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[…] re removed, fragmenting the genome into many smaller pieces. Chromosome quotients were calculated for the fragmented autosome and X sequences from the AgamP3 genome assembly (Figure ). The autosomal sequences had chromosome quotients distributed around one, and the X chromosome sequences had chromosome quotients distributed around two. Chromosome quotients were calculated for the fragmented Y chromosome sequences from the AgamP3 genome assembly. Of the 42 known An. gambiae Y sequences, 37 had chromosome quotients less than 0.3., The An. gambiae sequences that were unable to be anchored to chromosomes, known as UNKN in the AgamP3 assembly, were fragmented by removing the repeats indicated by RepeatMasker. Chromosome quotients were calculated for these UNKN sequences. From the UNKN sequences, we identified 16 novel candidate Y sequences, encompassing more than 9,000 bases (Figure )., We also tested the CQ method de novo by generating a genome assembly from male G3 strain Illumina sequence data using ABySS. Chromosome quotients were calculated for all the sequences in the Illumina assembly. From the Illumina assembly, we identified 17 novel candidate Y sequences encompassing more than 6,000 bases (Figure ). All Y sequences reported in this study are provided in the additional files (Additional file )., Comparison of the Y sequences to An. stephensi and An. gambiae RNA-sequencing data with blastn led to the identification of six novel Y genes, three from each species (Table ). The An. stephensi and An. gambiae Y genes were given the names sYG (An. stephensi Y gene) and gYG (An. gambiae Y gene) respectively, followed by a number designating the order in which they were discovered. All six Y genes amplified a product exclusively in male genomic DNA (Figure ). Sequencing of RT-PCR products (Figure ) confirmed transcription of all six genes. cDNA sequences for genes with confirmed introns were used to determine the structure of these genes, and are provided in Additional file (Figure ). Interestingly, all six genes were expressed in the early embryo, 2–12 hours after egg depositi […]

Pipeline specifications

Software tools RepeatMasker, ABySS, BLASTN
Organisms Homo sapiens, Drosophila melanogaster, Anopheles stephensi
Diseases Malaria