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| Selected Publications |
Ren Y, He Z, Liu P, Traw MB, Sun S, Tian D, Yang S, Jia Y*, Wang L* (2021) Somatic Mutation Analysis in Salix Suchowensis Reveals Early-Segregated Cell Lineages. Mol Biol Evol no.msab286. doi.org/10.1093/molbev/msab286
| Yu L, Ma S, Zhang X, Tian D, Yang S*, Jia X*, Traw MB* (2021) Ancient Rapid Functional Differentiation and Fixation of the Duplicated Members in Rice Dof Genes after Whole Genome Duplication. Plant J doi.org/10.1111/tpj.15516
| Jia X, Zhang Q, Jiang M, Huang J, Yu L, Traw MB, Tian D, Hurst LD*, Yang S* (2021) Mitotic gene conversion can be as important as meiotic conversion in driving genetic variability in plants and other species without early germline segregation. PLoS Biol 19(3): e3001164
| Jiang M, He Y, Chen X, Zhang X, Guo Y, Yang S, Huang J*, Traw M* (2020) CRISPR-based assessment of genomic structure in the conserved SQUAMOSA promoter-binding-like gene clusters in rice. Plant J 104(5):1301-1314
| Wang L, Sun Y, Sun X, Yu L, Xue L, He Z, Huang J, Tian D, Hurst LD* & Yang S* (2020) Repeat-Induced Point Mutation in Neurospora Crassa Causes the Highest Known Mutation Rate and Mutational Burden of Any Cellular Life. Genome Biology 21(1):142. doi:10.1186/s13059-020-02060-w.
| Chen J, Hao Z, Guang X, Zhao C, Wang P, Xue L, Zhu Q, Yang L, Yu Sheng1 , Zhou Y, Xu H, Xie H, Long X, Zhang J, Wang Z, Shi M, Lu Y, Liu S, Guan L, Zhu Q, Yang L, Ge S , Cheng T, Laux T, Gao Q, Peng Y, Liu N*, Yang S*, Shi J* (2019) Liriodendron genome sheds light on angiosperm phylogeny and species-pair differentiation. Nature Plants 10.1038/s41477-018-0323-6
| Wang L, Zhao L, Zhang X, Zhang Q, Jia Y, Wang G, Li S, Tian D, Li W-H* & Yang S*. (2019). Large-Scale Identification and Functional Analysis of NLR Genes in Blast Resistance in the Tetep Rice Genome Sequence. PNAS August, 201910229. doi:10.1073/pnas.1910229116.
| Jia X, Zhang Y, Zhang Q, Zhao Q, Wang L, Traw M, Tian D, Wang C*, Yang S*. (2019) High resolution insight into recombination events at the SD1 locus in rice. Plant J DOI: 10.1111/tpj.14154
| Chen X, Tian X, Xue L, Zhang X, Yang S, Traw MB & Huang J*. (2019). CRISPR-Based Assessment of Gene Specialization in the Gibberellin Metabolic Pathway in Rice. Plant Physiology 180(4):2091–2105. doi:10.1104/pp.19.00328.
| Wang L, Ji Y, Hu Y, Hu H, Jia X, Jiang M, Zhang X, Zhao L, Zhang Y, Jia Y, Qin C, Yu L, Huang J, Yang S*, Hurst LD* & Tian D*. (2019). The architecture of intra-organism mutation rate variation in plants. PLOS Biology 17(4):e3000191.
