Research

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.

Highlighted

Re-evaluating evidence for adaptive mutation rate variation

Wang L, Ho AT, Hurst LD, Yang S

Nature  ·  01 Jan 2023  ·  manual-wang-2023-reevaluating

All

2023

Re-evaluating evidence for adaptive mutation rate variation

Wang L, Ho AT, Hurst LD, Yang S

Nature  ·  01 Jan 2023  ·  manual-wang-2023-reevaluating

2022

In rice splice variants that restore the reading frame after frameshifting indel introduction are common, often induced by the indels and sometimes lead to organism-level rescue

Jia Y, Qin C, Traw MB, Chen X, He Y, Kai J, Yang S, Wang L, Hurst LD

PLOS Genetics  ·  01 Jan 2022  ·  manual-jia-2022-rice-splice

2021

Ancient rapid functional differentiation and fixation of the duplicated members in riceDofgenes after whole genome duplication

Luyao Yu, Shiying Ma, Xiaohui Zhang, Dacheng Tian, Sihai Yang, Xianqing Jia, Milton Brian Traw

The Plant Journal  ·  15 Oct 2021  ·  doi:10.1111/tpj.15516

Somatic Mutation Analysis in Salix suchowensis Reveals Early-Segregated Cell Lineages

Yifan Ren, Zhen He, Pingyu Liu, Brian Traw, Shucun Sun, Dacheng Tian, Sihai Yang, Yanxiao Jia, Long Wang

Molecular Biology and Evolution  ·  25 Sep 2021  ·  doi:10.1093/molbev/msab286

Mitotic gene conversion can be as important as meiotic conversion in driving genetic variability in plants and other species without early germline segregation

Jia X, Zhang Q, Jiang M, Huang J, Yu L, Traw MB, Tian D, Hurst LD, Yang S

PLoS Biol  ·  01 Jan 2021  ·  manual-jia-2021-mitotic-gene

2020

Repeat-induced point mutation in Neurospora crassa causes the highest known mutation rate and mutational burden of any cellular life

Long Wang, Yingying Sun, Xiaoguang Sun, Luyao Yu, Lan Xue, Zhen He, Ju Huang, Dacheng Tian, Laurence D. Hurst, Sihai Yang

Genome Biology  ·  16 Jun 2020  ·  doi:10.1186/s13059-020-02060-w

Pleiotropic changes revealed by in situ recovery of the semi-dwarf gene sd1 in rice

Xianqing Jia, Luyao Yu, Menglu Tang, Dacheng Tian, Sihai Yang, Xiaohui Zhang, M. Brian Traw

Journal of Plant Physiology  ·  01 May 2020  ·  doi:10.1016/j.jplph.2020.153141

Pleiotropic Changes Revealed by in Situ Recovery of the Semi-Dwarf Gene Sd1 in Rice

Jia X, Yu L, Tang M, Tian D, Yang S, Zhang X, Traw MB

Journal of Plant Physiology  ·  01 Jan 2020  ·  manual-jia-2020-pleiotropic-changes

CRISPR-based assessment of genomic structure in the conserved SQUAMOSA promoter-binding-like gene clusters in rice

Jiang M, He Y, Chen X, Zhang X, Guo Y, Yang S, Huang J, Traw M

Plant J  ·  01 Jan 2020  ·  manual-jiang-2020-crispr-based

2019

Large-scale identification and functional analysis of NLR genes in blast resistance in the Tetep rice genome sequence

Long Wang, Lina Zhao, Xiaohui Zhang, Qijun Zhang, Yanxiao Jia, Guan Wang, Simin Li, Dacheng Tian, Wen-Hsiung Li, Sihai Yang

Proceedings of the National Academy of Sciences  ·  26 Aug 2019  ·  doi:10.1073/pnas.1910229116

CRISPR-Based Assessment of Gene Specialization in the Gibberellin Metabolic Pathway in Rice

Xiao Chen, Xuejian Tian, Lan Xue, Xiaohui Zhang, Sihai Yang, M. Brian Traw, Ju Huang

Plant Physiology  ·  03 Jun 2019  ·  doi:10.1104/pp.19.00328

Different Knockout Genotypes of OsIAA23 in Rice Using CRISPR/Cas9 Generating Different Phenotypes

