Journal: Applied and Environmental Microbiology

Article Title: Convergent reductive evolution in bee-associated lactic acid bacteria

doi: 10.1128/aem.01257-24

Figure Lengend Snippet: Phylogenomic tree of the Lactobacillaceae. ( A ) Maximum likelihood phylogenomic tree comprising 369 LAB species inferred from the concatenated alignment of 180 single-copy orthogroups and rooted with Lactococcus lactis and Enterococcus massiliensis . The isolation source and predicted environment are depicted in the first two rings, respectively. The species isolated from bee-associated environments are highlighted in yellow. Presence/absence of adhE , number of protein-coding genes, and genome size are also shown in the other three rings. ( B ) Boxplots depicting comparisons between bee-associated species and others regarding genome size, number of protein-coding genes, and GC content. The respective statistical significance after phylogenetically informed phylANOVA is displayed for each feature. * P < 0.05, ** P < 0.01.

Article Snippet: A total of 369 representative genomes of the family Lactobacillaceae and two outgroups ( Lactococcus lactis and Enterococcus massiliensis ) were retrieved from the National Center for Biotechnology Information (NCBI) (19 January 2023).

Techniques: Isolation

Journal: bioRxiv

Article Title: Coherence of Microcystis species revealed through population genomics

doi: 10.1101/541755

Figure Lengend Snippet: A core genome of 152 homologous genes shared by 79 Microcystis genomes and the outgroups ( Anabaena variabilis ATCC 29413 and Synechocystis sp. PCC6803) was identified using software Roary . The eight hierBAPS clusters are highlighted in colored boxes. The genomes from the same isolate at a different time have letter “D or T” at the end of their names and are indicated with a black asterisk. The genomes from a bulk culture and a single colony from the same cultured are indicated with a hash. The three genomes from uncultured colonies from Lake Champlain (Quebec, Canada) are indicated with a red asterisk and “Col” at the end of their name. The font colors indicate the geographical origin (Brazil: orange, Canada: blue, USA: purple, other: black). The abbreviated hierBAPS cluster names Mpn, Mwe, Mfl, Mvi and Mae correspond to M. panniformis , M. wesenbergii M. flos-aquae, M. viridis and M. aeruginosa , respectively. The tree bar scale indicates number of nucleotide substitutions per site.

Article Snippet: A core genome of 222 homologous genes shared by 53 Microcystis genomes and the outgroups ( Anabaena variabilis ATCC 29413 and Synechocystis sp .

Techniques: Software, Cell Culture

Journal: Journal of Integrative Plant Biology

Article Title: Haplotype‐resolved genome of a papeda provides insights into the geographical origin and evolution of Citrus

doi: 10.1111/jipb.13819

Figure Lengend Snippet: Genome analysis of a wild papeda DYC002 and representative citrus species (A) Phylogenetic analysis of DYC002 and nine other representative citrus species using genome‐wide SNPs on the degenerated sites after the resequencing data were mapped to the assembled DYC002 monoploid genome. Pie charts associated with each species show the proportions of gene families that underwent expansion (red) or contraction (green). (B) GO enrichment analysis of the genes in rapidly expanded families in DYC002. (C) K s value distribution of the paralogous gene pairs in the DYC002, P. trifoliata , C. sinensis , and C. grandis genomes. The black vertical line indicates the whole‐genome duplication event that occurred in the Citrus – Poncirus lineage ( K s = 1.25).

Article Snippet: Chinese box orange ( Atalantia buxifolia ) was used as the outgroup, and its genomic resequencing data were downloaded from the National Center for Biotechnology Information (NCBI; SRR4253620).

Techniques: Genome Wide