e-journal

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

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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 x 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 silicagel-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.

ADDITIONAL KEYWORDS: assembly likelihood estimation – chloroplast DNA – organelle genome assembly – Pelargonium – Rinorea.

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Informasi Detail

Judul Seri

Biological Journal of the Linnean Society

No. Panggil

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Penerbit

London : The Linnean Society of London., 2016

Deskripsi Fisik

Biological Journal of the Linnean Society, 2016, 117, 33–43.

Bahasa

English

ISBN/ISSN

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Klasifikasi

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Tipe Isi

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Tipe Media

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Tipe Pembawa

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Edisi

2016, 117

Subjek

BIOLOGI

Info Detail Spesifik

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Pernyataan Tanggungjawab

agus

Versi lain/terkait

Lampiran Berkas

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