Jiang M, Hu H, Kai J, Traw MB, Yang S, Zhang X

Plant Mol Biol  ·  01 Jan 2019  ·  manual-jiang-2019-different-knockout

The architecture of intra-organism mutation rate variation in plants

Wang L, Ji Y, Hu Y, Hu H, Jia X, …, Yu L, Huang J, Yang S, Hurst LD, Tian D

PLOS Biology  ·  01 Jan 2019  ·  manual-chen-2019-architecture

2018

High‐resolution insight into recombination events at the SD1 locus in rice

Xianqing Jia, Yadong Zhang, Qijun Zhang, Qingyong Zhao, Milton Brian Traw, Long Wang, Dacheng Tian, Cailin Wang, Sihai Yang

The Plant Journal  ·  18 Dec 2018  ·  doi:10.1111/tpj.14154

Liriodendron genome sheds light on angiosperm phylogeny and species–pair differentiation

Jinhui Chen, Zhaodong Hao, Xuanmin Guang, Chenxi Zhao, Pengkai Wang, …, Qiang Gao, Ye Peng, Na Liu, Sihai Yang, Jisen Shi

Nature Plants  ·  17 Dec 2018  ·  doi:10.1038/s41477-018-0323-6

Phylogenetic and CRISPR/Cas9 Studies in Deciphering the Evolutionary Trajectory and Phenotypic Impacts of Rice ERECTA Genes

Zhang Y, Li S, Xue S, Yang S, Huang J, Wang L

Frontiers in Plant Science  ·  01 Jan 2018  ·  manual-zhang-2018-phylogenetic

Tetrad Analysis in Plants and Fungi Finds Large Differences in Gene Conversion Rates but No GC Bias

Liu H, Huang J, Sun X, Li J, Hu Y, Yu L, Liti G, Tian D, Hurst LD, Yang S

Nature Ecology & Evolution  ·  01 Jan 2018  ·  manual-liu-2018-tetrad-analysis

Identifying a Large Number of High-Yield Genes in Rice by Pedigree Analysis, Whole-Genome Sequencing, and CRISPR-Cas9 Gene Knockout

Huang J, Li J, Zhou J, Wang L, Yang S, Hurst LD, Li W-H, Tian D

PNAS  ·  01 Jan 2018  ·  manual-huang-2018-identifying

2017

Selective Sweep with Significant Positive Selection Serves as the Driving Force for the Differentiation of Japonica and Indica Rice Cultivars

Yuan Y, Zhang Q, Zeng S, Gu L, Si W, Zhang X, Tian D, Yang S, Wang L

BMC Genomics  ·  01 Jan 2017  ·  manual-yuan-2017-selective-sweep

Direct determination of the mutation rate in the bumblebee reveals evidence for weak recombination-associated mutation and an approximate rate constancy in insects

Liu H, Jia Y, Sun X, Tian D, Hurst LD, Yang S

Mol Biol Evol  ·  01 Jan 2017  ·  manual-liu-2017-direct-determination

2016

Insertions/deletions-associated nucleotide polymorphism in Arabidopsis thaliana

Guo C, Du J, Wang L, Yang S, Mauricio R, Tian D, Gu T

Frontiers in Plant Science  ·  01 Jan 2016  ·  manual-guo-2016-insertions-deletions

Insertion DNA accelerates meiotic inerchromosomal recombination in Arabidopsis thaliana

Sun XQ, Li DH, Xue JY, Yang SH, Zhang YM, Li MM, Hang Y

Mol Biol Evol  ·  01 Jan 2016  ·  manual-sun-2016-insertion-dna

Mutation rate analysis via parent-progeny sequencing of the perennial peach II: No evidence for recombination-associated mutation

Wang L, Zhang Y, Qing C, Tian D, Yang S, Hurst LD

P Roy Soc B-Biol Sci  ·  01 Jan 2016  ·  manual-wang-2016-mutation-rate-peach-ii

Mutation rate analysis via parent-progeny sequencing of the perennial peach I. A low rate in woody perennials and a higher mutagenicity in hybrids

