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White-collared manakin (Manacus candei) assembly release notes##The white-collared manakin (family Pipridae) is a small frugivorous bird of tropical lowland forest understories ranging from southern Mexico to western Panama. Adult males have black wings, tail, and cap, a yellow belly, ... and a white collar consisting of the throat, breast, and upper back feathers. Immature males and females are uniformly olive green. There are no described subspecies.##White-collared manakins, like most manakins, are lekking birds: males aggregate to perform courtship displays for females, who evaluate different males in the lek. Males maintain a display court on the forest floor which they clear of all leaves and other debris. The male performs a display by jumping between small vertical stems in the court and landing with an upright posture with throat feathers flared out in a "beard." Before each jump, the male will strike its wings together over its back, making a loud "snap." When a female visits, the pair will jump back and forth between stems. The display ends with one of the birds leaving the court or with copulation, where the male performs a cartwheel to the ground, jumps up above the female on the court's central stem and finally slides down the stem to her.##This species has been studied primarily at the eastern edge of its range where it hybridizes with M. vitellinus, the golden-collared manakin. Plumage traits of golden-collared manakins, including a yellow collar and green belly, have introgressed 
50 km into genetic white-collared manakin populations under positive sexual selection. Active areas of research include the selective drivers and constraints on introgression, the genetic basis of introgressing plumage traits, and genomic factors contributing to partial reproductive isolation between white- and golden-collared manakins.##The adult male individual used for this assembly was collected 8 km southwest of Guabito, Bocas del Toro Province, Panama (9'28''N 82'40''W) on April 28, 1994. The voucher specimen (USNM #608988) and cryopreserved tissue samples are deposited at the US National Museum of Natural History, Smithsonian Institution in Washington DC USA. DNA was isolated by phenol-chloroform extraction and stored at -80degC prior to sequencing. DNA libraries were prepared and sequenced by the University of Maryland Institute for Genome Sciences on two PacBio Sequel II 8M SMRT Cells in CCS/HiFi mode using a 15 kb insert size. ###Sequencing/assembly stats ##The total sequence coverage for M. candei using (instrument- Pacbio HiFi) was 45x. The reads were combined into one file and remnant PacBio adapter sequences were removed using HiFiAdapterFilt (Sim et al 2022). The reads were then assembled using the de novo Hifiasm assembler (Cheng et al 2021). The resulting assembly contained 643 contigs with an N50 contig length of 15991245 bp. The assembly spans 1.12 Gb. ##*** Contiguity: Contig ***#Total contig number: 643#Total contig bases: 1121284527#Average contig length: 1743832#Maximum contig length: 83188583 bp#N50 contig length: 15991245 bp#N50 contig number: 19##This work was supported by a Core Grant for Science from the National Museum of Natural History, Smithsonian Institution to Michael Braun (braunm@si.edu) and Kevin Bennett (BennettKF@si.edu)##Mailing Address: Dept. of Vertebrate Zoology National Museum of Natural History Smithsonian Institution- MRC 163 P.O. Box 37012 Washington DC 20013-7012##Manacus candei 1.0 Sequence and Assembly Credits:##WGS Source DNA - Dr. Michael J. Braun, National Museum of Natural History Smithsonian Institution, Washington DC. ##Genome Sequence - Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201.##Sequence Assembly - Madeline Bursell (BursellM@si.edu) and Dr. Rebecca Dikow (DikowR@si.edu), Research Computing- OCIO, Smithsonian Institution, Herndon VA  more

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