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Blue-crowned Manakin Sequence Assembly Release Notes
 Background: The blue-crowned manakin (Lepidothrix coronata) is a species of bird in the Pipridae family which ranges from the Pacific slope of Costa Rica to northwestern Ecuador and in western Amazonia from Venezuela, ... Colombia, Ecuador, Peru, Brazil to Bolivia. The males have a brilliant blue crown and a black body throughout much of its range, while in the subspecies found in southeastern Peru, southwestern Brazil and northern Bolivia males have a blue crown and green body (L. coronata caelestileata, regalis, exquisita); females of all subspecies are green. Relationships among the currently recognized 8 subspecies are not well understood. It's natural habitats are primarily tropical and occasionally subtropical moist forests (0-1350 m). 
 Blue-crowned manakin males aggregate in leks, where they engage in competitive displays that may entice visiting females who are surveying prospective partners for copulation. Females appear to select males for mating based on both song and display rates, and often only one male within a given lek is reproductively successful. High reproductive skew among males has led to the question why males join leks when their chances of reproductive success are so low. 
 Avian plumage traits are the targets of both natural and sexual selection. Consequently, genetic changes resulting in plumage variation among closely related taxa as in the blue-crowned manakin subspecies might represent important evolutionary events. The molecular basis of such differences in the blue-crowned manakin is an active area of research.
 The blue-crowned manakin DNA for shotgun sequencing is derived from an adult male (Lepidothrix coronata; B3197) from the genetic resources collection of the Louisiana State University Museum of Natural Science. Locality data for the voucher specimen (LSUMZ #110521) are as follows: Peru: Loreto Department; 1.5 km S Libertad, S. bank Rio Napo, 80 km N Iquitos.
 Total sequence genome input coverage on the Illumina HiSeq instrument was approx. 61x (41x fragments, 17x 3kb, and 3x 8kb) using a genome size estimate of 1Gb. The combined sequence reads were assembled using ALLPATHS-LG software (Gnerre et al 2011) and where possible, scaffold gaps were closed by mapping with 20X coverage of Illumina sequences and local gap assembly. Long insert reads were used to link assembled sequences into scaffolds using the program SSPACE (Boetzer 2011). This Lepidothrix coronata 1.0 version has been cleaned of contaminating contigs, and contigs 200bp and less were removed. The assembly is made up of a total of 4620 scaffolds (including single contig scaffolds) with an N50 scaffold length of 5.01Mb (N50 contig length is 142kb). The assembly spans 1.0.8Gb. 
 This work was supported by the following labs: 
 Dr. Bette Loiselle1,2 & Dr. John G. Blake1 1Center for Latin American Studies Professor, 2Department of Wildlife Ecology & Conservation University of Florida Gainesville, FL
 Dr. T. Brandt Ryder National Zoological Park Migratory Bird Center P.O. Box 37012- MRC 5503 Washington, DC 20013
 Dr. Michael J. Braun Dept. of Vertebrate Zoology National Museum of Natural History Smithsonian Institution- MRC 163 P.O. Box 37012 Washington DC 20013-7012
 DNA Source Contact: Dr. Michael J. Braun, braunm@si.edu, mailing address above
 Lepidothrix coronata 1.0 Sequence and Assembly Credits:
 WGS Source DNA - Dr. Michael J. Braun, National Museum of Natural History Smithsonian Institution, Washington DC. Genome Sequence - McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO. Sequence Assembly - McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO.

 Citation upon use of this assembly in a manuscript:
 It is requested that users of this Lepidothrix coronata 1.0 sequence assembly acknowledge Wesley Warren and McDonnell Genome Institute, Washington University School of Medicine in any publications that result from use of this sequence assembly. 

 Lepidothrix coronata 1.0 assembly statistics: (scaffold = supercontig)
 *** Contiguity: Contig *** Total contig number: 23511 Total contig bases: 1057205722 bp Average contig length: 44966 bp Maximum contig length: 1071009 bp N50 contig length: 141849 bp N50 contig number: 2198 
 *** Contiguity: Supercontig *** Total supercontig number: 4620 Average supercontig length: 228832 bp Maximum supercontig length: 19162435 bp N50 supercontig length: 5009311 bp N50 supercontig number: 68 
 *** Scaffold Distribution *** Scaffolds > 1M: 254 Scaffold 250K--1M: 101 Scaffold 100K--250K: 47 Scaffold 10--100K: 227 Scaffold 5--10K: 394 Scaffold 2--5K: 1869 Scaffold 0--2K: 1728  more

Global statistics