Comparative genomics and transcriptomic response to root exudates of six rice root-associated Burkholderia sensu lato species by Wallner, Adrian, Klonowska, Agnieszka, Guigard, Ludivine, King, Eoghan, Rimbault, Isabelle, Ngonkeu, Eddy, Nguyen, Phuong, Béna, Gilles, Moulin, Lionel

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Genomic insights and comparative analysis of Colletotrichum species associated with anthracnose fruit rot and crown rot of strawberry in North Carolina by Tika B. Adhikari, Norman Muzhinji, Ashley N. Philbrick, Frank J. Louws, Frank J. Louws

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A Near Complete Genome Assembly of the Oshima Cherry Cerasus speciosa by Kazumichi Fujiwara, Atsushi Toyoda, Bhim B. Biswa, Takushi Kishida, Momi Tsuruta, Yasukazu Nakamura, Noriko Kimura, Shoko Kawamoto, Yutaka Sato, Toshio Katsuki, Sakura 100 Genome Consortium, Tsuyoshi Koide

“…Detailed structural analysis of these putative centromeric regions revealed that the centromeric regions of C. speciosa comprised repetitive sequences with monomer lengths of 166 or 167 bp. Comparative genomic analysis with Prunus sensu lato genome revealed structural variations and conserved syntenic regions. …”
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Fine-mapping of PmHHM, a broad-spectrum allele from a wheat landrace conferring both seedling and adult resistance to powdery mildew by Bisheng Fu, Bisheng Fu, Bisheng Fu, Zhixin Lin, Lijuan Yan, Qiaofeng Zhang, Caiyun Liu, Caiyun Liu, Jin Cai, Jin Cai, Wei Guo, Wei Guo, Ying Liu, Wenling Zhai, Shuangjun Gong, Feng Xu, Jizhong Wu, Jizhong Wu, Jizhong Wu

“…To map its PM resitance gene, bulked segregant analysis, molecular mapping and comparative genomic analysis were also used in the present study.ResultsHHM shows remarkable adult resistance in the field and is nearly immune to all 25 Bgt isolates used in seedling tests, making it an excellent source of PM resistance. …”
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Screen of propionate-producing probiotic strains in attenuating murine colitis by modulating immune response and restoring the intestinal barrier by Ting Shu, Xizi Song, Silu Zhang, Xiaoli Zhou, Zhizhu Zhang, Pengfei Wang, Hu Canying, Jie Pan, Xiaoshuang Dai, Yan Tan, Wu Xiyang, Huicui Meng, Guoxun Xiao, Huaijie Hao

“…Probiotics produce propionate, a short-chain fatty acid that restores intestinal balance and reduces inflammation.Comparative genomic analysis of propionate pathway integrity was performed to nominate 41 candidate strains. …”
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Comparative analysis of chloroplast genomes reveals molecular evolution and phylogenetic relationships within the Papilionoideae of Fabaceae by Qian Qin, Yanjing Dong, Jialong Chen, Bo Wang, Yuxin Peng, XinPeng Zhang, Xiaoyun Wang, Jinxiang Zeng, Guoyue Zhong, Shouwen Zhang, Xiaolang Du

“…These species exhibit pronounced differences in their non-coding regions. Comparative genomic variations at cpDNA sites were identified. …”
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Insights into the origin, hybridisation and adaptation of Candida metapsilosis hybrid pathogens. by Valentina Del Olmo, Álvaro Redondo-Río, Alicia Benavente García, Savitree Limtong, Ester Saus, Toni Gabaldón

“…Here, we sequenced the genomes of five new C. metapsilosis isolates, one representing the first African isolate for this species, and four environmental isolates from marine niches. Our comparative genomic analyses, including a total of 29 sequenced strains, shed light on the phylogenetic relationships between C. metapsilosis hybrid isolates and show that environmental strains are closely related to clinical ones and belong to different clades, suggesting multiple independent colonisations. …”
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Genomic epidemiology and phenotypic characterization of Staphylococcus aureus isolated from atopic dermatitis patients in South China by Chao Yang, Xiaowei Chen, Min Li, Wenchang Yuan, Shunguang Li, Dexing Han, Junhui Feng, Haimin Luo, Minling Zheng, Jiaqi Liang, Cha Chen, Pinghua Qu, Song Li

