Biodiversity assessment: State-of-the-art techniques in phylogenomics and species identification

P. Roxanne Steele, J. Chris Pires

Research output: Contribution to journalArticle

46 Citations (Scopus)

Abstract

Premise of the study: Biodiversity assessment is the first step in protecting the complete range of morphological and genetic diversity of species on Earth, and in reaching the goals of conservation biology. Assessment begins with identifying organisms that make up biological communities and understanding evolutionary histories. Scientific advancements in molecular sequencing can help clarify and provide support for identifications. Massively parallel DNA sequencing technologies are being used to sequence complete genomes of model organisms; however, this resource has not been fully used for species identifications. Animal researchers commonly use one mitochondrial region, and groups of plant scientists have proposed numerous combinations of two or three chloroplast markers as genomic identifiers. Yet, nearly as many studies have reported that the proposed regions are uninformative in some plant groups and at various taxonomic levels. Methods: We propose a combination of whole (or nearly whole) chloroplast genomes, mitochondrial genes, and nuclear repeat regions for both species identifications and phylogenetic analyses, obtained from a simple total DNA extraction and one run on massively parallel DNA sequencing machines. Key results: We have recovered both coding and noncoding sequences from multiple genetic sources, providing genomic information for comparisons within and between multiple taxonomic levels. Conclusions: In combination with morphological and other data, this abundance of genomic information will have a broad range of applications, including not only helping conservation biologists understand ecosystem biodiversity, but also understanding the evolutionary histories of organisms, mending damaged landscapes, and investigating interactions of plants with pollinators and pests.

Original languageEnglish (US)
Pages (from-to)415-425
Number of pages11
JournalAmerican Journal of Botany
Volume98
Issue number3
DOIs
StatePublished - Mar 1 2011

Fingerprint

Biodiversity
High-Throughput Nucleotide Sequencing
genomics
biodiversity
DNA Sequence Analysis
DNA
chloroplast
organisms
sequence analysis
genome
Chloroplast Genome
Biota
history
Mitochondrial Genes
Chloroplasts
pollinator
pollinators
biologists
Ecosystem
chloroplasts

Keywords

  • Citizen science
  • DNA barcoding
  • Genome
  • Genome survey sequencing
  • Handheld field device
  • Mitochondria
  • Nextgeneration sequencing
  • Nuclear ribosomal DNA
  • Plastome
  • Whole genome shotgun

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Plant Science

Cite this

Biodiversity assessment : State-of-the-art techniques in phylogenomics and species identification. / Roxanne Steele, P.; Chris Pires, J.

In: American Journal of Botany, Vol. 98, No. 3, 01.03.2011, p. 415-425.

Research output: Contribution to journalArticle

@article{f47465ae16464789a769aed08d407c66,
title = "Biodiversity assessment: State-of-the-art techniques in phylogenomics and species identification",
abstract = "Premise of the study: Biodiversity assessment is the first step in protecting the complete range of morphological and genetic diversity of species on Earth, and in reaching the goals of conservation biology. Assessment begins with identifying organisms that make up biological communities and understanding evolutionary histories. Scientific advancements in molecular sequencing can help clarify and provide support for identifications. Massively parallel DNA sequencing technologies are being used to sequence complete genomes of model organisms; however, this resource has not been fully used for species identifications. Animal researchers commonly use one mitochondrial region, and groups of plant scientists have proposed numerous combinations of two or three chloroplast markers as genomic identifiers. Yet, nearly as many studies have reported that the proposed regions are uninformative in some plant groups and at various taxonomic levels. Methods: We propose a combination of whole (or nearly whole) chloroplast genomes, mitochondrial genes, and nuclear repeat regions for both species identifications and phylogenetic analyses, obtained from a simple total DNA extraction and one run on massively parallel DNA sequencing machines. Key results: We have recovered both coding and noncoding sequences from multiple genetic sources, providing genomic information for comparisons within and between multiple taxonomic levels. Conclusions: In combination with morphological and other data, this abundance of genomic information will have a broad range of applications, including not only helping conservation biologists understand ecosystem biodiversity, but also understanding the evolutionary histories of organisms, mending damaged landscapes, and investigating interactions of plants with pollinators and pests.",
keywords = "Citizen science, DNA barcoding, Genome, Genome survey sequencing, Handheld field device, Mitochondria, Nextgeneration sequencing, Nuclear ribosomal DNA, Plastome, Whole genome shotgun",
author = "{Roxanne Steele}, P. and {Chris Pires}, J.",
year = "2011",
month = "3",
day = "1",
doi = "10.3732/ajb.1000296",
language = "English (US)",
volume = "98",
pages = "415--425",
journal = "American Journal of Botany",
issn = "0002-9122",
publisher = "Botanical Society of America Inc.",
number = "3",

