Unbiased anchors for reliable genome-wide synteny detection.

Authors: Käther, Karl K.^1,2 (AUTHOR) karl@bioinf.uni-leipzig.de, Remmel, Andreas^2,3 (AUTHOR) andreas.remmel@cos.uni-heidelberg.de, Lemke, Steffen^2,3 (AUTHOR) steffen.lemke@uni-hohenheim.de, Stadler, Peter F.^1,2,4,5,6,7 (AUTHOR) studla@bioinf.uni-leipzig.de

Source: Algorithms for Molecular Biology. 4/5/2025, Vol. 20 Issue 1, p1-12. 12p.

Subject Terms: *COMPARATIVE genomics, *LIFE sciences, *GENOMES, *GENETICS, *LOCUS (Genetics)

Structural and Functional Characterization of a Putative Type VI Secretion System Protein in Cronobacter sakazakii as a Potential Therapeutic Target: A Computational Study.

Authors: Akter, Nurun Nahar¹ (AUTHOR), Uddin, Md. Moin² (AUTHOR), Uddin, Nesar³ (AUTHOR), Asha, Israt Jahan¹ (AUTHOR), Uddin, Md Soyeb⁴ (AUTHOR), Hossain, Md. Arju⁵ (AUTHOR), Alam, Fahadul⁶ (AUTHOR), Shifat, Siratul Kubra⁷ (AUTHOR), Zihad, Md. Abu⁸ (AUTHOR), Rahman, Md Habibur^9,10 (AUTHOR) habib@iu.ac.bd

Source: Evolutionary Bioinformatics. 3/31/2025, p1-17. 17p.

Subject Terms: *BACTERIAL proteins, *COMPARATIVE genomics, *BACTERIAL genomes, *PROTEIN-protein interactions, *PROTEIN structure

Phylogenetic analysis of Asiatic species in the tropical genus Beilschmiedia (Lauraceae).

Authors: Zhu, Wen¹ (AUTHOR), Ma, Jurong² (AUTHOR), Tan, Yunhong³ (AUTHOR) tyh@xtbg.org.cn, Song, Yu² (AUTHOR) songyu@gxnu.edu.cn, Xin, Peiyao¹ (AUTHOR) xpytgyx@163.com

Source: BMC Genomics. 3/8/2025, Vol. 26 Issue 1, p1-13. 13p.

Subject Terms: *MICROSATELLITE repeats, *COMPARATIVE genomics, *TROPICAL forests, *LIFE sciences, *BAYESIAN field theory, *CHLOROPLAST DNA

Tracing the path from conservation to expansion evolutionary insights into NLR genes in oleaceae.

Authors: Parvez, Saba¹ (AUTHOR), Asif, Maryam¹ (AUTHOR), Ahmad, Alizay¹ (AUTHOR), Javaid, Iqra¹ (AUTHOR), Rasheed, Muhammad Zaman¹ (AUTHOR), Iftikhar, Romana¹ (AUTHOR), Aljarba, Nada H.² (AUTHOR), Zafar, Rabia¹ (AUTHOR), sarwar, Aqsa¹ (AUTHOR), Khan, Rao Sohail Ahmed¹ (AUTHOR), Serfraz, Saad¹ (AUTHOR) serfraz.saad@gmail.com

Source: BMC Plant Biology. 2/26/2025, Vol. 25 Issue 1, p1-16. 16p.

Subject Terms: *COMPARATIVE genomics, *ASH (Tree), *CONSERVATION genetics, *LIFE sciences, *OLEACEAE

Discovery of Evolutionary Loss of the Ubiquitin-like Autophagy-Related ATG12 System in a Lineage of Apicomplexa.

Authors: Lin, Xiaoxia X.¹ (AUTHOR) lxx870611@yahoo.co.jp, Bai, Yun D.¹ (AUTHOR) baiyun426@yeah.net, Wang, Sichang T.¹ (AUTHOR) 23fm0104@student.gs.chiba-u.jp, Nozawa, Akira² (AUTHOR) nozawa.akira.my@ehime-u.ac.jp, Sawasaki, Tatsuya² (AUTHOR) sawasaki.tatsuya.mf@ehime-u.ac.jp, Masatani, Tatsunori^3,4,5 (AUTHOR) masatani.tatsunori.j9@f.gifu-u.ac.jp, Hikosaka, Kenji¹ (AUTHOR) hikosaka@chiba-u.jp, Asada, Masahito⁶ (AUTHOR) masada@obihiro.ac.jp, Sakamoto, Hirokazu¹ (AUTHOR) hzsakamoto@chiba-u.jp

Source: Cells (2073-4409). Jan2025, Vol. 14 Issue 2, p121. 15p.

