Release notes
Notes for Build 2.1 back to top


Assembly
This build uses the Nvit_2.0 assembly from the Baylor College of Medicine Human Genome Sequencing Center, which includes updates to split a few erroneously assembled scaffolds and partially assemble scaffolds into 5 chromosomes based on the genetic mapping data of Niehuis et al, 2010.


Annotation
Transcript and protein predictions were computed using Gnomon, NCBI's genome annotation program. The model evidence used for this build included all publicly available Nasonia transcripts, as well as a set of transcriptome assemblies generated by Don Gilbert using Velvet with unpublished RNAseq data provided by Xu Wang and Jack Werren. It also included known and model RefSeq proteins from the latest NCBI annotation of Apis mellifera, and proteins from other insects. Curated transcript models are represented by RefSeq accessions with NM or NR prefixes, whereas computational predictions that are partially or fully supported by alignments are represented by RefSeq accessions with XM or XR prefixes. Additional ab initio models predicted by Gnomon that currently lack supporting alignments are also available for browsing on the model RNA track.


Map Viewer
The OGS_RNA map displays alignments of the Official Gene Set v1.2 (OGSv1.2) transcripts to the Nvit_2.0 assembly, as published by Werren et al 2010. The OGS is a set of gene predictions made by various research groups in the Nasonia Genome Working Group using the Baylor jewel wasp genome assembly version 1 (Nvit_1.0). The NCBI RefSeq predictions from build 1.1 plus a set of GLEAN and ab initio models were combined to create a non-redundant, consensus set of genes. This consensus set was aligned to the Nvit_2.0 assembly using Splign. An updated Official Gene Set based on the latest assembly and new gene models was still in progress at the time of release in Map Viewer.

The Repeats map includes both low complexity sequences and the positions of repetitive elements identified by Chris Smith at SFSU using PILER (Table_S30_Repeat-Library.fasta), placed on the Nvit_2.0 assembly using RepeatMasker


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