The Influence of Specific Neighboring Bases on Substitution Bias in Noncoding Regions of the Plant Chloroplast Genome View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

1997-09

AUTHORS

Brian R. Morton, Virginia M. Oberholzer, Michael T. Clegg

ABSTRACT

Substitutions occurring in noncoding sequences of the plant chloroplast genome violate the independence of sites that is assumed by substitution models in molecular evolution. The probability that a substitution at a site is a transversion, as opposed to a transition, increases significantly with increasing A + T content of the two adjacent nucleotides. In the present study, this dependency of substitutions on local context is examined further in a number of noncoding regions from the chloroplast genome of members of the grass family (Poaceae). Two features were examined; the influence of specific neighboring bases, as opposed to the general A + T content, on transversion proportion and an influence on substitutions by nucleotides other than the two immediately adjacent to the site of substitution. In both cases, a significant effect was found. In the case of specific nucleotides, transversion proportion is significantly higher at sites with a pyrimidine immediately 5' on either strand. Substitutions at sites of the type YNR, where N is the site of substitution, have the highest rate of transversion. This specific effect is secondary to the A + T content effect such that, in terms of proportion of substitutions that are transversions, the nucleotides are ranked T > A > C > G as to their effect when they are immediately 5' to the site of substitution. In the case of nucleotides other than the immediate neighbors, a significant influence on substitution dynamics is observed in the case where the two neighboring bases are both A and/or T. Thus, substitutions are primarily, but not exclusively, influenced by the composition of the two nucleotides that are immediately adjacent. These results indicate that the pattern of molecular evolution of the plant chloroplast genome is extremely complex as a result of a variety of inter-site dependencies. More... »

PAGES

227-231

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/pl00006224

DOI

http://dx.doi.org/10.1007/pl00006224

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1000719586

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/9302315


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Chloroplasts", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Evolution, Molecular", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genes, Plant", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genome, Plant", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Models, Genetic", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Open Reading Frames", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Purines", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Pyrimidines", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Columbia University", 
          "id": "https://www.grid.ac/institutes/grid.21729.3f", 
          "name": [
            "Department of Biological Sciences, Barnard College, Columbia University, 3009 Broadway, New York, NY 10027, USA, US"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Morton", 
        "givenName": "Brian R.", 
        "id": "sg:person.0733151570.08", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0733151570.08"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of California, Riverside", 
          "id": "https://www.grid.ac/institutes/grid.266097.c", 
          "name": [
            "Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA, US"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Oberholzer", 
        "givenName": "Virginia M.", 
        "id": "sg:person.01021644533.47", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01021644533.47"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of California, Riverside", 
          "id": "https://www.grid.ac/institutes/grid.266097.c", 
          "name": [
            "Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA, US"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Clegg", 
        "givenName": "Michael T.", 
        "id": "sg:person.01146631174.19", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01146631174.19"
        ], 
        "type": "Person"
      }
    ], 
    "datePublished": "1997-09", 
    "datePublishedReg": "1997-09-01", 
    "description": "Substitutions occurring in noncoding sequences of the plant chloroplast genome violate the independence of sites that is assumed by substitution models in molecular evolution. The probability that a substitution at a site is a transversion, as opposed to a transition, increases significantly with increasing A + T content of the two adjacent nucleotides. In the present study, this dependency of substitutions on local context is examined further in a number of noncoding regions from the chloroplast genome of members of the grass family (Poaceae). Two features were examined; the influence of specific neighboring bases, as opposed to the general A + T content, on transversion proportion and an influence on substitutions by nucleotides other than the two immediately adjacent to the site of substitution. In both cases, a significant effect was found. In the case of specific nucleotides, transversion proportion is significantly higher at sites with a pyrimidine immediately 5' on either strand. Substitutions at sites of the type YNR, where N is the site of substitution, have the highest rate of transversion. This specific effect is secondary to the A + T content effect such that, in terms of proportion of substitutions that are transversions, the nucleotides are ranked T > A > C > G as to their effect when they are immediately 5' to the site of substitution. In the case of nucleotides other than the immediate neighbors, a significant influence on substitution dynamics is observed in the case where the two neighboring bases are both A and/or T. Thus, substitutions are primarily, but not exclusively, influenced by the composition of the two nucleotides that are immediately adjacent. These results indicate that the pattern of molecular evolution of the plant chloroplast genome is extremely complex as a result of a variety of inter-site dependencies.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1007/pl00006224", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": false, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.2513351", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1016442", 
        "issn": [
          "0022-2844", 
          "1432-1432"
        ], 
        "name": "Journal of Molecular Evolution", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "3", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "45"
      }
    ], 
    "name": "The Influence of Specific Neighboring Bases on Substitution Bias in Noncoding Regions of the Plant Chloroplast Genome", 
    "pagination": "227-231", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "036d2ab5f0a2a2ec619128f190f57abda7a9bcf8410d5557e3e40130e29658cd"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "9302315"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "0360051"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/pl00006224"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1000719586"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1007/pl00006224", 
      "https://app.dimensions.ai/details/publication/pub.1000719586"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T20:46", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8684_00000509.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://link.springer.com/10.1007%2FPL00006224"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/pl00006224'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/pl00006224'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/pl00006224'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/pl00006224'


