马红教授菊科核基因系统分类文章在MBE上在线 关键词: 核基因 系统发育 十字花科 菊科 被子植物 HuangCH,SunR,HuY,ZengL,ZhangN,CaiL,ZhangQ,Koch MA,AlShehbazI,EdgerPP,...Hong Ma*2015.Resolution of Brassicaceae phylogeny using nuclear genes uncovers nested radiations and supports convergent morphological evolution. Mol Biol Evol doi:10.1093/molbev/ msv1226. Zeng L, Zhang Q, Sun R, Kong H, Zhang N*, Ma H*. 2014. Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times. Nat Commum. 5:4956. Zhang N, Zeng L, Shan H, Ma H*. 2012. Highly conserved low copy nuclear genes as effective markers for phylogenetic analyses in angiosperms. New Phytol. 195:923–937. Phylogenetic Resolution of Deep Eukaryotic and Fungal Relationships Using Highly Conserved Low-Copy Nuclear Genes. Ren R, Sun Y, Zhao Y, Geiser D, Ma H, Zhou X. Genome Biol Evol . 2016 Sep 6. pii: evw196. 加上之前的三篇,10分以上的核基因系统分类发了三篇。 这篇是对菊科进行了分析,之前一篇MBE是对十字花科进行了研究,更早一篇NC是对被子植物的分类进行了研究。 这些研究都是基于转录组数据,使用几十个或更多的核基因对这些物种进行了分类。由于之前系统分类大都是基于叶绿体基因,所以核基因结果势必更反映基因组的变化,应该是分类结果更可靠。 具体结果,见文章。 马红实验室2016年在线文章: 1. Phylogenetic Resolution of Deep Eukaryotic and Fungal Relationships Using Highly Conserved Low-Copy Nuclear Genes. Ren R, Sun Y, Zhao Y, Geiser D, Ma H, Zhou X. Genome Biol Evol . 2016 Sep 6. pii: evw196. Select item 27604225 2. Multiple polyploidization events across Asteraceae with two nested events in the early history revealed by nuclear phylogenomics. Huang CH, Zhang C, Liu M, Hu Y, Gao T, Qi J, Ma H. Mol Biol Evol . 2016 Sep 7. pii: msw157. Select item 27531888 3. Abundant protein phosphorylation potentially regulates Arabidopsis anther development. Ye J, Zhang Z, You C, Zhang X, Lu J, Ma H. J Exp Bot . 2016 Sep;67(17):4993-5008. doi: 10.1093/jxb/erw293. Epub 2016 Aug 16. Select item 27385818 4. The PHD Finger Protein MMD1/DUET Ensures the Progression of Male Meiotic Chromosome Condensation and Directly Regulates the Expression of the Condensin Gene CAP-D3. Wang J, Niu B, Huang J, Wang H, Yang X, Dong A, Makaroff C, Ma H, Wang Y. Plant Cell . 2016 Aug;28(8):1894-909. doi: 10.1105/tpc.16.00040. Epub 2016 Jul 6. Select item 27337541 5. MID1 plays an important role in response to drought stress during reproductive development. Guo C, Yao L, You C, Wang S, Cui J, Ge X, Ma H. Plant J . 2016 Jun 23. doi: 10.1111/tpj.13250. Select item 27113773 6. Feedback Regulation of DYT1 by Interactions with Downstream bHLH Factors Promotes DYT1 Nuclear Localization and Anther Development. Cui J, You C, Zhu E, Huang Q, Ma H, Chang F. Plant Cell . 2016 May;28(5):1078-93. doi: 10.1105/tpc.15.00986. Epub 2016 Apr 25. Select item 27095111 Select item 26940208 7. Proteomics and transcriptomics analyses of Arabidopsis floral buds uncover important functions of ARABIDOPSIS SKP1-LIKE1. Lu D, Ni W, Stanley BA, Ma H. BMC Plant Biol . 2016 Mar 3;16:61. doi: 10.1186/s12870-015-0571-9. 8. Resolution of Brassicaceae Phylogeny Using Nuclear Genes Uncovers Nested Radiations and Supports Convergent Morphological Evolution. Huang CH, Sun R, Hu Y, Zeng L, Zhang N, Cai L, Zhang Q, Koch MA, Al-Shehbaz I, Edger PP, Pires JC, Tan DY, Zhong Y, Ma H. Mol Biol Evol . 2016 Feb;33(2):394-412. doi: 10.1093/molbev/msv226. Epub 2015 Oct 29. PMID: 9. Evolution and protein interactions of AP2 proteins in Brassicaceae: Evidence linking development and environmental responses. Zeng L, Yin Y, You C, Pan Q, Xu D, Jin T, Zhang B, Ma H. J Integr Plant Biol . 2016 Jun;58(6):549-63. doi: 10.1111/jipb.12439. Epub 2015 Dec 4. PMID: 26472270
为什么线粒体基因的进化速率快于核基因 the nucleotide substitution rate in mitochondrial genes is often faster than rates of many nuclear genes (Moritz et al., 1987). The rate difference was previously thought to be due to the lack a proof reading activity by the mitochondrial DNA polymerase Polγ, but recent work suggests the replication machinery does indeed proof read , . A current theory posits that free radicals or reactive oxygen species, which are a byproduct of superoxide production by complexes of the oxidative phosphorylation system , damage the mitochondrial DNA (mtDNA) , and produce a higher mutation rate.