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Microsynteny analysis to understand evolution and impact of polyploidization on MIR319 family within Brassicaceae
The availability of a large number of whole-genome sequences allows comparative genomic analysis to reveal and understand evolution of regulatory regions and elements. The role played by events such as whole-genome and segmental duplications followed by genome fractionation in shaping genomic landsc...
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Published in: | Development genes and evolution 2018-12, Vol.228 (6), p.227-242 |
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description | The availability of a large number of whole-genome sequences allows comparative genomic analysis to reveal and understand evolution of regulatory regions and elements. The role played by events such as whole-genome and segmental duplications followed by genome fractionation in shaping genomic landscape and in expansion of gene families is crucial toward developing insights into evolutionary trends and consequences such as sequence and functional diversification. Members of Brassicaceae are known to have experienced several rounds of whole-genome duplication (WGD) that have been termed as paleopolyploidy, mesopolyploidy, and neopolyploidy. Such repeated events led to the creation and expansion of a large number of gene families.
MIR319
is reported to be one of the most ancient and conserved plant
MIRNA
families and plays a role in growth and development including leaf development, seedling development, and embryo patterning. We have previously reported functional diversification of members of
miR319
in
Brassica oleracea
affecting leaf architecture; however, the evolutionary history of the
MIR319
gene family across Brassicaceae remains unknown and requires investigation. We therefore identified homologous and homeologous segments of ca. 100 kb, with or without
MIR319
, performed comparative synteny analysis and genome fractionation studies. We detected variable rates of gene retention across members of Brassicaceae when genomic blocks of
MIR319a
,
MIR319b
, and
MIR319c
were compared either between themselves or against
Arabidopsis thaliana
genome which was taken as the base genome. The highest levels of shared genes were found between
A. thaliana
and
Capsella rubella
in both
MIR319b
- and
MIR319c
-containing genomic segments, and with the closest species of
A. thaliana
,
A. lyrata
, only in
MIR319a
-containing segment. Synteny analysis across 12 genomes (with 30 sub-genomes) revealed
MIR319c
to be the most conserved
MIRNA
loci (present in 27 genomes/sub-genomes) followed by
MIR319a
(present in 23 genomes/sub-genomes);
MIR319b
was found to be frequently lost (present in 20 genomes/sub-genomes) and thus is under least selection pressure for retention. Genome fractionation revealed extensive and differential loss of
MIRNA
homeologous loci and flanking genes from various sub-genomes of
Brassica
species that is in accordance with their older history of polyploidy when compared to
Camelina sativa,
a recent neopolyploid, where the effect of genome fractionation was |
doi_str_mv | 10.1007/s00427-018-0620-0 |
format | article |
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MIR319
is reported to be one of the most ancient and conserved plant
MIRNA
families and plays a role in growth and development including leaf development, seedling development, and embryo patterning. We have previously reported functional diversification of members of
miR319
in
Brassica oleracea
affecting leaf architecture; however, the evolutionary history of the
MIR319
gene family across Brassicaceae remains unknown and requires investigation. We therefore identified homologous and homeologous segments of ca. 100 kb, with or without
MIR319
, performed comparative synteny analysis and genome fractionation studies. We detected variable rates of gene retention across members of Brassicaceae when genomic blocks of
MIR319a
,
MIR319b
, and
MIR319c
were compared either between themselves or against
Arabidopsis thaliana
genome which was taken as the base genome. The highest levels of shared genes were found between
A. thaliana
and
Capsella rubella
in both
MIR319b
- and
MIR319c
-containing genomic segments, and with the closest species of
A. thaliana
,
A. lyrata
, only in
MIR319a
-containing segment. Synteny analysis across 12 genomes (with 30 sub-genomes) revealed
MIR319c
to be the most conserved
MIRNA
loci (present in 27 genomes/sub-genomes) followed by
MIR319a
(present in 23 genomes/sub-genomes);
MIR319b
was found to be frequently lost (present in 20 genomes/sub-genomes) and thus is under least selection pressure for retention. Genome fractionation revealed extensive and differential loss of
MIRNA
homeologous loci and flanking genes from various sub-genomes of
Brassica
species that is in accordance with their older history of polyploidy when compared to
Camelina sativa,