Subject Terms: *COMPARATIVE genomics, *RECOMBINANT proteins, *COVALENT bonds, *FUNCTIONAL analysis, *APICOMPLEXA, *BABESIA

Genomic characteristics and genetic manipulation of the marine yeast Scheffersomyces spartinae.

Authors: Sharma, Awkash¹, Liu, Xing¹, Yin, Jun¹, Yu, Pei-Jing¹, Qi, Lei¹, He, Min¹, Li, Ke-Jing¹, 22034192@zju.edu.cn, Zheng, Dao-Qiong¹, zhengdaoqiong@zju.edu.cn

Source: Applied Microbiology & Biotechnology; 12/19/2024, Vol. 108 Issue 1, p1-14, 14p

Assessment of the whole genome sequencing of Lactiplantibacillus plantarum 13-3 for elucidation of novel bacteriocin producing gene cluster and confirmation of its potential probiotic functionality and safety applications.

Authors: Aziz, Tariq^1,2 (AUTHOR) iwockd@gmail.com, Naveed, Muhammad³ (AUTHOR), Shabbir, Muhammad Aqib^3,4 (AUTHOR), Khan, Ayaz Ali⁵ (AUTHOR), Sarwar, Abid¹ (AUTHOR), Haq, Taqweem Ul⁵ (AUTHOR), Zhennai, Yang¹ (AUTHOR) yangzhennai@163.com, Alharbi, Metab⁶ (AUTHOR), Alasmari, Abdullah F.⁶ (AUTHOR), Albekairi, Thamer H.⁶ (AUTHOR)

Source: CyTA: Journal of Food. 2024, Vol. 22 Issue 1, p1-10. 10p.

Subject Terms: *BIOTECHNOLOGY, *COMPARATIVE genomics, *WHOLE genome sequencing, *GENE clusters, *PAN-genome

Chromosome level assemblies of Nakaseomyces (Candida) bracarensis uncover two distinct clades and define its adhesin repertoire.

Authors: Marcet-Houben, Marina^1,2,3 (AUTHOR), Księżopolska, Ewa^1,2,3 (AUTHOR), Gabaldón, Toni^1,2,3,4 (AUTHOR) toni.gabaldon@bsc.es

Source: BMC Genomics. 11/7/2024, Vol. 25 Issue 1, p1-13. 13p.

Subject Terms: *COMPARATIVE genomics, *CHROMOSOMES, *CANDIDA, *GENOMICS, *SPECIES

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation.

Authors: Kosch, Tiffany A.¹ (AUTHOR) tiffany.kosch@gmail.com, Torres-Sánchez, María² (AUTHOR) torressanchez.maria@gmail.com, Liedtke, H. Christoph³ (AUTHOR), Summers, Kyle⁴ (AUTHOR), Yun, Maximina H.^5,6 (AUTHOR), Crawford, Andrew J.^7,8 (AUTHOR), Maddock, Simon T.^9,10 (AUTHOR), Ahammed, Md. Sabbir¹¹ (AUTHOR), Araújo, Victor L. N.⁷ (AUTHOR), Bertola, Lorenzo V.¹² (AUTHOR), Bucciarelli, Gary M.¹³ (AUTHOR), Carné, Albert¹⁴ (AUTHOR), Carneiro, Céline M.¹⁵ (AUTHOR), Chan, Kin O.¹⁶ (AUTHOR), Chen, Ying¹⁷ (AUTHOR), Crottini, Angelica^18,19,20 (AUTHOR), da Silva, Jessica M.^21,22 (AUTHOR), Denton, Robert D.²³ (AUTHOR), Dittrich, Carolin²⁴ (AUTHOR), Espregueira Themudo, Gonçalo²⁵ (AUTHOR)

Source: BMC Genomics. 11/1/2024, Vol. 25 Issue 1, p1-19. 19p.

Subject Terms: *COMPARATIVE genomics, *BIOLOGICAL extinction, *GERMPLASM, *BIODIVERSITY conservation, *GENOME size, *GENETIC sex determination

Quinolone Resistance Genes qnr, aac(6′)-Ib-cr, oqxAB, and qepA in Environmental Escherichia coli: Insights into Their Genetic Contexts from Comparative Genomics: Quinolone Resistance Genes qnr, aac(6′)-Ib-cr, oqxAB, and qepA in Environmental Escherichia coli: Insights into Their Genetic Contexts from Comparative Genomics: R. Gomi and F. Adachi

Authors: Gomi, Ryota¹, gomi.ryota.34v@kyoto-u.jp, Adachi, Fumie²

Source: Microbial Ecology; 2/17/2025, Vol. 88 Issue 1, p1-13, 13p

Rethinking asexuality: the enigmatic case of functional sexual genes in Lepraria (Stereocaulaceae).