| Huang J, Li J, Zhou J, Wang L, Yang S, Hurst LD*, Li W-H* & Tian D*. (2018) Identifying a Large Number of High-Yield Genes in Rice by Pedigree Analysis, Whole-Genome Sequencing, and CRISPR-Cas9 Gene Knockout. PNAS 115(32): E7559-E7567
| Liu H, Huang J, Sun X, Li J, Hu Y, Yu L, Liti G, Tian D, Hurst LD* & Yang S*. (2018) Tetrad Analysis in Plants and Fungi Finds Large Differences in Gene Conversion Rates but No GC Bias. Nature Ecology & Evolution 2, 164–173
| Liu H, Jia Y, Sun X, Tian D, Hurst LD*, Yang S*. (2017) Direct determination of the mutation rate in the bumblebee reveals evidence for weak recombination-associated mutation and an approximate rate constancy in insects. Mol Biol Evol 34(1):119-130
| Gu L, Wu Y, Jiang M, Si W, Zhang X, Tian D*, Yang S*. (2016) Dissimilar Manifestation of Heterosis in Super Hybrid Rice at Early-Tillering Stage under Nutrient-Deficient and Nutrient-Sufficient Condition. Plant Physiol 172: 1142-1153
| Xie Z, Wang L, Wang L, Wang Z, Lu, Z, Tian D, Yang S*, Hurst LD.* (2016) Mutation rate analysis via parent-progeny sequencing of the perennial peach I. A low rate in woody perennials and a higher mutagenicity in hybrids. P Roy Soc B-Biol Sci 283: 20161016.
| Wang L, Zhang Y, Qing C, Tian D, Yang S*, Hurst LD.* (2016) Mutation rate analysis via parent-progeny sequencing of the perennial peach II: No evidence for recombination-associated mutation. P Roy Soc B-Biol Sci 283: 20161785
| Yang S, Wang L, Huang J, Zhang X, Yuan Y, Chen J-Q, Hurst LD*, Tian D* (2015). Parent-progeny sequencing indicates higher mutation rates in heterozygotes. Nature 523: 463–467 | Zhang X#, Yang S#, Wang J#, Jia Y#, Huang J#, Zhong Y, Tan S, Wang L, Gu L, Chen JQ, Pan QH*, Bergelson J*, Tian D* (2015). A genome-wide survey reveals abundant rice blast R-genes in resistant cultivars. Plant J 84 :20-28 | Liu H#, Zhang X#, Huang J, Chen JQ, Tian D, Hurst LD*, Yang S*. (2015) Causes and consequences of crossing-over evidenced via a high-resolution recombinational landscape of the honey bee. Genome Biology 16:15 | Si W, Yuan Y, Huang J, Zhang X, Zhang Y, Zhang Y, Tian D, Wang C, Yang YH*, Yang S*. (2015) Widely distributed hot and cold spots in meiotic recombination as shown by sequencing of rice F2 plants. New Phytologist 206 :1491-1502 | Yang S, Li J, Zhang X, Zhang Q, Huang J, Chen J-Q, Hartl DL, Tian D. (2013) Rapidly evolving R genes in diverse grass species confer resistance to rice blast disease. PNAS 110: 18572-18577 | Yang S, Yuan Y, Wang L, Li J, Wang W, Liu H, Chen JQ, Hurst LD, Tian D. (2012) Great majority of recombination events in Arabidopsis are gene conversion events. PNAS 109 :20992-20997 | Yue J-X, Meyers BC, Chen J-Q, Tian D, Yang S. (2012) Tracing the origin and evolutionary history of plant nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes. New Phytologist 193: 1049–1063 | Gu T, Tan S, Gou X, Araki H, Tian D. (2010) Avoidance of long mononucleotide repeats in codon pair usage. Genetics 186:1077-1084 | Zhu L, Wang Q, Tang P, Araki H, Tian D. (2009) Genome-wide association between insertions/deletions and the nucleotide diversity in bacteria. Mol Biol Evol 26:2353-2361 | Chen JQ, Wu Y, Yang