Chromosomal Mapping of Anopheline Genomes

Methods for chromosomal mapping of scaffolds [92 , 93 (link)] are detailed for A. albimanus [27 ], A. atroparvus [25 , 26 , 58 (link)], A. stephensi (SDA-500) [25 ], A. stephensi (Indian) [21 ], and A. sinensis (Chinese) [23 ]. A. funestus mapping built on previous results [59 (link)–61 (link)] with additional FISH mapping (Additional file 1: Figure S11) used to further develop the physical map by considering several different types of mapping results. A. stephensi mapping also extended previous efforts [94 (link)] by aligning FISH probes to the AsteI2 scaffolds with BLAST, and designing and hybridising new probes targeting specific scaffolds to increase the coverage. The complete ‘frozen’ input datasets of the physically mapped scaffolds for each of the six assemblies are presented in Additional file 4, with the usable scaffold pair adjacencies in Additional file 1: Table S6, the definitive mapped A. funestus scaffolds in Additional file 1: Table S7, and the definitive chromosome-mapped scaffolds for each of the six assemblies as well as for A. arabiensis in Additional file 5. These adjacencies were compared with the Camsa-generated two-way consensus assemblies, as well as the predictions from each method and the conservative and liberal consensus assemblies (Fig. 4a; Additional file 1: Table S8). RNAseq-based scaffolding has been employed for very large genomes such as the Norway spruce [95 (link)] and the Loblolly pine [96 (link)], but is also applicable to smaller genomes where more compact gene structures would make it less likely to erroneously skip intervening intronic scaffolds/contigs. The RNAseq-based adjacency predictions used genome-mapped paired-end sequencing data for 13 of the anophelines available from VectorBase [53 , 54 (link)] (Release VB-2017-02), including those from the Anopheles 16 Genomes Project [25 ] and an A. stephensi (Indian) male/female study [97 (link)]. Agouti [62 (link)] analyses were performed (requiring unique read mapping and a minimum coverage of 5 reads) to identify transcript-supported scaffold adjacencies for these 13 anophelines, complemented with Rascaf [98 (link)] predictions (Additional file 1: Table S9). These adjacencies were compared with the Camsa-generated two-way consensus assemblies, as well as the predictions from each method and the conservative and liberal consensus assemblies (Fig. 4b; Additional file 1: Table S10). See Additional file 1 for further details for physical mapping and Agouti adjacencies and their comparisons.

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Waterhouse R.M., Aganezov S., Anselmetti Y., Lee J., Ruzzante L., Reijnders M.J., Feron R., Bérard S., George P., Hahn M.W., Howell P.I., Kamali M., Koren S., Lawson D., Maslen G., Peery A., Phillippy A.M., Sharakhova M.V., Tannier E., Unger M.F., Zhang S.V., Alekseyev M.A., Besansky N.J., Chauve C., Emrich S.J, & Sharakhov I.V. (2020). Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies. BMC Biology, 18, 1.

Publication 2020

Agouti Anopheles Chinese Chromosome Female Fish Frozen Gene structures Genomes Intronic Loblolly pine Male Physical Spruce

Corresponding Organization : National Research Tomsk State University

Other organizations : Princeton University, Johns Hopkins University, Université de Montpellier, École Pratique des Hautes Études, Centre National de la Recherche Scientifique, Institut de Recherche pour le Développement, Institut des Sciences de l'Evolution de Montpellier, Indiana University Bloomington, Centers for Disease Control and Prevention, Tarbiat Modares University, National Human Genome Research Institute, National Institutes of Health, European Bioinformatics Institute, Centre de Recherche en Informatique, Laboratoire de Biométrie et Biologie Evolutive, Université Claude Bernard Lyon 1, University of Notre Dame, George Washington University Virginia Campus, Simon Fraser University, University of Tennessee at Knoxville

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Variable analysis

independent variables

Chromosomal mapping methods for scaffolds
RNAseq-based scaffolding

dependent variables

Chromosomal positions of scaffolds
Transcript-supported scaffold adjacencies

control variables

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