Xie Z, Wang L, Wang L, Wang Z, Lu Z, Tian D, Yang S, Hurst LD

P Roy Soc B-Biol Sci  ·  01 Jan 2016  ·  manual-xie-2016-mutation-rate-peach-i

Dissimilar Manifestation of Heterosis in Super Hybrid Rice at Early-Tillering Stage under Nutrient-Deficient and Nutrient-Sufficient Condition

Gu L, Wu Y, Jiang M, Si W, Zhang X, Tian D, Yang S

Plant Physiol  ·  01 Jan 2016  ·  manual-gu-2016-dissimilar-manifestation

2015

Relationship between Amino Acid Usage and Amino Acid Evolution in Primates

Liu H, Xie Z, Tan S, Zhang X, Yang S

Gene  ·  01 Jan 2015  ·  manual-liu-2015-amino-acid-usage

Ancient origins and rapid evolution of RB/Rpi-blb1 locus in Solanaceae

Xie Z, Si W, Gao R, Zhang X, Yang S

Mol Genet Genomics  ·  01 Jan 2015  ·  manual-xie-2015-ancient-origins

Extreme expansion of NBS-encoding genes in Rosaceae

Jia Y, Yuan Y, Zhang Y, Yang S, Zhang X

BMC Genetics  ·  01 Jan 2015  ·  manual-jia-2015-extreme-expansion

Dynamic evolution of NBS-LRR genes in bread wheat and its progenitors

Gu L, Si W, Zhao L, Yang S, Zhang X

Mol Genet Genomics  ·  01 Jan 2015  ·  manual-gu-2015-dynamic-evolution-nbs-lrr

High genetic abundance of Rpi-blb2/Mi-1.2/Cami gene family in Solanaceae

Zhao L, Zhang Q, Gao R, Yang S, Liu H, Zhang X

BMC Evol Biol  ·  01 Jan 2015  ·  manual-zhao-2015-high-genetic-abundance

GC-content of synonymous codons profoundly infulences amino acid usage

Li J, Zhou J, Wu Y, Yang S, Tian D

G3 : Genes|Genomes|Genetics  ·  01 Jan 2015  ·  manual-li-2015-gc-content

Novel rice blast resistance genes cloning from two rapidly evolving NBS-LRR gene families in rice

Guo C, Sun X, Chen X, Yang S, Li J, Wang L, Zhang X

Plant Mol Biol  ·  01 Jan 2015  ·  manual-guo-2015-novel-rice-blast

Widely distributed hot and cold spots in meiotic recombination as shown by sequencing of rice F2 plants

Si W, Yuan Y, Huang J, Zhang X, Zhang Y, Zhang Y, Tian D, Wang C, Yang YH, Yang S

New Phytologist  ·  01 Jan 2015  ·  manual-si-2015-widely-distributed-hot-spots

Causes and consequences of crossing-over evidenced via a high-resolution recombinational landscape of the honey bee

Liu H, Zhang X, Huang J, Chen JQ, Tian D, Hurst LD, Yang S

Genome Biology  ·  01 Jan 2015  ·  manual-liu-2015-gene-conversion-honeybee

A genome-wide survey reveals abundant rice blast R-genes in resistant cultivars

Zhang X, Yang S, Wang J, Jia Y, Huang J, …, Gu L, Chen JQ, Pan QH, Bergelson J, Tian D

Plant J  ·  01 Jan 2015  ·  manual-zhang-2015-rice-blast-r-genes

Parent-progeny sequencing indicates higher mutation rates in heterozygotes

Yang S, Wang L, Huang J, Zhang X, Yuan Y, Chen J-Q, Hurst LD, Tian D

Nature  ·  01 Jan 2015  ·  manual-yang-2015-higher-mutation-rates

2014

Allele-mining of rice blast resistance genes at AC134922 locus

Wang D, Guo CJ, Huang J, Yang S, Tian D, Zhang X

BBRC  ·  01 Jan 2014  ·  manual-wang-2014-allele-mining

Rapid evolution of avirulence genes in rice blast fungus Magnaporthe oryzae

Huang J, Si W, Deng Q, Li P, Yang S

BMC Genetics  ·  01 Jan 2014  ·  manual-huang-2014-rapid-evolution

2013

Functional requirements driving the gene duplication in 12 Drosophila species

Zhong Y, Jia Y, Gao Y, Tian D, Yang S, Zhang X

BMC Genomics  ·  01 Jan 2013  ·  manual-zhong-2013-functional-requirements

Rapidly evolving R genes in diverse grass species confer resistance to rice blast disease