H, Bergelson J, Kreitman M, Tian D. (2009) Variation in the ratio of nucleotide substitution and indel rates across genomes in mammals and bacteria. Mol Biol Evol 26:1523-31 | Tian D, Wang Q, Zhang P, Araki H, Yang S, Kreitman M, Nagylaki T, Hudson R, Bergelson J & Chen JQ. (2008) Single-nucleotide mutation rate increases close to indels in eukaryotes. Nature 455:105-108 | Sun X, Zhang Y, Yang S, Chen JQ, Hohn B, Tian D (2008) Insertion DNA promotes ectopic recombination during meiosis in Arabidopsis. Mol Biol Evol 25:2079-2083 | Araki H, Tian D, Goss EM, Jakob K, Halldorsdottir SS, Kreitman M and Bergelson J. (2006) Presence/absence polymorphism for alternative pathogenicity islands in Pseudomonas viridiflava, a pathogen of Arabidopsis. Proc Natl Acad Sci 103:5587-5892 | Shen J, Araki H, Chen L, Chen JQ, Tian D (2006) Unique evolutionary mechanism in R-genes under the presence/absence polymorphism in Arabidopsis thaliana. Genetics 172 (2):1243-50 | Tian D, Shaw B, Chen J, Kreitman M, Bergelson J (2003) Fitness cost of R-gene mediated resistance in Arabidopsis thaliana. Nature 424:74-77 | Mauricio R, Stahl E, Korves T, Tian D, Kreitman M & Bergelson J (2003) Natural selection for polymorphism in the disease resistance gene RPS2 of Arabidopsis. Genetics 163(2):735-746 | Tian D, Akashi H, Stahl E, Bergelson J, Kreitman M (2002) Signature of balancing selection in Arabidopsis. Proc Natl Acad Sci 99:11525-1153 | Bergelson J, Kreitman M, Stahl E, Tian D (2001) Evolutionary dynamics of plant R-genes. Science 292:2281-2285 | |
| Other Publications |
Jia X, Yu L, Tang M, Tian D, Yang S, Zhang X* & Traw MB* (2020) Pleiotropic Changes Revealed by in Situ Recovery of the Semi-Dwarf Gene Sd1 in Rice. Journal of Plant Physiology 248(May):153141. doi:10.1016/j.jplph.2020.153141.
| Jiang M, Hu H, Kai J, Traw MB, Yang S* & Zhang X*. (2019). Different Knockout Genotypes of OsIAA23 in Rice Using CRISPR/Cas9 Generating Different Phenotypes. Plant Mol Biol 100(4):467–479. doi:10.1007/s11103-019-00871-5.
| Zhang Y, Li S, Xue S, Yang S, Huang J* & Wang L*. (2018) Phylogenetic and CRISPR/Cas9 Studies in Deciphering the Evolutionary Trajectory and Phenotypic Impacts of Rice ERECTA Genes. Frontiers in Plant Science 9(473)
| Yuan Y, Zhang Q, Zeng S, Gu L, Si W, Zhang X, Tian D, Yang S* & Wang L*. (2017) Selective Sweep with Significant Positive Selection Serves as the Driving Force for the Differentiation of Japonica and Indica Rice Cultivars. BMC Genomics 18:307
| Sun XQ, Li DH, Xue JY, Yang SH, Zhang YM, Li MM, Hang Y. (2016) Insertion DNA accelerates meiotic inerchromosomal recombination in Arabidopsis thaliana. Mol Biol Evol 33:2044-53
| Guo C, Du J, Wang L, Yang S, Mauricio R, Tian D, Gu T*. (2016) Insertions/deletions-associated nucleotide polymorphism in Arabidopsis thaliana. Frontiers in Plant Science 7:1792
