A new approach for comprehensively describing heterogametic sex chromosomes

Abstract Notwithstanding the rapid developments in sequencing techniques, Y and W sex chromosomes have still been mostly excluded from whole genome sequencing projects due to their high repetitive DNA content. Therefore, Y and W chromosomes are poorly described in most species despite their biological importance. Several methods were developed for identifying Y or W-linked sequences among unmapped scaffolds. However, it is not enough to discover functional regions from short unmapped scaffolds. Here, we provide a new and simple strategy based on k-mer comparison for comprehensive analysis of the W chromosome in Bombyx mori. Using this novel method, we effectively assembled de novo 1281 W-derived genome contigs (totaling 1.9 Mbp), and identified 156 W-linked transcript RNAs and 345 W-linked small RNAs. This method will help in the elucidation of mechanisms of sexual development and exploration of W chromosome biological functions, and provide insights into the evolution of sex chromosomes. Moreover, we showed this method can be employed in identifying heterogametic sex chromosomes (W and Y chromosomes) in many other species where genomic information is still scarce.

[1]  K. Makova,et al.  Y and W Chromosome Assemblies: Approaches and Discoveries. , 2017, Trends in Genetics.

[2]  Lauren A. Assour,et al.  Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes , 2016, Proceedings of the National Academy of Sciences.

[3]  Q. Xia,et al.  Systematic Identification and Characterization of Long Non-Coding RNAs in the Silkworm, Bombyx mori , 2016, PloS one.

[4]  M. Schartl,et al.  Dynamics of vertebrate sex chromosome evolution: from equal size to giants and dwarfs , 2015, Chromosoma.

[5]  Carlos G Schrago,et al.  Long-Read Single Molecule Sequencing to Resolve Tandem Gene Copies: The Mst77Y Region on the Drosophila melanogaster Y Chromosome , 2015, G3: Genes, Genomes, Genetics.

[6]  Sumio Sugano,et al.  A single female-specific piRNA is the primary determiner of sex in the silkworm , 2014, Nature.

[7]  F. Aoki,et al.  Identification of the key stages for sex determination in the silkworm, Bombyx mori , 2013, Development Genes and Evolution.

[8]  Michael Roberts,et al.  The MaSuRCA genome assembler , 2013, Bioinform..

[9]  E. Hartmann,et al.  High-throughput sequencing of a single chromosome: a moth W chromosome , 2013, Chromosome Research.

[10]  Andrew G Clark,et al.  Efficient identification of Y chromosome sequences in the human and Drosophila genomes , 2013, Genome research.

[11]  Yi Zhao,et al.  Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts , 2013, Nucleic acids research.

[12]  Yumin Qi,et al.  Six novel Y chromosome genes in Anopheles mosquitoes discovered by independently sequencing males and females , 2013, BMC Genomics.

[13]  A. Sinclair,et al.  RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome , 2013, Genome Biology.

[14]  Nancy F. Chen,et al.  Identification of avian W-linked contigs by short-read sequencing , 2012, BMC Genomics.

[15]  Ryan K. Dale,et al.  Mediation of Drosophila autosomal dosage effects and compensation by network interactions , 2012, Genome Biology.

[16]  M. Long,et al.  Retrogenes Moved Out of the Z Chromosome in the Silkworm , 2012, Journal of Molecular Evolution.

[17]  K. Kadota,et al.  The silkworm W chromosome is a source of female-enriched piRNAs. , 2011, RNA.

[18]  N. Friedman,et al.  Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.

[19]  Carl Kingsford,et al.  A fast, lock-free approach for efficient parallel counting of occurrences of k-mers , 2011, Bioinform..

[20]  B. Langmead,et al.  Aligning Short Sequencing Reads with Bowtie , 2010, Current protocols in bioinformatics.

[21]  David R. Kelley,et al.  Quake: quality-aware detection and correction of sequencing errors , 2010, Genome Biology.

[22]  Huanming Yang,et al.  De novo assembly of human genomes with massively parallel short read sequencing. , 2010, Genome research.

[23]  Kazuei Mita,et al.  The genome of a lepidopteran model insect, the silkworm Bombyx mori. , 2009, Insect biochemistry and molecular biology.

[24]  F. Marec,et al.  Sex Chromosomes and Sex Determination in Lepidoptera , 2008, Sexual Development.

[25]  K. Mita,et al.  End-sequencing and characterization of silkworm (Bombyx mori) bacterial artificial chromosome libraries , 2007, BMC Genomics.

[26]  Manolis Kellis,et al.  Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila , 2007, Cell.

[27]  Kuniaki Saito,et al.  Specific association of Piwi with rasiRNAs derived from retrotransposon and heterochromatic regions in the Drosophila genome. , 2006, Genes & development.

[28]  H. Abe,et al.  Partial deletions of the W chromosome due to reciprocal translocation in the silkworm Bombyx mori , 2005, Insect molecular biology.

[29]  Colin N. Dewey,et al.  Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution , 2004, Nature.

[30]  James A. Birchler,et al.  Heterochromatic Silencing and HP1 Localization in Drosophila Are Dependent on the RNAi Machinery , 2004, Science.

[31]  T. Graves,et al.  The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes , 2003, Nature.

[32]  Zhong-yi Hu,et al.  Rapid Detection of rpoB Gene Mutations in Rifampin-Resistant Mycobacterium tuberculosis Isolates in Shanghai by Using the Amplification Refractory Mutation System , 2003, Journal of Clinical Microbiology.

[33]  Shuichi Asakawa,et al.  DMY is a Y-specific DM-domain gene required for male development in the medaka fish , 2002, Nature.

[34]  A. Clark,et al.  Identification of five new genes on the Y chromosome of Drosophila melanogaster , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[35]  A. Spradling,et al.  A novel group of pumilio mutations affects the asymmetric division of germline stem cells in the Drosophila ovary. , 1997, Development.

[36]  T. Shimada,et al.  Linkage map of random amplified polymorphic DNAs (RAPDs) in the silkworm, Bombyx mori , 1995 .

[37]  D. Page,et al.  The human Y chromosome: overlapping DNA clones spanning the euchromatic region. , 1992, Science.

[38]  N. Friedman,et al.  Trinity : reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2016 .