title: First report of Y-linked genes in the kissing bug Rhodnius prolixus.
abstract: BACKGROUND
  Due to an abundance of repetitive DNA, the annotation of heterochromatic regions of the genome such as the Y chromosome is problematic. The Y chromosome is involved in key biological functions such as male-fertility and sex-determination and hence, accurate identification of its sequences is vital. The hemipteran insect Rhodnius prolixus is an important vector of Chagas disease, a trypanosomiasis affecting 6-7 million people worldwide. Here we report the identification of the first Y-linked genes of this species.
  
  
  RESULTS
  The R. prolixus genome was recently sequenced using separate libraries for each sex and the sequences assembled only with male reads are candidates for Y linkage. We found 766 such candidates and PCR tests with the ten largest ones, confirmed Y-linkage for all of them, suggesting that "separate libraries" is a reliable method for the identification of Y-linked sequences. BLAST analyses of the 766 candidate scaffolds revealed that 568 scaffolds contained genes or part of putative genes. We tested Y-linkage for 36 candidates and found that nine of them are Y-linked (the PCR results for the other 25 genes were inconclusive or revealed autosomal/X-linkage). Hence, we describe in this study, for the first time, Y-linked genes in the R. prolixus genome: two zinc finger proteins (Znf-Y1 and Znf-Y2), one metalloproteinase (Met-Y), one aconitase/iron regulatory protein (Aco-Y) and five genes devoid of matches in any database (Rpr-Y1 to Rpr-Y5). Expression profile studies revealed that eight genes are expressed mainly in adult testis (some of which presented a weak expression in the initial developmental stages), while Aco-Y has a gut-restricted expression.
  
  
  CONCLUSIONS
  In this study we showed that the approach used for the R. prolixus genome project (separate sequencing of male and female DNA) is key to easy and fast identification of sex-specific (e.g. Y chromosome sequences). The nine new R. prolixus Y-linked genes reported here provide unique markers for population and phylogenetic analysis and further functional studies of these genes may answer some questions about sex determination, male fertility and Y chromosome evolution in this important species.
authors: Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil. lbkoerich@gmail.com.|Departamento de Parasitologia, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil. lbkoerich@gmail.com.
authors: Leonardo B
authors: LB
authors: Koerich
authors: Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil. edudupim@gmail.com.
authors: Eduardo G
authors: EG
authors: Dupim
authors: Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil. leo_nardo1991@yahoo.com.br.
authors: Leonardo L
authors: LL
authors: Faria
authors: Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil. felipe.dias@bioqmed.ufrj.br.
authors: Felipe A
authors: FA
authors: Dias
authors: Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil. dias.anaferreira@gmail.com.
authors: Ana F
authors: AF
authors: Dias
authors: Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil. gstrindade@live.com.
authors: Gabriela S
authors: GS
authors: Trindade
authors: Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil. rdmesquita@iq.ufrj.br.
authors: Rafael D
authors: RD
authors: Mesquita
authors: Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil. bernardo@biologia.ufrj.br.
authors: Antonio B
authors: AB
authors: Carvalho
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D005260:Female; D017344:Genes, Insect; D050173:Genes, Y-Linked; D049750:Genome, Insect; D023281:Genomics; D008297:Male; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D012239:Rhodnius / Q000145:classification / Q000235:genetics*; D014998:Y Chromosome