“…S. aureus of Chinese AD patients was mainly distributed in SC2, SC7, and SC12. Comparative genomic highlighted genes linked to AD, including enterotoxins (seh, selk, selq, entH), adhesion genes (fnbA, fnbB, sdrD, map, fib, narH). …”
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Ammonifying and phosphorus-solubilizing function of Aliikangiella maris sp. nov. isolated from Phaeocystis globosa bloom and algal–bacterial interactions by Fei Li, Fei Li, Ming-Ben Xu, Liang-Hao Pan, Jie Li, Cai-Bi Lan, Zhe Li, Shan Lu, Jun-Xiang Lai, Jun-Xiang Lai, Peng-Fu Li

“…According to phenotypic, chemotaxonomic, phylogenomic, and comparative genomic analyses data, strains GXAS 306T and GXAS 311 were considered to represent a novel species of the genus Aliikangiella. …”
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Decoding mutational signatures in breast cancer: Insights from a multi-cohort study by Margaux Betz, Andréa Witz, Julie Dardare, Cassandra Michel, Vincent Massard, Romain Boidot, Pauline Gilson, Jean-Louis Merlin, Alexandre Harlé

“…This work aims to compare genomic data and signatures extracted from tissue samples collected in the CICLADES study to existing cohorts. …”
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Correlation among blastocoel fluid DNA level, apoptotic genes expression and preimplantation aneuploidy by Fattaneh Khajehoseini, Zahra Noormohammadi, Poopak Eftekhari-Yazdi, Hamid Gourabi, Reza Pazhoomand, Shirzad Hosseinishenatal, Masood Bazrgar

“…Human blastocysts were classified into three groups; survivable embryo (SE), fatal single and double aneuploidy (FSDA) and multiple aneuploidy (MA) using array comparative genomic hybridization (array-CGH) by trophectoderm biopsy. …”
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Genomic changes during the evolution of the Coxiella genus along the parasitism-mutualism continuum by Santos-Garcia, Diego, Morel, Olivier, Henri, Hélène, El Filali, Adil, Buysse, Marie, Noël, Valérie, McCoy, Karen D., Gottlieb, Yuval, Klasson, Lisa, Zenner, Lionel, Duron, Olivier, Vavre, Fabrice

“…Using these newly sequenced Coxiella-LEs and 43 Coxiellaceae genomes, we conducted comparative genomic and phylogenomic analyses to increase our knowledge of C. burnetii pathogenicity and the emergence of Coxiella-LEs. …”
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Proteogenomic annotation of T6SS components identified in Bacteroides fragilis secretome by Natalya B. Zakharzhevskaya, Olga Yu Shagaleeva, Daria A. Kashatnikova, Daria A. Kashatnikova, Anton O. Goncharov, Anton O. Goncharov, Daria V. Evsyutina, Dmitry A. Kardonsky, Elizaveta A. Vorobeva, Artemiy S. Silantiev, Viktoria D. Kazakova, Irina V. Kolesnikova, Ivan O. Butenko, Anna A. Vanyushkina, Svetlana V. Smirnova, Andrei V. Chaplin, Andrei V. Chaplin, Boris A. Efimov, Boris A. Efimov

“…Proteogenomic annotation and comparative genomic study of the T6SS loci of the toxigenic Bf BOB25 were carried out by comparison with the reference genomes of the following Bf strains: JIM10, NCTC 9343 and 638R.ResultsAccording to the data obtained, T6SS components were represented in all types of the analysed samples. …”
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Virulence factor discovery identifies associations between the Fic gene family and Fap2+ fusobacteria in colorectal cancer microbiomes by Geicho Nakatsu, Duhyun Ko, Monia Michaud, Eric A. Franzosa, Xochitl C. Morgan, Curtis Huttenhower, Wendy S. Garrett

“…We demonstrate that Fic family genes expand with the presence of Fap2 in the fusobacterial pangenome. Through comparative genomic analysis, we find that Fap2+ Fusobacteriota are highly enriched with Fic gene families compared to other cancer-associated and human gut microbiome bacterial taxa. …”
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