Yang S, Li J, Zhang X, Zhang Q, Huang J, Chen J-Q, Hartl DL, Tian D

PNAS  ·  01 Jan 2013  ·  manual-yang-2013-rapidly-evolving-r-genes

2012

Recent duplications drive the rapid diversification of trypsin genes in 12 Drosophila

Li L, Memon S, Fan Y, Yang S, Tan S

Genetica  ·  01 Jan 2012  ·  manual-li-2012-recent-duplications

Heterogeneous evolutionary rates of Pi2/9 genes in rice lines

Wu K, Xu T, Guo C, Zhang X, Yang S

BMC Genetics  ·  01 Jan 2012  ·  manual-wu-2012-heterogeneous-rates

Genome-wide survey of pseudogenes in 80 fully re-sequenced Arabidopsis thaliana accessions

Wang L, Si W, Yao Y, Tian D, Araki H, Yang S

Plos One  ·  01 Jan 2012  ·  manual-wang-2012-genome-wide

Variation of presence/absence genes among Arabidopsis populations

Tan S, Zhong Y, Hou H, Yang S, Tian D

BMC Evol Biol  ·  01 Jan 2012  ·  manual-tan-2012-variation-presence

Tracing the origin and evolutionary history of plant nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes

Yue J-X, Meyers BC, Chen J-Q, Tian D, Yang S

New Phytologist  ·  01 Jan 2012  ·  manual-yue-2012-tracing-origin

Great majority of recombination events in Arabidopsis are gene conversion events

Yang S, Yuan Y, Wang L, Li J, Wang W, Liu H, Chen JQ, Hurst LD, Tian D

PNAS  ·  01 Jan 2012  ·  manual-yang-2012-gene-conversion-events

2011

Relative evolutionary rates of NBS-encoding genes revealed by soybean segmental duplication

Zhang X, Feng Y, Chen H, Tian D, Yang S, Chen J-Q

Mol Genet Genomics  ·  01 Jan 2011  ·  manual-zhang-2011-relative-evolutionary-rates

Rapid copy number expansion and recent recruitment of domains in S-receptor kinase-like genes contribute to the origin of self-incompatibility

Zhang X, Wang L, Yuan Y, Tian D, Yang S

FEBS J  ·  01 Jan 2011  ·  manual-zhang-2011-rapid-copy-number

Increased complexity of gene structure and base composition in vertebrates

Wu Y, Yuan HZ, Tan SJ, Chen JQ, Tian D, Yang HW

Journal of Genetics and Genomics  ·  01 Jan 2011  ·  manual-wu-2011-increased-complexity

Co-Variation Among Major Classes of LRR-Encoding Genes in Two Pairs of Plant Species

Wang J, Tan SJ, Zhang L, Li P, Tian D

J Mol Evol  ·  01 Jan 2011  ·  manual-wang-2011-co-variation

Unusual signatures of highly adaptable R-loci in closely-related Arabidopsis species

Wang J, Zhang L, Li P, Tian D

Gene  ·  01 Jan 2011  ·  manual-wang-2011-unusual-signatures

Adaptive evolution of Xa21 homologs in gramineae

Tan S, Wang D, Ding J, Tian D, Zhang XH, Yang S

Genteica  ·  01 Jan 2011  ·  manual-tan-2011-adaptive-evolution

2010

Disease resistance signature of the leucine-rich repeat receptor-like kinase genes in four plant species

Tang P, Zhang Y, Sun X, Tian D, Yang S, Ding J

Plant Sci  ·  01 Jan 2010  ·  manual-tang-2010-disease-resistance-signature

Strong positive selection drives rapid diversification of R-genes in Arabidopsis relatives

