A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global … – Nature.com

Weischenfeldt, J., Symmons, O., Spitz, F. & Korbel, J. O. Phenotypic impact of genomic structural variation: insights from and for human disease. Nat. Rev. Genet. 14, 125138 (2013).

Article CAS PubMed Google Scholar

Alonge, M. et al. Major impacts of widespread structural variation on gene expression and crop improvement in tomato. Cell 182, 145161 e23 (2020).

Article CAS PubMed PubMed Central Google Scholar

Jiao, W. B. & Schneeberger, K. Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics. Nat. Commun. 11, 989 (2020).

Article CAS PubMed PubMed Central Google Scholar

Lian, Q. et al. The megabase-scale crossover landscape is largely independent of sequence divergence. Nat. Commun. 13, 3828 (2022).

Article CAS PubMed PubMed Central Google Scholar

Zapata, L. et al. Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms. Proc. Natl Acad. Sci. USA 113, E4052E4060 (2016).

Article CAS PubMed PubMed Central Google Scholar

Capilla-Perez, L. et al. The synaptonemal complex imposes crossover interference and heterochiasmy in Arabidopsis. Proc. Natl Acad. Sci. USA 118, e2023613118 (2021).

Article CAS PubMed PubMed Central Google Scholar

Durand, S. et al. Joint control of meiotic crossover patterning by the synaptonemal complex and HEI10 dosage. Nat. Commun. 13, 5999 (2022).

Article CAS PubMed PubMed Central Google Scholar

Schmidt, C. et al. Changing local recombination patterns in Arabidopsis by CRISPR/Cas mediated chromosome engineering. Nat. Commun. 11, 4418 (2020).

Article CAS PubMed PubMed Central Google Scholar

Lowry, D. B. & Willis, J. H. A widespread chromosomal inversion polymorphism contributes to a major life-history transition, local adaptation, and reproductive isolation. PLoS Biol. 8, e1000500 (2010).

Article PubMed PubMed Central Google Scholar

Lamichhaney, S. et al. Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax). Nat. Genet. 48, 8488 (2016).

Article CAS PubMed Google Scholar

Harringmeyer, O. S. & Hoekstra, H. E. Chromosomal inversion polymorphisms shape the genomic landscape of deer mice. Nat. Ecol. Evol. 6, 19651979 (2022).

Article PubMed PubMed Central Google Scholar

Tong, X. et al. High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation. Nat. Commun. 13, 5619 (2022).

Article CAS PubMed PubMed Central Google Scholar

Goel, M., Sun, H., Jiao, W. B. & Schneeberger, K. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biol. 20, 277 (2019).

Article PubMed PubMed Central Google Scholar

Nattestad, M. & Schatz, M. C. Assemblytics: a web analytics tool for the detection of variants from an assembly. Bioinformatics 32, 30213023 (2016).

Article CAS PubMed PubMed Central Google Scholar

Bayer, P. E., Golicz, A. A., Scheben, A., Batley, J. & Edwards, D. Plant pan-genomes are the new reference. Nat. Plants 6, 914920 (2020).

Article PubMed Google Scholar

De Coster, W., Weissensteiner, M. H. & Sedlazeck, F. J. Towards population-scale long-read sequencing. Nat. Rev. Genet. 22, 572587 (2021).

Article PubMed PubMed Central Google Scholar

Della Coletta, R., Qiu, Y., Ou, S., Hufford, M. B. & Hirsch, C. N. How the pan-genome is changing crop genomics and improvement. Genome Biol. 22, 3 (2021).

Article PubMed PubMed Central Google Scholar

Jayakodi, M., Schreiber, M., Stein, N. & Mascher, M. Building pan-genome infrastructures for crop plants and their use in association genetics. DNA Res. 28, dsaa030 (2021).

Article PubMed PubMed Central Google Scholar

Liu, Y. et al. Pan-genome of wild and cultivated soybeans. Cell 182, 162176 e13 (2020).

Article CAS PubMed Google Scholar

Gao, L. et al. The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nat. Genet. 51, 10441051 (2019).

Article CAS PubMed Google Scholar

Zhou, Y. et al. Graph pangenome captures missing heritability and empowers tomato breeding. Nature 606, 527534 (2022).

Article CAS PubMed PubMed Central Google Scholar

Tang, D. et al. Genome evolution and diversity of wild and cultivated potatoes. Nature 606, 535541 (2022).

Article CAS PubMed PubMed Central Google Scholar

Shang, L. et al. A super pan-genomic landscape of rice. Cell Res. 32, 878896 (2022).

