François Michel's research while affiliated with Université Paris-Saclay and other places

... In Tel3c and Ll.ltrB introns, the length is 2 bp and 1 bp, respectively ( Fig. 1B) (10,13,24). Recently, a new EBS2a-IBS2a base pair (adjacent to EBS2/IBS2) was found in the EcI5 intron, and this paring could greatly affect intron migration on the chromosome, suggesting these adjacent key sequences could play a vital role in target DNA recognition and splicing (29). In our previous experience, the randomized base pairing of -8 and -7 sites in the interval of IBS2 and IBS1 of Tel3c/4c intron of TMT results in an undesirable success rate of gene inactivation. ...

... A similar clustering pattern is observed across the different catalytic states with three key clusters emerging highlighted in purple, yellow and green (and for those intron structures without broken chains additionally a cluster in blue). Exceptions to this are the chimeras (5j01 and 5j02), which were created by replacing part of the O. iheyensis sequence with intron AV.I.2 ( 17 ). In those cases, the yellow cluster does not break off and instead appears as part of larger purple clusters (Figure 3 ). ...

... In the present paper, we focus on three closely related genera (Nazari et al. 2007;Michel et al. 2008;Omoto et al. 2009): Zerynthia, Allancastria and Bhutanitis. We examine a considerably larger series of specimens than previous authors with a view to documenting the occurrence of overlooked or little-known sphragides. ...

... Splicing events can be divided into four main reaction steps: assembly, activation, catalysis and disassembly [60,61]. The catalytic centre of spliceosomes highly resembles Group II introns, and even the splicing mechanism is quite like the latter [62]. ...

... . We conclude that examination of additional taxa within and outside Boloriini is needed to confirm the status of Clossiana and Boloriina. The efforts ofWarren (1944Warren ( , 1955)Warren et al. (1946)and DosPassos & Grey (1945)produced a detailed generic classification for fritillaries that is used widely (see also ShiroˆzuShiroˆzu & Saigusa, 1973). Aubert et al. (1996tested this classification using molecular-based cladistic analyses (enzymes and ND1 sequence) for nineteen European species, and corroborated the traditional morphology-based argynnine classification, except for considering true Issoria close to Clossiana. Our analyses uncovered three main patterns among the fritillaries. First, argynni ...

... In this latter case, in which no or few homologs have been reported, the secondary structure can be explored using folding algorithms (Zuker 1989, 2003). The term " secondary structure " may carry some ambiguity because it includes not only all segments that can build helices formed by any combination of the isosteric Watson-Crick pairings but also, in variable proportions, Watson-Crick as well as non-Watson-Crick pairs involved in tertiary structure (Westhof and Michel 1994). A secondary structure can be broken down into recognizable elementary modules such as the helical regions (stems and pseudoknots) and nonhelical linking elements (hairpin and internal loops, bulges, and multiple junctions). ...

... The most prominent symptoms of fir broom rust are a greenish-yellow-coloured proliferation of branches in summer which is known as witches' brooms, cankers and spherical swellings on the trunk and branches (Podner & Metzler, 2009;Selik, 1980;Wilson & Henderson, 1966). Melampsorella caryophyllacearum typically has five different spore stages in its life) cycle: spermagonium, aecium, uredinium, telium and basidium (Cummins & Hiratsuka, 2003;Pei & Shang, 2005;Tian et al., 1991). (Cummins & Hiratsuka, 2003;Savile, 1973). ...

... Thirteen protein-coding genes (PCGs) and 2 rRNAs were obtained from all 102 individuals, and detailed information on the four concatenated datasets that were selected to reconstruct phylogenetic trees is available in supplementary materials and methods. These mitochondrial datasets were commonly used for previous Parnassius phylogeny inference (e.g., Allio et al., 2021;Condamine, Nabholz, et al., 2018;Condamine, Rolland, et al., 2018;Katoh et al., 2005;Michel et al., 2008;Omoto et al., 2004;Tao et al., 2020). ...

... Thus, various morphological lineages, subspecies, and hybrid forms have been described for E. pronoe (e.g. [11][12][13][14]. Recently, three of these described lineages have been confirmed by genetic markers 1,7 . ...

... Indeed, whereas organelle genome annotation typically involves automated gene prediction tools, manual analysis and curation by skilled experts are usually necessary to produce accurate results. In the case of mtDNA, the challenges stem from numerous Group I and Group II introns, twintrons (Hafez et al., 2013b), difficult-to-recognize mini-exons, marginally conserved genes, such as rps3, rnpB, ssrA (Bullerwell et al., 2000;Seif et al., 2003;Hafez et al., 2013a;Donath et al., 2019), and structurally reduced rRNAs and tRNAs (Okimoto et al., 1994). Furthermore, intron identification and classification is often only possible using elaborate and manually-refined computational models (Prince et al., 2022). ...