Works about PAN-genome

Results: 394

APAV: An advanced pangenome analysis and visualization toolkit.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 7, p. 1, doi. 10.1371/journal.pcbi.1013288

By:

Dong, Xiaorui;
Jiao, Du;
Xue, Hongzhang;
Fan, Shiyu;
Wei, Chaochun

Publication type:

Article

Homologous recombination and evolutionary arms race drive the adaptive evolution of African swine fever virus.

Published in:

Veterinary Research, 2025, v. 56, n. 1, p. 1, doi. 10.1186/s13567-025-01573-1

By:

Wang, Wenqiang;
Liu, Qinqiu;
Zhao, Qilin;
Zhu, Zhenbang;
Wen, Wei;
Zhang, Zhendong;
Li, Xiangdong

Publication type:

Article

Pairwise graph edit distance characterizes the impact of the construction method on pangenome graphs Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 6, p. 1, doi. 10.1093/bioinformatics/btaf291

By:

Dubois, Siegfried;
Zytnicki, Matthias;
Lemaitre, Claire;
Faraut, Thomas

Publication type:

Article

Genetic Diversity of Clinical Bordetella Pertussis ST2 Strains in comparison with Vaccine Reference Strains of India.

Published in:

Journal of Genomics, 2021, v. 9, p. 38, doi. 10.7150/jgen.58823

By:

Sharma, Naresh Chand;
Anandan, Shalini;
Devanga Ragupathi, Naveen Kumar;
Muthuirulandi Sethuvel, Dhiviya Prabaa;
Vasudevan, Karthick;
Kumar, Dhirendra;
Gupta, Sushil Kumar;
Sangal, Lucky;
Veeraraghavan, Balaji

Publication type:

Article

Analysis of Genome Sequences of Coagulase-Negative Staphylococci Isolates from South Africa and Nigeria Highlighted Environmentally Driven Heterogeneity.

Published in:

Journal of Genomics, 2021, v. 9, p. 26, doi. 10.7150/jgen.53019

By:

Maguvu, Tawanda Elias;
Oladipo, Adegboyega Oyedele;
Bezuidenhout, Cornelius Carlos

Publication type:

Article

Gossypium latifolium genome reveals the genetic basis of domestication of upland cotton from semi-wild races to cultivars.

Published in:

Crop Journal (2095-5421), 2025, v. 13, n. 3, p. 929, doi. 10.1016/j.cj.2025.02.014

By:

Chao Fu;
Nian Wang;
Qingying Meng;
Zhiyong Xu;
Yu Le;
Xianlong Zhang;
Yangyang Wei;
Renhai Peng;
Chao Shen;
Zhongxu Lin

Publication type:

Article

Genetic Analysis of Lodging Resistance in 1892S Based on the T2T Genome: Providing a Genetic Approach for the Improvement of Two-Line Hybrid Rice Varieties.

Published in:

Plants (2223-7747), 2025, v. 14, n. 12, p. 1873, doi. 10.3390/plants14121873

By:

Zhang, Wei;
Zhou, Liang;
Ni, Dahu;
Ni, Jinlong;
Song, Fengshun;
Yang, Liansong;
Zhang, Dewen

Publication type:

Article

Comparative Genomics Reveals Intra and Inter Species Variation in the Pathogenic Fungus Batrachochytrium dendrobatidisOpen Access.

Published in:

Genome Biology & Evolution, 2025, v. 17, n. 6, p. 1, doi. 10.1093/gbe/evaf114

By:

Yacoub, Mark N;
Stajich, Jason E

Publication type:

Article

Benchmarking pangenome dynamics and horizontal gene transfer in Mycobacterium marinum evolution.

Published in:

Frontiers in Microbiology, 2025, p. 1, doi. 10.3389/fmicb.2025.1537826

By:

Shahed, Khandker;
Islam, Sk Injamamul;
Sangsawad, Papungkorn;
Jung, Won-Kyo;
Permpoonpattana, Patima;
Linh, Nguyen Vu

Publication type:

Article

Phage-encoded enzymes found in Acinetobacter baumannii convert pseudaminic acid to 8-epipseudaminic acid.

Published in:

Communications Biology, 2025, v. 8, n. 1, p. 1, doi. 10.1038/s42003-025-08114-8

By:

Sharar, Nowshin S.;
Iovine, Andrea;
De Castro, Cristina;
Hall, Ruth M.;
Kenyon, Johanna J.