a recent neopolyploid, where the effect of genome fractionation was least. Finally, estimation of phylogenetic relationship using precursor sequences of
MIR319
reveals
MIR319a
and
MIR319b
form sister clades, with
MIR319c
forming a separate clade. An intra-species synteny analysis between
MIR319a
-,
MIR319b-
, and
MIR319c-
containing genomic segments suggests segmental duplications at the base of Brassicaceae to be responsible for the origin of
MIR319a
and
MIR319b
.</description><identifier>ISSN: 0949-944X</identifier><identifier>EISSN: 1432-041X</identifier><identifier>DOI: 10.1007/s00427-018-0620-0</identifier><identifier>PMID: 30242472</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Animal Genetics and Genomics ; Biomedical and Life Sciences ; Brassicaceae ; Cell Biology ; Developmental Biology ; Evolutionary Biology ; Evolutionary genetics ; Gene families ; Genes ; Genomes ; Genomic analysis ; Leaves ; Life Sciences ; miRNA ; Original Article ; Pattern formation ; Phylogeny ; Plant Genetics and Genomics ; Polyploidy ; Regulatory sequences ; Seedlings ; Species ; Synteny ; Zoology</subject><ispartof>Development genes and evolution, 2018-12, Vol.228 (6), p.227-242</ispartof><rights>Springer-Verlag GmbH Germany, part of Springer Nature 2018</rights><rights>Development Genes and Evolution is a copyright of Springer, (2018). All Rights Reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c372t-377ebd1a100a9b97efc12a67627ccb982a21fbe1915864497c7697d2f445838d3</citedby><cites>FETCH-LOGICAL-c372t-377ebd1a100a9b97efc12a67627ccb982a21fbe1915864497c7697d2f445838d3</cites><orcidid>0000-0002-9241-2613</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30242472$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Joshi, Gauri</creatorcontrib><creatorcontrib>Chauhan, Chetan</creatorcontrib><creatorcontrib>Das, Sandip</creatorcontrib><title>Microsynteny analysis to understand evolution and impact of polyploidization on MIR319 family within Brassicaceae</title><title>Development genes and evolution</title><addtitle>Dev Genes Evol</addtitle><addtitle>Dev Genes Evol</addtitle><description>The availability of a large number of whole-genome sequences allows comparative genomic analysis to reveal and understand evolution of regulatory regions and elements. The role played by events such as whole-genome and segmental duplications followed by genome fractionation in shaping genomic landscape and in expansion of gene families is crucial toward developing insights into evolutionary trends and consequences such as sequence and functional diversification. Members of Brassicaceae are known to have experienced several rounds of whole-genome duplication (WGD) that have been termed as paleopolyploidy, mesopolyploidy, and neopolyploidy. Such repeated events led to the creation and expansion of a large number of gene families.
MIR319
is reported to be one of the most ancient and conserved plant
MIRNA
families and plays a role in growth and development including leaf development, seedling development, and embryo patterning. We have previously reported functional diversification of members of
miR319
in
Brassica oleracea
affecting leaf architecture; however, the evolutionary history of the
MIR319
gene family across Brassicaceae remains unknown and requires investigation. We therefore identified homologous and homeologous segments of ca. 100 kb, with or without
MIR319
, performed comparative synteny analysis and genome fractionation studies. We detected variable rates of gene retention across members of Brassicaceae when genomic blocks of
MIR319a
,
MIR319b
, and
MIR319c
were compared either between themselves or against
Arabidopsis thaliana
genome which was taken as the base genome. The highest levels of shared genes were found between
A. thaliana
and
Capsella rubella
in both
MIR319b
- and
MIR319c
-containing genomic segments, and with the closest species of
A. thaliana
,
A. lyrata
, only in
MIR319a
-containing segment. Synteny analysis across 12 genomes (with 30 sub-genomes) revealed
MIR319c
to be the most conserved
MIRNA
loci (present in 27 genomes/sub-genomes) followed by
MIR319a
(present in 23 genomes/sub-genomes);
MIR319b
was found to be frequently lost (present in 20 genomes/sub-genomes) and thus is under least selection pressure for retention. Genome fractionation revealed extensive and differential loss of
MIRNA
homeologous loci and flanking genes from various sub-genomes of
Brassica
species that is in accordance with their older history of polyploidy when compared to
Camelina sativa,
a recent neopolyploid, where the effect of genome fractionation was least. Finally, estimation of phylogenetic relationship using precursor sequences of
MIR319
reveals
MIR319a
and
MIR319b
form sister clades, with
MIR319c
forming a separate clade. An intra-species synteny analysis between
MIR319a
-,
MIR319b-
, and
MIR319c-
containing genomic segments suggests segmental duplications at the base of Brassicaceae to be responsible for the origin of
MIR319a
and
MIR319b