}

TY - JOUR

T1 - Biodiversity assessment

T2 - State-of-the-art techniques in phylogenomics and species identification

AU - Roxanne Steele, P.

AU - Chris Pires, J.

PY - 2011/3/1

Y1 - 2011/3/1

N2 - Premise of the study: Biodiversity assessment is the first step in protecting the complete range of morphological and genetic diversity of species on Earth, and in reaching the goals of conservation biology. Assessment begins with identifying organisms that make up biological communities and understanding evolutionary histories. Scientific advancements in molecular sequencing can help clarify and provide support for identifications. Massively parallel DNA sequencing technologies are being used to sequence complete genomes of model organisms; however, this resource has not been fully used for species identifications. Animal researchers commonly use one mitochondrial region, and groups of plant scientists have proposed numerous combinations of two or three chloroplast markers as genomic identifiers. Yet, nearly as many studies have reported that the proposed regions are uninformative in some plant groups and at various taxonomic levels. Methods: We propose a combination of whole (or nearly whole) chloroplast genomes, mitochondrial genes, and nuclear repeat regions for both species identifications and phylogenetic analyses, obtained from a simple total DNA extraction and one run on massively parallel DNA sequencing machines. Key results: We have recovered both coding and noncoding sequences from multiple genetic sources, providing genomic information for comparisons within and between multiple taxonomic levels. Conclusions: In combination with morphological and other data, this abundance of genomic information will have a broad range of applications, including not only helping conservation biologists understand ecosystem biodiversity, but also understanding the evolutionary histories of organisms, mending damaged landscapes, and investigating interactions of plants with pollinators and pests.

AB - Premise of the study: Biodiversity assessment is the first step in protecting the complete range of morphological and genetic diversity of species on Earth, and in reaching the goals of conservation biology. Assessment begins with identifying organisms that make up biological communities and understanding evolutionary histories. Scientific advancements in molecular sequencing can help clarify and provide support for identifications. Massively parallel DNA sequencing technologies are being used to sequence complete genomes of model organisms; however, this resource has not been fully used for species identifications. Animal researchers commonly use one mitochondrial region, and groups of plant scientists have proposed numerous combinations of two or three chloroplast markers as genomic identifiers. Yet, nearly as many studies have reported that the proposed regions are uninformative in some plant groups and at various taxonomic levels. Methods: We propose a combination of whole (or nearly whole) chloroplast genomes, mitochondrial genes, and nuclear repeat regions for both species identifications and phylogenetic analyses, obtained from a simple total DNA extraction and one run on massively parallel DNA sequencing machines. Key results: We have recovered both coding and noncoding sequences from multiple genetic sources, providing genomic information for comparisons within and between multiple taxonomic levels. Conclusions: In combination with morphological and other data, this abundance of genomic information will have a broad range of applications, including not only helping conservation biologists understand ecosystem biodiversity, but also understanding the evolutionary histories of organisms, mending damaged landscapes, and investigating interactions of plants with pollinators and pests.

KW - Citizen science

KW - DNA barcoding

KW - Genome

KW - Genome survey sequencing

KW - Handheld field device

KW - Mitochondria

KW - Nextgeneration sequencing

KW - Nuclear ribosomal DNA

KW - Plastome

KW - Whole genome shotgun

UR - http://www.scopus.com/inward/record.url?scp=79952766189&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79952766189&partnerID=8YFLogxK

U2 - 10.3732/ajb.1000296

DO - 10.3732/ajb.1000296

M3 - Article

C2 - 21613135

AN - SCOPUS:79952766189

VL - 98

SP - 415

EP - 425

JO - American Journal of Botany

JF - American Journal of Botany

SN - 0002-9122

IS - 3

ER -