Chen Q, Han Z, Jiang H, Tian D, Yang S

J Mol Evol  ·  01 Jan 2010  ·  manual-chen-2010-strong-positive-selection

Unique pattern of number evolution in gramineous NBS-LRR genes

Li J, Ding J, Zhang W, Zhang Y, Tang P, Chen JQ, Tian D, Yang S

Mol Genet Genomics  ·  01 Jan 2010  ·  manual-li-2010-unique-pattern-number

Genome-wide investigation reveals high evolutionary rates in annual plants

Yue J-X, Li J, Wang D, Araki H, Tian D, Yang S

BMC Plant Biol  ·  01 Jan 2010  ·  manual-yue-2010-genome-wide-investigation

Important role of indels in somatic mutations of human cancer genes

Yang H, Zhong Y, Peng C, Chen JQ, Tian D

BMC Med Genet  ·  01 Jan 2010  ·  manual-yang-2010-important-role-indels

Avoidance of long mononucleotide repeats in codon pair usage

Gu T, Tan S, Gou X, Araki H, Tian D

Genetics  ·  01 Jan 2010  ·  manual-gu-2010-avoidance-repeats

2009

Evolutionary pattern of protein architecture in mammal and fruit fly genomes

Yang H, Wu Y, Feng J, Yang S, Tian D

Genomics  ·  01 Jan 2009  ·  manual-yang-2009-evolutionary-pattern

Patterns of exon-intron architecture variation of genes in eukaryotic genomes

Zhu L, Zhang Y, Zhang W, Yang S, Chen JQ, Tian D

BMC Genomics  ·  01 Jan 2009  ·  manual-zhu-2009-patterns-exon-intron

Genetic signature of rice domestication shown by a variety of genes

Zhang Y, Wang J, Zhang X, Chen JQ, Tian D, Yang S

J Mol Evol  ·  01 Jan 2009  ·  manual-zhang-2009-genetic-signature

Variation in the ratio of nucleotide substitution and indel rates across genomes in mammals and bacteria

Chen JQ, Wu Y, Yang H, Bergelson J, Kreitman M, Tian D

Mol Biol Evol  ·  01 Jan 2009  ·  manual-chen-2009-variation-ratio

Genome-wide association between insertions/deletions and the nucleotide diversity in bacteria

Zhu L, Wang Q, Tang P, Araki H, Tian D

Mol Biol Evol  ·  01 Jan 2009  ·  manual-zhu-2009-genome-wide

2008

Grouped nucleotide polymorphism: A major contributor to genetic variation in Arabidopsis

Du J, Gu T, Tian H, Araki H, Yang YH, Tian D

Gene  ·  01 Jan 2008  ·  manual-du-2008-grouped-nucleotide

Recent duplication dominates the expansion of the NBS-encoding genes in two woody species

Yang S, Zhang X, Yue JX, Tian D, Chen JQ

Mol Genet Genomics  ·  01 Jan 2008  ·  manual-yang-2008-recent-duplication

The pattern of insertion/deletion polymorphism in Arabidopsis thaliana

Zhang W, Sun X, Yuan H, Araki H, Wang J, Tian D

Mol Genet Genomics  ·  01 Jan 2008  ·  manual-zhang-2008-pattern-insertion

Genetic variation of NBS-LRR class resistance genes in rice lines

Yang S, Gu T, Pan C, Feng Z, Ding J, Hang Y, Chen JQ, Tian D

Theor Appl Genet  ·  01 Jan 2008  ·  manual-yang-2008-genetic-variation

Insertion DNA promotes ectopic recombination during meiosis in Arabidopsis

Sun X, Zhang Y, Yang S, Chen JQ, Hohn B, Tian D

Mol Biol Evol  ·  01 Jan 2008  ·  manual-sun-2008-insertion-dna

Single-nucleotide mutation rate increases close to indels in eukaryotes

Tian D, Wang Q, Zhang P, Araki H, Yang S, Kreitman M, Nagylaki T, Hudson R, Bergelson J, Chen JQ