Article CAS PubMed PubMed Central Google Scholar

Zhang, F. et al. Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes. Genome Res. 32, 853863 (2022).

PubMed PubMed Central Google Scholar

Qin, P. et al. Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations. Cell 184, 35423558 e16 (2021).

Article CAS PubMed Google Scholar

Hufford, M. B. et al. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science 373, 655662 (2021).

Article CAS PubMed PubMed Central Google Scholar

Jayakodi, M. et al. The barley pan-genome reveals the hidden legacy of mutation breeding. Nature 588, 284289 (2020).

Article CAS PubMed PubMed Central Google Scholar

Walkowiak, S. et al. Multiple wheat genomes reveal global variation in modern breeding. Nature 588, 277283 (2020).

Article CAS PubMed PubMed Central Google Scholar

Sun, X. et al. Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication. Nat. Genet. 52, 14231432 (2020).

Article CAS PubMed PubMed Central Google Scholar

Liao, W. W. et al. A draft human pangenome reference. Nature 617, 312324 (2023).

Article CAS PubMed PubMed Central Google Scholar

Vollger, M. R. et al. Increased mutation and gene conversion within human segmental duplications. Nature 617, 325334 (2023).

Article CAS PubMed PubMed Central Google Scholar

Initiative, A. G. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796815 (2000).

Article Google Scholar

Cao, J. et al. Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat. Genet. 43, 956963 (2011).

Article CAS PubMed Google Scholar

Gan, X. et al. Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 477, 419423 (2011).

Article CAS PubMed PubMed Central Google Scholar

The 1001 Genomes Consortium. 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell 166, 481491 (2016).

Durvasula, A. et al. African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana. Proc. Natl Acad. Sci. USA 114, 52135218 (2017).

Article CAS PubMed PubMed Central Google Scholar

Zou, Y. P. et al. Adaptation of Arabidopsis thaliana to the Yangtze River basin. Genome Biol. 18, 239 (2017).

Article PubMed PubMed Central Google Scholar

Goktay, M., Fulgione, A. & Hancock, A. M. A new catalog of structural variants in 1,301 A. thaliana lines from Africa, Eurasia, and North America reveals a signature of balancing selection at defense response genes. Mol. Biol. Evol. 38, 14981511 (2021).

Article PubMed Google Scholar

Horton, M. W. et al. Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. Nat. Genet. 44, 212216 (2012).

Article CAS PubMed PubMed Central Google Scholar

Frachon, L. et al. Intermediate degrees of synergistic pleiotropy drive adaptive evolution in ecological time. Nat. Ecol. Evol. 1, 15511561 (2017).

Article PubMed Google Scholar

Fransz, P. et al. Molecular, genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana. Plant J. 88, 159178 (2016).

Article CAS PubMed PubMed Central Google Scholar

Barragan, A. C. et al. A truncated singleton NLR causes hybrid necrosis in Arabidopsis thaliana. Mol. Biol. Evol. 38, 557574 (2021).

Article CAS PubMed Google Scholar

Michael, T. P. et al. High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell. Nat. Commun. 9, 541 (2018).

Article PubMed PubMed Central Google Scholar

Pucker, B. et al. A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set. PLoS ONE 14, e0216233 (2019).

Article CAS PubMed PubMed Central Google Scholar

Rabanal, F. A. et al. Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes. Nucleic Acids Res. 50, 1230912327 (2022).

Article CAS PubMed PubMed Central Google Scholar

Kang, M. et al. The pan-genome and local adaptation of Arabidopsis thaliana. Nat. Commun. 14, 6259 (2023).

Article CAS PubMed PubMed Central Google Scholar

Hagmann, J. et al. Century-scale methylome stability in a recently diverged Arabidopsis thaliana lineage. PLoS Genet. 11, e1004920 (2015).

Article PubMed PubMed Central Google Scholar

Anastasio, A. E. et al. Source verification of mis-identified Arabidopsis thaliana accessions. Plant J. 67, 554566 (2011).

Article CAS PubMed Google Scholar

Simon, M. et al. DNA fingerprinting and new tools for fine-scale discrimination of Arabidopsis thaliana accessions. Plant J. 69, 10941101 (2012).

Article CAS PubMed Google Scholar

Long, Q. et al. Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden. Nat. Genet. 45, 884890 (2013).

Article CAS PubMed PubMed Central Google Scholar

Sun, H., Ding, J., Piednoel, M. & Schneeberger, K. findGSE: estimating genome size variation within human and Arabidopsis using k-mer frequencies. Bioinformatics 34, 550557 (2018).

See more here:
A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global ... - Nature.com

Related Posts