Herbarium genomics: plastome sequence assembly from a range of herbarium specimens using an Iterative Organelle Genome Assembly pipeline

TY - JOUR

T1 - Herbarium genomics

T2 - plastome sequence assembly from a range of herbarium specimens using an Iterative Organelle Genome Assembly pipeline

AU - Bakker, Freek T.

AU - Lei, Di

AU - Yu, Jiaying

AU - Mohammadin, Setareh

AU - Wei, Zhen

AU - van de Kerke, Sara

AU - Gravendeel, Barbara

AU - Nieuwenhuis, Mathijs

AU - Staats, Martijn

AU - Alquezar Planas, David Eugenio

AU - Holmer, Rens

N1 - Special Issue: Collections-Based Research in the Genomic Era

PY - 2016

Y1 - 2016

N2 - 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 × 1012 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.

AB - 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 × 1012 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.

KW - Pelargonium

KW - Rinorea

KW - Assembly likelihood estimation

KW - Chloroplast DNA

KW - Organelle genome assembly

U2 - 10.1111/bij.12642

DO - 10.1111/bij.12642

M3 - Journal article

AN - SCOPUS:84955384677

SN - 0024-4066

VL - 117

SP - 33

EP - 43

JO - Proceedings of the Linnean Society of London

JF - Proceedings of the Linnean Society of London

IS - 1

ER -