| Guo C, Sun X, Chen X, Yang S, Li J, Wang L, Zhang X. (2015) Novel rice blast resistance genes cloning from two rapidly evolving NBS-LRR gene families in rice. Plant Mol Biol 90: 95-105 | Li J, Zhou J, Wu, Y, Yang S, Tian D*. (2015) GC-content of synonymous codons profoundly infulences amino acid usage. G3 : Genes|Genomes|Genetics 5(10):2027-36 | Zhao L, Zhang Q, Gao R, Yang S, Liu H, Zhang X. (2015) High genetic abundance of Rpi-blb2/Mi-1.2/Cami gene family in Solanaceae. BMC Evol Biol 15:215 | Gu L, Si W, Zhao L, Yang S*, Zhang X*. (2015) Dynamic evolution of NBS-LRR genes in bread wheat and its progenitors. Mol Genet Genomics 290:727-738 | Jia Y, Yuan Y. Zhang Y. Yang S*, Zhang X*. (2015) Extreme expansion of NBS-encoding genes in Rosaceae. BMC Genetics 16 : 48 | Xie Z, Si W, Gao R, Zhang X*, Yang S*. (2015) Ancient origins and rapid evolution of RB/Rpi-blb1 locus in Solanaceae. Mol Genet Genomics DOI: 10.1007/s00438-015-1068-9 | Liu H, Xie Z, Tan S, Zhang X*, Yang S* (2015) Relationship between Amino Acid Usage and Amino Acid Evolution in Primates. Gene 557: 182-187 | Huang J, Si W, Deng Q, Li P*, Yang S*. (2014) Rapid evolution of avirulence genes in rice blast fungus Magnaporthe oryzae. BMC Genetics 15:45 | Wang D, Guo CJ, Huang J, Yang S, Tian D*, Zhang X*. (2014) Allele-mining of rice blast resistance genes at AC134922 locus. BBRC 446(4):1085-90 | Zhong Y, Jia Y, Gao Y, Tian D, Yang S, Zhang X. (2013) Functional requirements driving the gene duplication in 12 Drosophila species. BMC Genomics 14:555 | Tan S, Zhong Y, Hou H, Yang S, Tian D. (2012) Variation of presence/absence genes among Arabidopsis populations. BMC Evol Biol 12:86 | Wang L, Si W, Yao Y, Tian D, Araki H. Yang S. (2012) Genome-wide survey of pseudogenes in 80 fully re-sequenced Arabidopsis thaliana accessions. Plos One 7(12): e51769 | Wu K, Xu T, Guo C, Zhang X, Yang S. (2012) Heterogeneous evolutionary rates of Pi2/9 genes in rice lines. BMC Genetics 13:73 | Li L, Memon S, Fan Y, Yang S, Tan S. (2012) Recent duplications drive the rapid diversification of trypsin genes in 12 Drosophila. Genetica 140: 297-305 | Tan S, Wang D, Ding J, Tian D, Zhang XH, Yang S. (2011) Adaptive evolution of Xa21 homologs in gramineae. Genteica 139:1465-1475 | Wang J, Zhang L, Li J, Lawton-Rauh A, Tian D. (2011) Unusual signatures of highly adaptable R-loci in closely-related Arabidopsis species.Gene 482:24–33 | Wang J, Tan SJ, Zhang L, Li P, Tian D. (2011) Co-Variation Among Major Classes of LRR-Encoding Genes in Two Pairs of Plant Species.J Mol Evol 72:498–509 | Wu Y, Yuan HZ, Tan SJ, Chen JQ, Tian D, Yang HW (2011) Increased complexity of gene structure and base composition in vertebrates.Journal of Genetics and Genomics 38: 297-305 | Zhang X, Wang L, Yuan Y, Tian D, Yang S. (2011) Rapid copy number expansion and recent recruitment of domains in S-receptor kinase-like genes contribute to the origin of self-incompatibility. FEBS J 278: 4323-4337 | Zhang X, Feng Y, Chen H, Tian D, Yang S, Chen J-Q (2011) Relative evolutionary rates of NBS-encoding genes revealed by soybean segmental duplication.Mol Genet Genomics 285: 79-90 | Yang H, Zhong Y, Peng C, Chen JQ, Tian D. (2010) Important role of indels in somatic mutations of human cancer genes. BMC Med Genet 11:128 | Yue J-X, Li J, Wang D, Araki H, Tian D, Yang S (2010) Genome-wide investigation reveals high evolutionary rates in annual plants. BMC Plant Biol 10: 242 | Li J, Ding J, Zhang W, Zhang Y, Tang P, Chen JQ, Tian D, Yang S. (2010) Unique