Open AccessHerbarium genomics: plastome sequence assembly from a range of herbarium specimens using an Iterative Organelle Genome Assembly pipeline
Author(s) -
Bakker Freek T.,
Lei Di,
Yu Jiaying,
Mohammadin Setareh,
Wei Zhen,
Kerke Sara,
Gravendeel Barbara,
Nieuwenhuis Mathijs,
Staats Martijn,
AlquezarPlanas David E.,
Holmer Rens
Publication year - 2016
Publication title -
biological journal of the linnean society
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.906
H-Index - 112
eISSN - 1095-8312
pISSN - 0024-4066
DOI - 10.1111/bij.12642
Subject(s) - herbarium , chloroplast dna , biology , genome , sequence assembly , dna sequencing , contig , genomics , computational biology , botany , genetics , dna , gene , gene expression , transcriptome
Herbarium genomics is proving promising as next‐generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA . We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired‐end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different Angiosperm families, 73 of which were from herbarium material with ages up to 146 years old. For 84 specimens, a sufficient number of paired‐end reads were generated (in total 9.4 × 10 12 nucleotides), yielding successful plastome assemblies for 74 specimens. Those derived from herbarium specimens have lower fractions of plastome‐derived reads compared with those from fresh and silica‐gel‐dried specimens, but total herbarium assembly lengths are only slightly shorter. Specimens from wet‐tropical conditions appear to have a higher number of contigs per assembly and lower N50 values. We find no significant correlation between plastome coverage and nuclear genome size ( C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost‐effective (compared with Sanger sequencing or plastome‐enrichment approaches), and can be performed with limited sample destruction.