 

This table displays all metadata directly associated to this object as RDF triples.

120 TRIPLES      20 PREDICATES      37 URIs      29 LITERALS      17 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/pl00006224 schema:about N05b57461fbf94262bd36a7c022867f2f
2 N21fb114641c84ceeba0116683b11d4da
3 N35209b2d57834c91a8b37b69e1d746d2
4 N39cf4e5a5b114779950bd65c673265ca
5 Na2725de721b04fd8a26c16912a86fc1b
6 Nc806c58b2c404b9e84239d3183b6df20
7 Ne1afd3e5cfb444cb84c8631147d3b1c8
8 Nfef02e4bab1d44bea4b5fe026aa79613
9 anzsrc-for:06
10 anzsrc-for:0604
11 schema:author Na04427f54cc844178dbf00b3c03f70f9
12 schema:datePublished 1997-09
13 schema:datePublishedReg 1997-09-01
14 schema:description Substitutions occurring in noncoding sequences of the plant chloroplast genome violate the independence of sites that is assumed by substitution models in molecular evolution. The probability that a substitution at a site is a transversion, as opposed to a transition, increases significantly with increasing A + T content of the two adjacent nucleotides. In the present study, this dependency of substitutions on local context is examined further in a number of noncoding regions from the chloroplast genome of members of the grass family (Poaceae). Two features were examined; the influence of specific neighboring bases, as opposed to the general A + T content, on transversion proportion and an influence on substitutions by nucleotides other than the two immediately adjacent to the site of substitution. In both cases, a significant effect was found. In the case of specific nucleotides, transversion proportion is significantly higher at sites with a pyrimidine immediately 5' on either strand. Substitutions at sites of the type YNR, where N is the site of substitution, have the highest rate of transversion. This specific effect is secondary to the A + T content effect such that, in terms of proportion of substitutions that are transversions, the nucleotides are ranked T > A > C > G as to their effect when they are immediately 5' to the site of substitution. In the case of nucleotides other than the immediate neighbors, a significant influence on substitution dynamics is observed in the case where the two neighboring bases are both A and/or T. Thus, substitutions are primarily, but not exclusively, influenced by the composition of the two nucleotides that are immediately adjacent. These results indicate that the pattern of molecular evolution of the plant chloroplast genome is extremely complex as a result of a variety of inter-site dependencies.
15 schema:genre research_article
16 schema:inLanguage en
17 schema:isAccessibleForFree false
18 schema:isPartOf N36ca67d3878d49b09b2f8076f881b436
19 N9d5711dcacfc4e09b4dd32cdceee660c
20 sg:journal.1016442
21 schema:name The Influence of Specific Neighboring Bases on Substitution Bias in Noncoding Regions of the Plant Chloroplast Genome
22 schema:pagination 227-231
23 schema:productId N2d8577990af64fa6b166be88f372e04b
24 N3d928110040744d893eb927d0085ebe3
25 N9332b08b7593440b849f739fbcd5af62
26 Nc0eeeabab8bf40c7ad2695a23ed928e9
27 Nd17b8fad5fc946299d8dd418f86820ad
28 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000719586
29 https://doi.org/10.1007/pl00006224
30 schema:sdDatePublished 2019-04-10T20:46
31 schema:sdLicense https://scigraph.springernature.com/explorer/license/
32 schema:sdPublisher N6a69cd4c9d3043b584cfca242b38f39a
33 schema:url http://link.springer.com/10.1007%2FPL00006224
34 sgo:license sg:explorer/license/
35 sgo:sdDataset articles
36 rdf:type schema:ScholarlyArticle
37 N05b57461fbf94262bd36a7c022867f2f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
38 schema:name Models, Genetic
39 rdf:type schema:DefinedTerm
40 N21fb114641c84ceeba0116683b11d4da schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
41 schema:name Purines
42 rdf:type schema:DefinedTerm
43 N2d8577990af64fa6b166be88f372e04b schema:name dimensions_id