pattern of number evolution in gramineous NBS-LRR genes. Mol Genet Genomics 283:427–438 | Chen Q, Han Z, Jiang H, Tian D, Yang S. (2010) Strong positive selection drives rapid diversification of R-genes in Arabidopsis relatives. J Mol Evol 70: 137-148 | Tang P, Zhang Y, Sun X, Tian D, Yang S, Ding J. (2010) Disease resistance signature of the leucine-rich repeat receptor-like kinase genes in four plant species. Plant Sci 179: 399-406 | Zhang Y, Wang J, Zhang X, Chen JQ, Tian D, Yang S. (2009) Genetic signature of rice domestication shown by a variety of genes. J Mol Evol 68:393-402 | Zhu L, Zhang Y, Zhang W, Yang S, Chen JQ, Tian D. (2009) Patterns of exon-intron architecture variation of genes in eukaryotic genomes. BMC Genomics 10:47 | Yang H, Wu Y, Feng J, Yang S, Tian D (2009) Evolutionary pattern of protein architecture in mammal and fruit fly genomes. Genomics 93:90-97 | Yang S, Gu T, Pan C, Feng Z, Ding J, Hang Y, Chen JQ, Tian D (2008) Genetic variation of NBS-LRR class resistance genes in rice lines. Theor Appl Genet 116:165-177 | Zhang W, Sun X, Yuan H, Araki H, Wang J, Tian D (2008) The pattern of insertion/deletion polymorphism in Arabidopsis thaliana. Mol Genet Genomics 280:351-361 | Yang S, Zhang X, Yue JX, Tian D, Chen JQ. (2008) Recent duplication dominates the expansion of the NBS-encoding genes in two woody species Mol Genet Genomics 280: 187-198 | Du J, Gu T, Tian H, Araki H, Yang YH, Tian D (2008) Grouped nucleotide polymorphism: A major contributor to genetic variation in Arabidopsis. Gene 426:1-6 | Ding J, Zhang W, Jing Z, Chen JQ, Tian D (2007) Unique pattern of R-gene variation within populations in Arabidopsis. Mol Genet Genomics 277:619-629 | Yang S, Jiang K, Araki H, Ding J, Yang Y, Tian D (2007) A molecular isolation mechanism associated with high intra-specific diversity in rice. Gene 394:87-95 | Ding J., Cheng H., Jin Q., Araki H., Yang Y, Tian D (2007) Contrasting patterns of evolution between allelic groups at a single locus in Arabidopsis. Genetica 29:235-242 | Ding J, Araki H, Wang Q, Zhang P, Chen JQ, Tian D (2007) Highly asymmetric rice genomes. BMC Genomics 8:154 | Jiang H, Wang C, Ping L, Tian D, Yang S. (2007) Pattern of LRR nucleotide variation in plant resistance genes. Plant Science 173:253-261 | Yang S, Feng Z, Zhang X, Jiang K, Jin X, Hang Y, Chen JQ, Tian D (2006) Genome-wide investigation on the genetic variations of rice disease resistance genes. Plant Mol Biol 62:181-193 | Zhou T, Wang Y, Chen JQ, Araki H, Jing Z, Jiang K, Shen J, Tian D (2004). Genome-wide identification of NBS genes in rice reveals significant expansion of divergent non-TIR NBS Genes. Mol Genet Genomics 271:402-415 | Tian D, Niu C & Rose R. (2002) DNA transfer by highly asymmetric somatic hybridisation in Medicago truncatula x Medicago rugosa and Medicago truncatula x Medicago scutellata. Theo Appl Genet 104:9-16 | Tian D, & Rose R (1999) Plant regeneration of asymmetric somatic hybrids between annual Medicago truncatula and Medicago scutellata. Plant Cell Report 18:989-996 | Tian D (1994) 杂交水稻制种高产栽培技术. 四川科技出版社 | Tian D (1991) 水稻异交栽培学. 四川科技出版社 | |
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