Authors: Doellman, Meredith M.¹ (AUTHOR), Sun, Yukun¹ (AUTHOR), Barcenas-Peña, Alejandrina¹ (AUTHOR), Lumbsch, H. Thorsten¹ (AUTHOR), Grewe, Felix¹ (AUTHOR) fgrewe@fieldmuseum.org

Source: BMC Genomics. 10/26/2024, Vol. 25 Issue 1, p1-15. 15p.

Subject Terms: *SEXUAL cycle, *COMPARATIVE genomics, *GENOMICS, *ASEXUAL reproduction, *MEIOSIS, *REPRODUCTION

Comparative Phylogenomic Study of Malaxidinae (Orchidaceae) Sheds Light on Plastome Evolution and Gene Divergence.

Authors: Zeng, Meng-Yao¹ (AUTHOR) 62419052001@fafu.edu.cn, Li, Ming-He^1,2 (AUTHOR) fjalmh@fafu.edu.cn, Lan, Siren^1,2 (AUTHOR) lkzx@fafu.edu.cn, Yin, Wei-Lun^1,3 (AUTHOR) yinwl@bjfu.edu.cn, Liu, Zhong-Jian^1,2 (AUTHOR) yinwl@bjfu.edu.cn

Source: International Journal of Molecular Sciences. Oct2024, Vol. 25 Issue 20, p11181. 16p.

Subject Terms: *COMPARATIVE genomics, *NUCLEOTIDE sequencing, *PHYLOGENY, *ORCHIDS, *GENOMES

Candidate genes involved in biosynthesis and degradation of the main extracellular matrix polysaccharides of brown algae and their probable evolutionary history.

Authors: Mazéas, Lisa¹ (AUTHOR), Bouguerba-Collin, Ahlem¹ (AUTHOR), Cock, J. Mark¹ (AUTHOR), Denoeud, France² (AUTHOR), Godfroy, Olivier¹ (AUTHOR), Brillet-Guéguen, Loraine^1,3 (AUTHOR), Barbeyron, Tristan¹ (AUTHOR), Lipinska, Agnieszka P.⁴ (AUTHOR), Delage, Ludovic¹ (AUTHOR), Corre, Erwan³ (AUTHOR), Drula, Elodie^5,6,7 (AUTHOR), Henrissat, Bernard^5,6,8 (AUTHOR), Czjzek, Mirjam¹ (AUTHOR), Terrapon, Nicolas^5,6 (AUTHOR), Hervé, Cécile¹ (AUTHOR) cecile.herve@sb-roscoff.fr

Source: BMC Genomics. 10/10/2024, Vol. 25 Issue 1, p1-19. 19p.

Subject Terms: *COMPARATIVE genomics, *EXTRACELLULAR enzymes, *GENE families, *SULFOTRANSFERASES, *EXTRACELLULAR matrix

Genomes of diverse Actinidia species provide insights into cis-regulatory motifs and genes associated with critical traits.

Authors: Li, Xiaolong^1,2 (AUTHOR), Huo, Liuqing^1,2 (AUTHOR), Li, Xinyi^1,2 (AUTHOR), Zhang, Chaofan³ (AUTHOR), Gu, Miaofeng^1,2 (AUTHOR), Fan, Jialu⁴ (AUTHOR), Xu, Changbin^1,2 (AUTHOR), Gong, Jinli^1,2 (AUTHOR), Hu, Xiaoli^1,2 (AUTHOR), Zheng, Yi⁴ (AUTHOR), Sun, Xuepeng^1,2 (AUTHOR) xs57@zafu.edu.cn

Source: BMC Biology. 9/11/2024, Vol. 22 Issue 1, p1-16. 16p.

Subject Terms: *GENE families, *COMPARATIVE genomics, *PAN-genome, *VITAMIN C, *FRUIT development, *KIWIFRUIT

Marine sponge microbe provides insights into evolution and virulence of the tubercle bacillus.

Authors: Pidot, Sacha J.¹ (AUTHOR) sacha.pidot@unimelb.edu.au, Klatt, Stephan² (AUTHOR), Ates, Louis S.³ (AUTHOR), Frigui, Wafa³ (AUTHOR), Sayes, Fadel³ (AUTHOR), Majlessi, Laleh³ (AUTHOR), Izumi, Hiroshi⁴ (AUTHOR), Monk, Ian R.¹ (AUTHOR), Porter, Jessica L.¹ (AUTHOR), Bennett-Wood, Vicki¹ (AUTHOR), Seemann, Torsten¹ (AUTHOR), Otter, Ashley⁵ (AUTHOR), Taiaroa, George⁶ (AUTHOR), Cook, Gregory M.⁶ (AUTHOR), West, Nicholas⁴ (AUTHOR), Tobias, Nicholas J.¹ (AUTHOR), Fuerst, John A.⁴ (AUTHOR), Stutz, Michael D.⁷ (AUTHOR), Pellegrini, Marc⁷ (AUTHOR), McConville, Malcolm² (AUTHOR)

Source: PLoS Pathogens. 8/29/2024, Vol. 20 Issue 8, p1-27. 27p.

