references.citation: Proc Natl Acad Sci U S A. 2010 May 4;107(18):8063-70
references.pmid: 20385809
references.citation: Plant J. 2015 Jan;81(2):223-32
references.pmid: 25376953
references.citation: Plant Physiol. 2009 Sep;151(1):180-98
references.pmid: 19625634
references.citation: Plant Cell. 2006 Jan;18(1):29-39
references.pmid: 16339853
references.citation: Annu Rev Plant Physiol Plant Mol Biol. 1996 Jun;47:377-403
references.pmid: 15012294
references.citation: Plant Cell. 2007 Sep;19(9):2952-66
references.pmid: 17905899
references.citation: Cell Mol Life Sci. 2013 Feb;70(4):689-709
references.pmid: 22996258
references.citation: Nucleic Acids Res. 2010 Jul;38(Web Server issue):W64-70
references.pmid: 20435677
references.citation: Proc Natl Acad Sci U S A. 2014 Sep 30;111(39):E4096-102
references.pmid: 25225383