Genome Assemblies

Echinoderm Genome Assemblies by Species

Patiria miniata

V2.0 Assembly

We sought to improve the Patiria miniata genome assembly with additional PacBio sequences. We generated a new PacBio read dataset at the Duke University Sequencing Center using our reference individual DNA. The read dataset contains 2 million reads and 15.8 billion bp. The read N50 is 10.4 Kb. We used PBJelly2 to combine the PacBio reads with the previously assembled contigs. The results were an improvement in contig size and number with only a small reduction in the number of scaffolds (Table). The P. miniata Gene v2.0 set was generated using MAKER2 pipeline from v2.0 genome assembly.

	Pm v1.0	Pm v2.0
Scaffold number	60,183	57,698
Scaffold N50	52,6141	76,341
Contig number	179,756	131,779
Contig N50	9,466	18,676

V1.0 Assembly

What's New

Pmin_1.0 is the latest (as of Apr 11, 2012) assembly of the genome of Patiria Miniata. The assembly tools CABOG (Celera Assembler), Newbler, ATLAS-Link, and ATLAS-GapFill were used to assemble a combination of 454 reads (fragment and 2.5kb insert paired ends;~15x coverage) and Illumina reads (300bp insert and 2.5kb insert paired ends;~70x coverage).

Introduction

This information is for the first release (Pmin_1.0) of the draft genome sequence of the Patiria miniata . This is a draft sequence and may contain errors so users should exercise caution.Typical errors in draft genome sequences include misassemblies of repeated sequences, collapses of repeated regions, and unmerged overlaps(e.g. due to polymorphisms) creating artificial duplications.

With a goal of solving the polymorphism issues of the data while maintaining the sequence continuity, The Pmin_1.0 assembly was generated in the following steps:

1. 454 reads were assembled by CABOG using settings less strignent than the default (unitigger=bog utgErrorRate=0.03 ovlErrorRate=0.08 cnsErrorRate=0.08 cgwErrorRate=0.14 doExtendClearRanges=0)
2. Both contig and degenerate sequences from the previous step were chopped into fake reads with ~11x coverage (500bp long; 460bp overlap; 80bp minimal length) for ctgs and 8x coverage(450bp long; 400bp overlap; 80bp minimal length) for degs. The fake reads were then assembled by Newbler with the option of -large.
3. Both 454 and iIlumina pair end reads were mapped to the contigs from the previous step. We used BLAT to map the 454 data and bwa(aln+samse) to map the Illumina data, both with the default options. Based on the mapping locations of the paired ends, contigs were then ordered and oriented into scaffolds using ATLAS-Link.
4. ATLAS-GapFill was then used to assemble the reads locally in an attempt to fill the gaps among the contigs within the scaffolds.This final step produced 770.5Mb sequences with contig N50 size of 9.5kb and scaffold N50 size of 50.3kb.

Conditions for use

These data are made available before scientific publication with the following understanding:

• The data may be freely downloaded, used in analyses, and repackaged in databases.

• Users are free to use the data in scientific papers analyzing particular genes and regions if the providers of this data (Baylor College of Medicine Human Genome Sequencing Center) are properly acknowledged. Please cite the BCM-HGSC web site or publications from BCM-HGSC referring to the genome sequence.

• The BCM-HGSC plans to publish the assembly and genomic annotation of the dataset, including large-scale identification of regions of evolutionary conservation and other features.

• This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects and the resulting NHGRI policy statement (http://www.genome.gov/page.cfm?pageID=10506537).

• Any redistribution of the data should carry this notice.

Description of files

There are 2 directories.

1. Contigs/ directory
This directory has 2 files for assembled contigs in the genome, there is no chromosome assignment for the contigs in Pmin_1.0. Pmin_1.0.20120411.contigs.agp (agp file) Pmin_1.0.20120411.contigs.fa (fasta file) The Pmin_1.0.20120411.contigs.agp file describes the positions and orientations of the contigs in the group. It takes the standard NCBI format.
2. LinearScaffolds/ directory
This directory has 1 file Pmin_1.0.20120411.linear.fa The sequences are linearized scaffolds where the gaps between adjacent contigs within a scaffold are filled with 'N's and the captured gap size is estimated from the clone insert size.

Sequence Statistics

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Scaffolds/Contigs	Number	N50 (kb)	Bases (Mb)	Gap (Mb)
All Scaffolds	60,336	50.3	811.6	41.1
All Contigs	181,436	9.5	770.5	N/A

History

Pmin_1.0 (Apr, 2012) This release was the first assembly of the Patiria Miniata genome.