44 schema:value pub.1000719586
45 rdf:type schema:PropertyValue
46 N35209b2d57834c91a8b37b69e1d746d2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
47 schema:name Chloroplasts
48 rdf:type schema:DefinedTerm
49 N36ca67d3878d49b09b2f8076f881b436 schema:issueNumber 3
50 rdf:type schema:PublicationIssue
51 N39cf4e5a5b114779950bd65c673265ca schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
52 schema:name Genome, Plant
53 rdf:type schema:DefinedTerm
54 N3d928110040744d893eb927d0085ebe3 schema:name doi
55 schema:value 10.1007/pl00006224
56 rdf:type schema:PropertyValue
57 N6a69cd4c9d3043b584cfca242b38f39a schema:name Springer Nature - SN SciGraph project
58 rdf:type schema:Organization
59 N9332b08b7593440b849f739fbcd5af62 schema:name nlm_unique_id
60 schema:value 0360051
61 rdf:type schema:PropertyValue
62 N9d5711dcacfc4e09b4dd32cdceee660c schema:volumeNumber 45
63 rdf:type schema:PublicationVolume
64 Na04427f54cc844178dbf00b3c03f70f9 rdf:first sg:person.0733151570.08
65 rdf:rest Ncb1839d188634626b513c5d8b222a306
66 Na2725de721b04fd8a26c16912a86fc1b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
67 schema:name Open Reading Frames
68 rdf:type schema:DefinedTerm
69 Nc0eeeabab8bf40c7ad2695a23ed928e9 schema:name readcube_id
70 schema:value 036d2ab5f0a2a2ec619128f190f57abda7a9bcf8410d5557e3e40130e29658cd
71 rdf:type schema:PropertyValue
72 Nc806c58b2c404b9e84239d3183b6df20 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
73 schema:name Genes, Plant
74 rdf:type schema:DefinedTerm
75 Ncb1839d188634626b513c5d8b222a306 rdf:first sg:person.01021644533.47
76 rdf:rest Nfc9e55819b63411b8a4947638c74e363
77 Nd17b8fad5fc946299d8dd418f86820ad schema:name pubmed_id
78 schema:value 9302315
79 rdf:type schema:PropertyValue
80 Ne1afd3e5cfb444cb84c8631147d3b1c8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
81 schema:name Pyrimidines
82 rdf:type schema:DefinedTerm
83 Nfc9e55819b63411b8a4947638c74e363 rdf:first sg:person.01146631174.19
84 rdf:rest rdf:nil
85 Nfef02e4bab1d44bea4b5fe026aa79613 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
86 schema:name Evolution, Molecular
87 rdf:type schema:DefinedTerm
88 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
89 schema:name Biological Sciences
90 rdf:type schema:DefinedTerm
91 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
92 schema:name Genetics
93 rdf:type schema:DefinedTerm
94 sg:grant.2513351 http://pending.schema.org/fundedItem sg:pub.10.1007/pl00006224
95 rdf:type schema:MonetaryGrant
96 sg:journal.1016442 schema:issn 0022-2844
97 1432-1432
98 schema:name Journal of Molecular Evolution
99 rdf:type schema:Periodical
100 sg:person.01021644533.47 schema:affiliation https://www.grid.ac/institutes/grid.266097.c
101 schema:familyName Oberholzer
102 schema:givenName Virginia M.
103 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01021644533.47
104 rdf:type schema:Person
105 sg:person.01146631174.19 schema:affiliation https://www.grid.ac/institutes/grid.266097.c
106 schema:familyName Clegg
107 schema:givenName Michael T.
108 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01146631174.19
109 rdf:type schema:Person
110 sg:person.0733151570.08 schema:affiliation https://www.grid.ac/institutes/grid.21729.3f
111 schema:familyName Morton
112 schema:givenName Brian R.
113 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0733151570.08
114 rdf:type schema:Person
115 https://www.grid.ac/institutes/grid.21729.3f schema:alternateName Columbia University
116 schema:name Department of Biological Sciences, Barnard College, Columbia University, 3009 Broadway, New York, NY 10027, USA, US
117 rdf:type schema:Organization
118 https://www.grid.ac/institutes/grid.266097.c schema:alternateName University of California, Riverside
119 schema:name Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA, US
120 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...