Subject Terms: *BCG vaccines, *COMPARATIVE genomics, *TUBERCULOSIS vaccines, *DNA vaccines, *COMMUNICABLE diseases, *MYCOBACTERIUM tuberculosis, *MYCOBACTERIUM bovis, *MOUNTAIN soils

Insights into aging mechanisms from comparative genomics in orange and silver roughies.

Authors: Carrero, Dido¹, Pascual-Torner, Maria^1,2 mariapascual1.618@gmail.com, Álvarez-Puente, Diana¹, Quesada, Víctor¹, García-Gómez, Claudia¹, López-Otín, Carlos¹

Source: Scientific Reports. 8/26/2024, Vol. 14 Issue 1, p1-14. 14p.

Subject Terms: *COMPARATIVE genomics, *SILVER, *FISHERIES, *CELL communication, *LONGEVITY, *ORANGES, *TOXAPHENE, *GENOMES

Organellar Genomes of Sargassum hemiphyllum var. chinense Provide Insight into the Characteristics of Phaeophyceae.

Authors: Jia, Xuli¹ (AUTHOR) 18734539035@163.com, Chen, Weizhou² (AUTHOR) wzchen@stu.edu.cn, Liu, Tao³ (AUTHOR) liutao2021@xmu.edu.cn, Chen, Zepan² (AUTHOR) zepan@stu.edu.cn

Source: International Journal of Molecular Sciences. Aug2024, Vol. 25 Issue 16, p8584. 25p.

Subject Terms: *TANDEM repeats, *COMPARATIVE genomics, *CHLOROPLAST DNA, *SARGASSUM, *MITOCHONDRIAL DNA

Genomic diversity in Paenibacillus polymyxa: unveiling distinct species groups and functional variability.

Authors: Wallner, Adrian¹ (AUTHOR) adrian.wallner@ait.ac.at, Antonielli, Livio¹ (AUTHOR), Mesguida, Ouiza^2,3 (AUTHOR), Rey, Patrice² (AUTHOR), Compant, Stéphane¹ (AUTHOR)

Source: BMC Genomics. 7/25/2024, Vol. 25 Issue 1, p1-11. 11p.

Subject Terms: *FUNCTIONAL groups, *COMPARATIVE genomics, *PAENIBACILLUS, *NITROGEN fixation, *SECONDARY metabolism, *SPECIES

Puzzle Hi-C: An accurate scaffolding software.

Authors: Lin, Guoliang¹ (AUTHOR), Huang, Zhiru² (AUTHOR), Yue, Tingsong¹ (AUTHOR), Chai, Jing¹ (AUTHOR), Li, Yan¹ (AUTHOR), Yang, Huimin¹ (AUTHOR), Qin, Wanting¹ (AUTHOR), Yang, Guobing¹ (AUTHOR), Murphy, Robert W.³ (AUTHOR), Zhang, Ya-ping^1,4 (AUTHOR) jingluo@ynu.edu.cn, Zhang, Zijie^1,4 (AUTHOR) jingluo@ynu.edu.cn, Zhou, Wei⁵ (AUTHOR) jingluo@ynu.edu.cn, Luo, Jing^1,4 (AUTHOR) jingluo@ynu.edu.cn

Source: PLoS ONE. 7/15/2024, Vol. 19 Issue 7, p1-14. 14p.

Subject Terms: *COMPARATIVE genomics, *GENOMICS, *PUZZLES, *CHROMOSOMES, *COMPUTER software

Comparative genomics of Tn6411 transposons carrying the blaIMP-1 gene in Pseudomonas aeruginosa.

Authors: Zheng, Lin¹ (AUTHOR) xuejung2021@163.com, Wang, Zixian¹ (AUTHOR), Guo, Jingyi² (AUTHOR), Guan, Jiayao³ (AUTHOR), Lu, Gejin¹ (AUTHOR), Jing, Jie¹ (AUTHOR), Sun, Shiwen¹ (AUTHOR), Sun, Yang¹ (AUTHOR), Ji, Xue¹ (AUTHOR), Jiang, Bowen¹ (AUTHOR), Wang, Yongjie⁴ (AUTHOR), Zhao, Chuanfang⁵ (AUTHOR), Zhu, Lingwei¹ (AUTHOR) xuejung2021@163.com, Guo, Xuejun¹ (AUTHOR) xuejung2021@163.com

Source: PLoS ONE. 7/9/2024, Vol. 19 Issue 7, p1-9. 9p.

Subject Terms: *COMPARATIVE genomics, *PSEUDOMONAS aeruginosa, *TRANSPOSONS, *CARBAPENEM-resistant bacteria, *WHOLE genome sequencing, *MOBILE genetic elements, *BACTERIAL genomes