Publication type:

Article

Constructing a draft Indian cattle pangenome using short-read sequencing.

Published in:

Communications Biology, 2025, v. 8, n. 1, p. 1, doi. 10.1038/s42003-025-07978-0

By:

Azam, Sarwar;
Sahu, Abhisek;
Pandey, Naveen Kumar;
Neupane, Mahesh;
Van Tassell, Curtis P.;
Rosen, Benjamin D.;
Gandham, Ravi Kumar;
Rath, Subha Narayan;
Majumdar, Subeer S.

Publication type:

Article

The pan-genome of Spodoptera frugiperda provides new insights into genome evolution and horizontal gene transfer.

Published in:

Communications Biology, 2025, v. 8, n. 1, p. 1, doi. 10.1038/s42003-025-07707-7

By:

Huang, Yi-Xin;
Rao, He-Yan;
Su, Bao-Shan;
Lv, Ji-Mu;
Lin, Jun-Jie;
Wang, Xu;
Xu, Li-Na;
Kong, Xiang-Dong;
Sun, Yang

Publication type:

Article

Repeat-induced point mutations driving Parastagonospora nodorum genomic diversity are balanced by selection against non-synonymous mutations.

Published in:

Communications Biology, 2024, v. 7, n. 1, p. 1, doi. 10.1038/s42003-024-07327-7

By:

Jones, Darcy A. B.;
Rybak, Kasia;
Hossain, Mohitul;
Bertazzoni, Stefania;
Williams, Angela;
Tan, Kar-Chun;
Phan, Huyen T. T.;
Hane, James K.

Publication type:

Article

Correction to: Female space use correlates with extra-pair mating in barn swallow replacement clutches.

Published in:

2025

By:

Kenny-Duddela, Heather V.;
Schield, Drew R.;
Keller, Kayleigh P.;
Safran, Rebecca J.

Publication type:

Correction Notice

Trio-binning Assemblies of the Duroc and Landrace swine breeds.

Published in:

2024

By:

Ackerson, Leland K.;
Kuhn, Kristen;
Gondro, Cedric;
Jicai Jiang;
Maltecca, Christian;
Rohrer, Gary A.;
Rosen, Benjamin D.;
Smith, Timothy;
Tuggle, Christopher K.;
Wen Huang

Publication type:

Abstract

The Power of Pangenome Assemblies in Ruminants.

Published in:

Journal of Animal Science, 2023, v. 101, p. 47, doi. 10.1093/jas/skad281.057

By:

Murdoch, Brenda M.;
Rosen, Benjamin D.;
McKay, Stephanie;
Smith, Timothy

Publication type:

Article

New insights into the novel sequences of the chicken pan-genome by liquid chip.

Published in:

Journal of Animal Science, 2022, v. 100, n. 12, p. 1, doi. 10.1093/jas/skac336

By:

Wang, Fei;
Guo, Yingwei;
Liu, Zhenyu;
Wang, Qiao;
Jiang, Yu;
Zhao, Guiping

Publication type:

Article

RicePilaf: a post-GWAS/QTL dashboard to integrate pangenomic, coexpression, regulatory, epigenomic, ontology, pathway, and text-mining information to provide functional insights into rice QTLs and GWAS loci.

Published in:

GigaScience, 2024, v. 13, n. 1, p. 1, doi. 10.1093/gigascience/giae013

By:

Shrestha, Anish M S;
Gonzales, Mark Edward M;
Ong, Phoebe Clare L;
Larmande, Pierre;
Lee, Hyun-Sook;
Jeung, Ji-Ung;
Kohli, Ajay;
Chebotarov, Dmytro;
Mauleon, Ramil P;
Lee, Jae-Sung;
McNally, Kenneth L

Publication type:

Article

Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data.

Published in:

GigaScience, 2024, v. 13, n. 1, p. 1, doi. 10.1093/gigascience/giae010

By:

Hall, Michael B;
Coin, Lachlan J M

Publication type:

Article

Genome assembly of Musa beccarii shows extensive chromosomal rearrangements and genome expansion during evolution of Musaceae genomes.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad005

By:

Wang, Zheng-Feng;
Rouard, Mathieu;
Droc, Gaetan;
Heslop-Harrison, Pat (J S);
Ge, Xue-Jun

Publication type:

Article

The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features.

