---
identifier: LA2155.tcp.BTsx

provenance: "The files in this directory are the primary, initial source. The files here are held as part of the LegumeInfo, PeanutBase, and LegumeFederation projects."

synopsis: Transcriptome assemblies for Apios americana

scientific_name: Apios americana

taxid: 185702

scientific_name_abbrev: apiam

genotype:
  - AA-2155

description: "Files in this directory include the Trinity-derived transcriptome assemblies of the genotype indicated above. Assembly method: Trinity v 2.0.2, using default settings. Open reading frames (ORFs) using Transdecoder v 2.0.1 (https://transdecoder.github.io/) with parameters, -search_pfam and -m 67. The transcripts were scanned against the UniProt database with parameters (-e-value 1e-5 -num_threads 6 - -outfmt 6). The longest spliced variant was retained from each gene model to develop a set of unique transcripts. The remaining contigs were compared against each other to identify redundant contigs (sequence similarity >= 95%). Only the longest contigs from the latter analysis were used and placed with other unique contigs. The remaining contigs were compared again using the CD-Hit-EST program (Li and Godzik 2006) and the resulting unique sequences were used to create low-redundancy reduced reference transcriptome."

original_file_creation_date: "2015-09-27"

local_file_creation_date: "2017-05-19"

publication_doi: 10.1007/s00122-017-3004-3

dataset_release_date: "2017-05-19"

publication_title: "A Transcriptome-SNP-derived Linkage Map of Apios americana (Potato bean) Provides Insights about Genome Re-organization and Synteny Conservation in the Phaseolid Legumes"

contributors: "Jugpreet Singh, Scott R. Kalberer, Vikas Belamkar, Teshale Mamo, Matthew N. Nelson, Andrew D. Farmer, William J. Blackmon, Steven B. Cannon"

data_curators: Steven Cannon

public_access_level: public

license: Open access. 

keywords: Apios americana, potato bean, transcriptome

citation: "Jugpreet Singh, Scott R. Kalberer, Vikas Belamkar, Teshale Mamo, Matthew N. Nelson, Andrew D. Farmer, William J. Blackmon, Steven B. Cannon. A Transcriptome-SNP-derived Linkage Map of Apios americana (Potato bean) Provides Insights about Genome Re-organization and Synteny Conservation in the Phaseolid Legumes. Theoretical and Applied Genetics 131:333 (2018)."