Nature  ·  01 Jan 2008  ·  manual-tian-2008-singlenucleotide-mutation

2007

Pattern of LRR nucleotide variation in plant resistance genes

Jiang H, Wang C, Ping L, Tian D, Yang S

Plant Science  ·  01 Jan 2007  ·  manual-jiang-2007-pattern-lrr

Highly asymmetric rice genomes

Ding J, Araki H, Wang Q, Zhang P, Chen JQ, Tian D

BMC Genomics  ·  01 Jan 2007  ·  manual-ding-2007-highly-asymmetric

Contrasting patterns of evolution between allelic groups at a single locus in Arabidopsis

Ding J, Araki H, Wang Q, Zhang P, Chen JQ, Tian D

Genetica  ·  01 Jan 2007  ·  manual-ding-2007-contrasting-patterns

A molecular isolation mechanism associated with high intra-specific diversity in rice

Yang S, Jiang K, Araki H, Ding J, Yang Y, Tian D

Gene  ·  01 Jan 2007  ·  manual-yang-2007-molecular-isolation

Unique pattern of R-gene variation within populations in Arabidopsis

Ding J, Zhang W, Jing Z, Chen JQ, Tian D

Mol Genet Genomics  ·  01 Jan 2007  ·  manual-ding-2007-unique-pattern

2006

Genome-wide investigation on the genetic variations of rice disease resistance genes

Yang S, Feng Z, Zhang X, Jiang K, Jin X, Hang Y, Chen JQ, Tian D

Plant Mol Biol  ·  01 Jan 2006  ·  manual-yang-2006-genome-wide-investigation

Unique evolutionary mechanism in R-genes under the presence/absence polymorphism in Arabidopsis thaliana

Shen J, Araki H, Chen L, Chen JQ, Tian D

Genetics  ·  01 Jan 2006  ·  manual-shen-2006-unique-evolutionary-mechanism

Presence/absence polymorphism for alternative pathogenicity islands in Pseudomonas viridiflava, a pathogen of Arabidopsis

Araki H, Tian D, Goss EM, Jakob K, Halldorsdottir SS, Kreitman M, Bergelson J

Proc Natl Acad Sci  ·  01 Jan 2006  ·  manual-arakai-2006-presence-absence

2004

Genome-wide identification of NBS genes in rice reveals significant expansion of divergent non-TIR NBS Genes

Zhou T, Wang Y, Chen JQ, Araki H, Jing Z, Jiang K, Shen J, Tian D

Mol Genet Genomics  ·  01 Jan 2004  ·  manual-zhou-2004-genome-wide-identification

2003

Natural selection for polymorphism in the disease resistance gene RPS2 of Arabidopsis

Mauricio R, Stahl E, Korves T, Tian D, Kreitman M, Bergelson J

Genetics  ·  01 Jan 2003  ·  manual-mauricio-2003-natural-selection

Fitness cost of R-gene mediated resistance in Arabidopsis thaliana

Tian D, Shaw B, Chen J, Kreitman M, Bergelson J

Nature  ·  01 Jan 2003  ·  manual-tian-2003-fitness-cost

2002

DNA transfer by highly asymmetric somatic hybridisation in Medicago truncatula x Medicago rugosa and Medicago truncatula x Medicago scutellata

Tian D, Niu C, Rose R

Theo Appl Genet  ·  01 Jan 2002  ·  manual-tian-2002-dna-transfer

Signature of balancing selection in Arabidopsis

Tian D, Akashi H, Stahl E, Bergelson J, Kreitman M

Proc Natl Acad Sci  ·  01 Jan 2002  ·  manual-tian-2002-signature-balancing

2001

Evolutionary dynamics of plant R-genes

Bergelson J, Kreitman M, Stahl E, Tian D

Science  ·  01 Jan 2001  ·  manual-bergelson-2001-evolutionary-dynamics

1999

Plant regeneration of asymmetric somatic hybrids between annual Medicago truncatula and Medicago scutellata

Tian D, Rose R

Plant Cell Report  ·  01 Jan 1999  ·  manual-tian-1999-plant-regeneration

1994

杂交水稻制种高产栽培技术

Tian D

四川科技出版社  ·  01 Jan 1994  ·  manual-tian-1994-hybrid-rice-cultivation

1991

水稻异交栽培学

Tian D

四川科技出版社  ·  01 Jan 1991  ·  manual-tian-1991-rice-cross-breeding