Phototroph genomics ten years on

Jason Raymond, Wesley D. Swingley

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

The onset of the genome era means different things to different people, but it is clear that this new age brings with it paradigm shifts that will forever affect biological research. Less clear is just how these shifts are changing the scope and scale of research. Are gigabases of raw data more useful than a single well-understood gene? Do we really need a full genome to understand the physiology of a single organism? The photosynthetic field is poised at the periphery of the bulk of genome sequencing work-understandably skewed toward health-related disciplines-and, as such, is subject to different motivations, limitations, and primary focus for each new genome. To understand some of these differences, we focus here on various indicators of the impact that genomics has had on the photosynthetic community, now a full decade since the publication of the first photosynthetic genome. Many useful indicators are indexed in public databases, providing pre- and post-genome sequence snapshots of changes in factors such as publication rate, number of proteins characterized, and sequenced genome coverage versus known diversity. As more genomes are sequenced and metagenomic projects begin to pour out billions of bases, it becomes crucial to understand how to harness this data in order to accumulate possible benefits and avoid possible pitfalls, especially as resources become increasingly directed toward natural environments governed by photosynthetic activity, ranging from hot springs to tropical forest ecosystems to the open ocean.

Original languageEnglish (US)
Pages (from-to)5-19
Number of pages15
JournalPhotosynthesis Research
Volume97
Issue number1
DOIs
StatePublished - Jul 2008
Externally publishedYes

Fingerprint

Genomics
Genes
Genome
genomics
genome
Publications
Hot Springs
Metagenomics
Hot springs
harness
hot springs
Physiology
Research
Oceans and Seas
forest ecosystems
tropical forests
Ecosystem
Ecosystems
physiology
oceans

Keywords

  • Chlorobi
  • Chloroflexi
  • Cyanobacteria
  • Genome sequencing
  • Heliobacteria
  • Metagenomics
  • Proteobacteria

ASJC Scopus subject areas

  • Plant Science

Cite this

Phototroph genomics ten years on. / Raymond, Jason; Swingley, Wesley D.

In: Photosynthesis Research, Vol. 97, No. 1, 07.2008, p. 5-19.

Research output: Contribution to journalArticle

Raymond, J & Swingley, WD 2008, 'Phototroph genomics ten years on', Photosynthesis Research, vol. 97, no. 1, pp. 5-19. https://doi.org/10.1007/s11120-008-9308-z
Raymond, Jason ; Swingley, Wesley D. / Phototroph genomics ten years on. In: Photosynthesis Research. 2008 ; Vol. 97, No. 1. pp. 5-19.
@article{8c15cb0075ad4cb98539eff0c12d1bc0,
title = "Phototroph genomics ten years on",
abstract = "The onset of the genome era means different things to different people, but it is clear that this new age brings with it paradigm shifts that will forever affect biological research. Less clear is just how these shifts are changing the scope and scale of research. Are gigabases of raw data more useful than a single well-understood gene? Do we really need a full genome to understand the physiology of a single organism? The photosynthetic field is poised at the periphery of the bulk of genome sequencing work-understandably skewed toward health-related disciplines-and, as such, is subject to different motivations, limitations, and primary focus for each new genome. To understand some of these differences, we focus here on various indicators of the impact that genomics has had on the photosynthetic community, now a full decade since the publication of the first photosynthetic genome. Many useful indicators are indexed in public databases, providing pre- and post-genome sequence snapshots of changes in factors such as publication rate, number of proteins characterized, and sequenced genome coverage versus known diversity. As more genomes are sequenced and metagenomic projects begin to pour out billions of bases, it becomes crucial to understand how to harness this data in order to accumulate possible benefits and avoid possible pitfalls, especially as resources become increasingly directed toward natural environments governed by photosynthetic activity, ranging from hot springs to tropical forest ecosystems to the open ocean.",
keywords = "Chlorobi, Chloroflexi, Cyanobacteria, Genome sequencing, Heliobacteria, Metagenomics, Proteobacteria",
author = "Jason Raymond and Swingley, {Wesley D.}",
year = "2008",
month = "7",
doi = "10.1007/s11120-008-9308-z",
language = "English (US)",
volume = "97",
pages = "5--19",
journal = "Photosynthesis Research",
issn = "0166-8595",
publisher = "Springer Netherlands",
number = "1",

}

TY - JOUR

T1 - Phototroph genomics ten years on

AU - Raymond, Jason

AU - Swingley, Wesley D.

PY - 2008/7

Y1 - 2008/7

N2 - The onset of the genome era means different things to different people, but it is clear that this new age brings with it paradigm shifts that will forever affect biological research. Less clear is just how these shifts are changing the scope and scale of research. Are gigabases of raw data more useful than a single well-understood gene? Do we really need a full genome to understand the physiology of a single organism? The photosynthetic field is poised at the periphery of the bulk of genome sequencing work-understandably skewed toward health-related disciplines-and, as such, is subject to different motivations, limitations, and primary focus for each new genome. To understand some of these differences, we focus here on various indicators of the impact that genomics has had on the photosynthetic community, now a full decade since the publication of the first photosynthetic genome. Many useful indicators are indexed in public databases, providing pre- and post-genome sequence snapshots of changes in factors such as publication rate, number of proteins characterized, and sequenced genome coverage versus known diversity. As more genomes are sequenced and metagenomic projects begin to pour out billions of bases, it becomes crucial to understand how to harness this data in order to accumulate possible benefits and avoid possible pitfalls, especially as resources become increasingly directed toward natural environments governed by photosynthetic activity, ranging from hot springs to tropical forest ecosystems to the open ocean.

AB - The onset of the genome era means different things to different people, but it is clear that this new age brings with it paradigm shifts that will forever affect biological research. Less clear is just how these shifts are changing the scope and scale of research. Are gigabases of raw data more useful than a single well-understood gene? Do we really need a full genome to understand the physiology of a single organism? The photosynthetic field is poised at the periphery of the bulk of genome sequencing work-understandably skewed toward health-related disciplines-and, as such, is subject to different motivations, limitations, and primary focus for each new genome. To understand some of these differences, we focus here on various indicators of the impact that genomics has had on the photosynthetic community, now a full decade since the publication of the first photosynthetic genome. Many useful indicators are indexed in public databases, providing pre- and post-genome sequence snapshots of changes in factors such as publication rate, number of proteins characterized, and sequenced genome coverage versus known diversity. As more genomes are sequenced and metagenomic projects begin to pour out billions of bases, it becomes crucial to understand how to harness this data in order to accumulate possible benefits and avoid possible pitfalls, especially as resources become increasingly directed toward natural environments governed by photosynthetic activity, ranging from hot springs to tropical forest ecosystems to the open ocean.

KW - Chlorobi

KW - Chloroflexi

KW - Cyanobacteria

KW - Genome sequencing

KW - Heliobacteria

KW - Metagenomics

KW - Proteobacteria

UR - http://www.scopus.com/inward/record.url?scp=48449090797&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=48449090797&partnerID=8YFLogxK

U2 - 10.1007/s11120-008-9308-z

DO - 10.1007/s11120-008-9308-z

M3 - Article

VL - 97

SP - 5

EP - 19

JO - Photosynthesis Research

JF - Photosynthesis Research

SN - 0166-8595

IS - 1

ER -