Published in:

GigaScience, 2022, v. 11, p. 1, doi. 10.1093/gigascience/giac028

By:

Qi, Weihong;
Lim, Yi-Wen;
Patrignani, Andrea;
Schläpfer, Pascal;
Bratus-Neuenschwander, Anna;
Grüter, Simon;
Chanez, Christelle;
Rodde, Nathalie;
Prat, Elisa;
Vautrin, Sonia;
Fustier, Margaux-Alison;
Pratas, Diogo;
Schlapbach, Ralph;
Gruissem, Wilhelm

Publication type:

Article

A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae.

Published in:

GigaScience, 2022, v. 11, p. 1, doi. 10.1093/gigascience/giac027

By:

Wang, Ziwei;
Rouard, Mathieu;
Biswas, Manosh Kumar;
Droc, Gaetan;
Cui, Dongli;
Roux, Nicolas;
Baurens, Franc-Christophe;
Ge, Xue-Jun;
Schwarzacher, Trude;
Heslop-Harrison, Pat (J S);
Liu, Qing

Publication type:

Article

Genome evolution and diversity of wild and cultivated rice species.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-54427-3

By:

Long, Weixiong;
He, Qiang;
Wang, Yitao;
Wang, Yu;
Wang, Jie;
Yuan, Zhengqing;
Wang, Meijia;
Chen, Wei;
Luo, Lihua;
Luo, Laiyang;
Xu, Weibiao;
Li, Yonghui;
Li, Wei;
Yan, Longan;
Cai, Yaohui;
Du, Huilong;
Xie, Hongwei

Publication type:

Article

Analyzes of pan-genome and resequencing atlas unveil the genetic basis of jujube domestication.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-53718-z

By:

Guo, Mingxin;
Lian, Qun;
Mei, Ye;
Yang, Wangwang;
Zhao, Suna;
Zhang, Siyuan;
Xing, Xinfeng;
Zhang, Haixiang;
Gao, Keying;
He, Wentong;
Wang, Zhitong;
Wang, Huan;
Zhou, Jun;
Cheng, Lin;
Bao, Zhigui;
Huang, Sanwen;
Yan, Jianbin;
Zhao, Xusheng

Publication type:

Article

A unified framework to analyze transposable element insertion polymorphisms using graph genomes.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-53294-2

By:

Groza, Cristian;
Chen, Xun;
Wheeler, Travis J.;
Bourque, Guillaume;
Goubert, Clément

Publication type:

Article

Haplotype-based pangenomes reveal genetic variations and climate adaptations in moso bamboo populations.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-52376-5

By:

Hou, Yinguang;
Gan, Junwei;
Fan, Zeyu;
Sun, Lei;
Garg, Vanika;
Wang, Yu;
Li, Shanying;
Bao, Pengfei;
Cao, Bingchen;
Varshney, Rajeev K.;
Zhao, Hansheng

Publication type:

Article

Evolutionary dynamics of the successful expansion of pandemic Vibrio parahaemolyticus ST3 in Latin America.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-52159-y

By:

Campbell, Amy Marie;
Gavilan, Ronnie G.;
Abanto Marin, Michel;
Yang, Chao;
Hauton, Chris;
van Aerle, Ronny;
Martinez-Urtaza, Jaime

Publication type:

Article

Evolutionary dynamics of the successful expansion of pandemic Vibrio parahaemolyticus ST3 in Latin America.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-52159-y

By:

Campbell, Amy Marie;
Gavilan, Ronnie G.;
Abanto Marin, Michel;
Yang, Chao;
Hauton, Chris;
van Aerle, Ronny;
Martinez-Urtaza, Jaime

Publication type:

Article

The pan-tandem repeat map highlights multiallelic variants underlying gene expression and agronomic traits in rice.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-51854-0

By:

He, Huiying;
Leng, Yue;
Cao, Xinglan;
Zhu, Yiwang;
Li, Xiaoxia;
Yuan, Qiaoling;
Zhang, Bin;
He, Wenchuang;
Wei, Hua;
Liu, Xiangpei;
Xu, Qiang;
Guo, Mingliang;
Zhang, Hong;
Yang, Longbo;
Lv, Yang;
Wang, Xianmeng;
Shi, Chuanlin;
Zhang, Zhipeng;
Chen, Wu;
Zhang, Bintao

Publication type:

Article

Adaptive gene loss in the common bean pan-genome during range expansion and domestication.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-51032-2

By:

Cortinovis, Gaia;
Vincenzi, Leonardo;
Anderson, Robyn;
Marturano, Giovanni;
Marsh, Jacob Ian;
Bayer, Philipp Emanuel;
Rocchetti, Lorenzo;
Frascarelli, Giulia;
Lanzavecchia, Giovanna;
Pieri, Alice;
Benazzo, Andrea;
Bellucci, Elisa;
Di Vittori, Valerio;
Nanni, Laura;
Ferreira Fernández, Juan José;
Rossato, Marzia;
Aguilar, Orlando Mario;
Morrell, Peter Laurent;
Rodriguez, Monica;
Gioia, Tania

Publication type:

Article

Impact of whole-genome duplications on structural variant evolution in Cochlearia.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-49679-y

By:

Hämälä, Tuomas;
Moore, Christopher;
Cowan, Laura;
Carlile, Matthew;
Gopaulchan, David;
Brandrud, Marie K.;
Birkeland, Siri;
Loose, Matthew;
Kolář, Filip;
Koch, Marcus A.;
Yant, Levi

Publication type:

Article

euka : Robust tetrapodic and arthropodic taxa detection from modern and ancient environmental DNA using pangenomic reference graphs.

Published in:

Methods in Ecology & Evolution, 2023, v. 14, n. 11, p. 2717, doi. 10.1111/2041-210X.14214

By:

Vogel, Nicola Alexandra;
Rubin, Joshua Daniel;
Swartz, Mikkel;
Vlieghe, Juliette;
Sackett, Peter Wad;
Pedersen, Anders Gorm;
Pedersen, Mikkel Winther;
Renaud, Gabriel

Publication type:

Article

Pseudomonas Phage Lydia and the Evolution of the Mesyanzhinovviridae Family.

Published in:

Viruses (1999-4915), 2025, v. 17, n. 3, p. 369, doi. 10.3390/v17030369

By:

Troshin, Konstantin;
Sykilinda, Nina;
Shuraleva, Sofia;
Tokmakova, Anna;
Tkachenko, Nikolay;
Kurochkina, Lidia;
Miroshnikov, Konstantin;
Suzina, Natalia;
Brzhozovskaya, Ekaterina;
Petrova, Kristina;
Toshchakov, Stepan;
Evseev, Peter

Publication type:

Article

Genome Analysis of Anti-Phage Defense Systems and Defense Islands in Stenotrophomonas maltophilia : Preservation and Variability.

Published in:

Viruses (1999-4915), 2024, v. 16, n. 12, p. 1903, doi. 10.3390/v16121903

By:

Jdeed, Ghadeer;
Morozova, Vera V.;
Tikunova, Nina V.

Publication type:

Article

Redefining genomic view of Clostridioides difficile through pangenome analysis and identification of drug targets from its core genome.

Published in:

Drug Target Insights, 2022, v. 16, n. 1, p. 17, doi. 10.33393/dti.2022.2469

By:

Golchha, Nikita Chordia;
Nighojkar, Anand;
Nighojkar, Sadhana

Publication type:

Article

Complete genome sequence analysis and Pks genes identification of Brevibacillus brevis FJAT-0809-GLX with a broad inhibitory spectrum against phytopathogens.

Published in:

World Journal of Microbiology & Biotechnology, 2024, v. 40, n. 11, p. 1, doi. 10.1007/s11274-024-04139-z

By:

Che, Jianmei;
Lai, Chengchun;
Lai, Gongti;
Chen, Bingxing;
He, Liyuan;
Liu, Bo

Publication type:

Article

Population genomics of Lacticaseibacillus paracasei: pan-genome, integrated prophage, antibiotic resistance, and carbohydrate utilization.

Published in:

World Journal of Microbiology & Biotechnology, 2023, v. 39, n. 10, p. 1, doi. 10.1007/s11274-023-03722-0

By:

Pei, Zhangming;
Li, Xiaoshu;
Cui, Shumao;
Yang, Bo;
Lu, Wenwei;
Zhao, Jianxin;
Mao, Bingyong;
Chen, Wei

Publication type:

Article

Genome-wide survey of KT/HAK/KUP genes in the genus Citrullus and analysis of their involvement in K<sup>+</sup>-deficiency and drought stress responses in between C. lanatus and C. amarus.

Published in:

BMC Genomics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12864-024-10712-5

By:

Cheng, Rui;
Zhao, Zhengxiang;
Tang, Yan;
Gu, Yan;
Chen, Guodong;
Sun, Yudong;
Wang, Xuezheng

Publication type:

Article

Elucidating the biotechnological potential of the genera Parageobacillus and Saccharococcus through comparative genomic and pan-genome analysis.

