The Release 6 reference sequence of the Drosophila melanogaster genome

Roger A Hoskins,Maria Carmela Accardo,Ivonne Mendez,Joseph W Carlson,Kenneth H Wan,Elisabetta Damia,Barret D Pfeiffer,Gary H Karpen,Reed A George,Patrizio Dimitri,Evgeniya N Andreyeva,Giovanni Messina,Martin Krzywinski,Lidiya V Boldyreva,Benjamin W Booth,Gerald M Rubin,Beatriz De Pablos,María Méndez-Lago,Robert Svirskas,Olga V Demakova,Antonio Bernardo Carvalho ,Marco A Marra ,Alfredo Villasanté ,Samuel Galle ,Jacqueline E Schein ,Soohyung Park ,И Ф Жимулев ,S Celniker

doi:10.1101/gr.185579.114

Abstract

Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy and middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. Further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads.

Highlights

The genome sequence of the fruit fly Drosophila melanogaster was first reported in 2000 (Adams et al 2000)
Ished sequences and draft sequences of a tiling path of Bacterial Artificial Chromosomes (BACs) and P1 clones spanning the euchromatic portion of the genome (Adams et al 2000).WGS1 and Release 1 were validated by comparison to the available finished genomic sequences and to a BAC-based physical map of the major autosomes (Hoskins et al 2000)
In 2002, we reported BAC-based finishing of 116.9 Mb of genome sequence in 13 scaffolds spanning the euchromatic portions of the six chromosome arms (Celniker et al 2002) and an improved whole-genome shotgun (WGS) assembly (WGS3) including 20.7 Mb of draft-quality sequence in larger scaffolds in the heterochromatic portion of the genome (Celniker et al 2002; Hoskins et al 2002)

Summary

Introduction

The genome sequence of the fruit fly Drosophila melanogaster was first reported in 2000 (Adams et al 2000). In Release 5, scaffold CP000212 was mismapped to chromosome arm 3L based on analysis of a P-element transposon inserted in repeat-rich genomic sequence (Hoskins et al 2007); the new BAC FISH results show that CP000212 maps to the Y chromosome (Supplemental Fig. S5B).

Results

Conclusion