Published in:

BMC Genomics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12864-024-10635-1

By:

Mol, Michael;
de Maayer, Pieter

Publication type:

Article

Pangenome analysis of Shewanella xiamenensis revealed important genetic traits concerning genetic diversity, pathogenicity and antibiotic resistance.

Published in:

BMC Genomics, 2024, v. 25, p. 1, doi. 10.1186/s12864-024-10146-z

By:

Wang, Haichen;
Xia, Fengjun;
Xia, Yubing;
Li, Jun;
Hu, Yongmei;
Deng, Yating;
Zou, Mingxiang

Publication type:

Article

Multiple variation patterns of terpene synthases in 26 maize genomes.

Published in:

BMC Genomics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12864-023-09137-3

By:

Sun, Yang;
Xiao, Wenqing;
Wang, Qing-nan;
Wang, Jing;
Kong, Xiang-dong;
Ma, Wen-hui;
Liu, Si-xian;
Ren, Ping;
Xu, Li-na;
Zhang, Yong-Jun

Publication type:

Article

Genome analysis of haloalkaline isolates from the soda saline crater lake of Isabel Island; comparative genomics and potential metabolic analysis within the genus Halomonas.

Published in:

BMC Genomics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12864-023-09800-9

By:

Hernández-Soto, Luis Mario;
Martínez-Abarca, Francisco;
Ramírez-Saad, Hugo;
López-Pérez, Marcos;
Aguirre-Garrido, José Félix

Publication type:

Article

The pan-genome of Mycobacterium avium subsp. paratuberculosis (Map) confirms ancestral lineage and reveals gene rearrangements within Map Type S.

Published in:

BMC Genomics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12864-023-09752-0

By:

Hodgeman, Rachel;
Mann, Rachel;
Djitro, Noel;
Savin, Keith;
Rochfort, Simone;
Rodoni, Brendan

Publication type:

Article

Genomic characterization and comparative genomic analysis of HS-associated Pasteurella multocida serotype B:2 strains from Pakistan.

Published in:

BMC Genomics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12864-023-09626-5

By:

Mahboob, Sadia;
Ullah, Nimat;
Farhan Ul Haque, Muhammad;
Rauf, Waqar;
Iqbal, Mazhar;
Ali, Amjad;
Rahman, Moazur

Publication type:

Article

Effectidor II: a pan-genomic AI-based algorithm for the prediction of type III secretion system effectors Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf272

By:

Wagner, Naama;
Baumer, Ella;
Lyubman, Iris;
Shimony, Yair;
Bracha, Noam;
Martins, Leonor;
Potnis, Neha;
Chang, Jeff H;
Teper, Doron;
Koebnik, Ralf;
Pupko, Tal

Publication type:

Article

Pitfalls of bacterial pan-genome analysis approaches: a case study of Mycobacterium tuberculosis and two less clonal bacterial species Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf219

By:

Marin, Maximillian G;
Quinones-Olvera, Natalia;
Wippel, Christoph;
Behruznia, Mahboobeh;
Jeffrey, Brendan M;
Harris, Michael;
Mann, Brendon C;
Rosenthal, Alex;
Jacobson, Karen R;
Warren, Robin M;
Li, Heng;
Meehan, Conor J;
Farhat, Maha R

Publication type:

Article

Generating multiple alignments on a pangenomic scale.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf104

By:

Olbrich, Jannik;
Büchler, Thomas;
Ohlebusch, Enno

Publication type:

Article

Fast and exact gap-affine partial order alignment with POASTA.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae757

By:

Dijk, Lucas R van;
Manson, Abigail L;
Earl, Ashlee M;
Garimella, Kiran V;
Abeel, Thomas

Publication type:

Article

SCARAP: scalable cross-species comparative genomics of prokaryotes.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae735

By:

Wittouck, Stijn;
Eilers, Tom;
Noort, Vera van;
Lebeer, Sarah

Publication type:

Article

Panacus: fast and exact pangenome growth and core size estimation.

Published in:

Bioinformatics, 2024, v. 40, n. 12, p. 1, doi. 10.1093/bioinformatics/btae720

By:

Parmigiani, Luca;
Garrison, Erik;
Stoye, Jens;
Marschall, Tobias;
Doerr, Daniel

Publication type:

Article