.</description><subject>Animal Genetics and Genomics</subject><subject>Biomedical and Life Sciences</subject><subject>Brassicaceae</subject><subject>Cell Biology</subject><subject>Developmental Biology</subject><subject>Evolutionary Biology</subject><subject>Evolutionary genetics</subject><subject>Gene families</subject><subject>Genes</subject><subject>Genomes</subject><subject>Genomic analysis</subject><subject>Leaves</subject><subject>Life Sciences</subject><subject>miRNA</subject><subject>Original Article</subject><subject>Pattern formation</subject><subject>Phylogeny</subject><subject>Plant Genetics and Genomics</subject><subject>Polyploidy</subject><subject>Regulatory sequences</subject><subject>Seedlings</subject><subject>Species</subject><subject>Synteny</subject><subject>Zoology</subject><issn>0949-944X</issn><issn>1432-041X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><recordid>eNp1kV9LHDEUxUOp1K3tB_BFAr74MvXmz04mj7poKyiCKOxbyGQybWQmGZMZy_TTN7urFYSGCyHc3z3hnoPQIYFvBECcJgBORQGkKqCkUMAHtCCc0QI4WX9EC5BcFpLz9T76nNIjAKGSLT-hfQaUUy7oAj3dOBNDmv1o_Yy1192cXMJjwJNvbEyj9g22z6GbRhc83rxcP2gz4tDiIXTz0AXXuD962851c3XHiMSt7l03499u_OU8Po86JWe0sdp-QXut7pL9-nIfoIfLi_vVj-L69vvV6uy6MEzQsWBC2LohOi-qZS2FbQ2huhQlFcbUsqKakra2RJJlVXIuhRGlFA1tOV9WrGrYATrZ6Q4xPE02jap3ydiu096GKSlK8skuEJnR43foY5hi9mJLAZO8KqtMkR21MSxF26ohul7HWRFQmzzULg-V81CbPBTkmaMX5anubfNv4jWADNAdkHLL_7Tx7ev_q_4FW3CV3w</recordid><startdate>20181201</startdate><enddate>20181201</enddate><creator>Joshi, Gauri</creator><creator>Chauhan, Chetan</creator><creator>Das, Sandip</creator><general>Springer Berlin Heidelberg</general><general>Springer Nature B.V</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QP</scope><scope>7SS</scope><scope>7TK</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-9241-2613</orcidid></search><sort><creationdate>20181201</creationdate><title>Microsynteny analysis to understand evolution and impact of polyploidization on MIR319 family within Brassicaceae</title><author>Joshi, Gauri ; Chauhan, Chetan ; Das, Sandip</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c372t-377ebd1a100a9b97efc12a67627ccb982a21fbe1915864497c7697d2f445838d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Animal Genetics and Genomics</topic><topic>Biomedical and Life Sciences</topic><topic>Brassicaceae</topic><topic>Cell Biology</topic><topic>Developmental Biology</topic><topic>Evolutionary Biology</topic><topic>Evolutionary genetics</topic><topic>Gene families</topic><topic>Genes</topic><topic>Genomes</topic><topic>Genomic analysis</topic><topic>Leaves</topic><topic>Life Sciences</topic><topic>miRNA</topic><topic>Original Article</topic><topic>Pattern formation</topic><topic>Phylogeny</topic><topic>Plant Genetics and Genomics</topic><topic>Polyploidy</topic><topic>Regulatory sequences</topic><topic>Seedlings</topic><topic>Species</topic><topic>Synteny</topic><topic>Zoology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Joshi, Gauri</creatorcontrib><creatorcontrib>Chauhan, Chetan</creatorcontrib><creatorcontrib>Das, Sandip</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>ProQuest_Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>AUTh Library subscriptions: ProQuest Central</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>PML(ProQuest Medical Library)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>ProQuest Biological Science Journals</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Development genes and evolution</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Joshi, Gauri</au><au>Chauhan, Chetan</au><au>Das, Sandip</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Microsynteny analysis to understand evolution and impact of polyploidization on MIR319 family within Brassicaceae</atitle><jtitle>Development genes and evolution</jtitle><stitle>Dev Genes Evol</stitle><addtitle>Dev Genes Evol</addtitle><date>2018-12-01</date><risdate>2018</risdate><volume>228</volume><issue>6</issue><spage>227</spage><epage>242</epage><pages>227-242</pages><issn>0949-944X</issn><eissn>1432-041X</eissn><abstract>The availability of a large number of whole-genome sequences allows comparative genomic analysis to reveal and understand evolution of regulatory regions and elements. The role played by events such as whole-genome and segmental duplications followed by genome fractionation in shaping genomic landscape and in expansion of gene families is crucial toward developing insights into evolutionary trends and consequences such as sequence and functional diversification. Members of Brassicaceae are known to have experienced several rounds of whole-genome duplication (WGD) that have been termed as paleopolyploidy, mesopolyploidy, and neopolyploidy. Such repeated events led to the creation and expansion of a large number of gene families.
MIR319
is reported to be one of the most ancient and conserved plant
MIRNA
families and plays a role in growth and development including leaf development, seedling development, and embryo patterning. We have previously reported functional diversification of members of
miR319
in
Brassica oleracea
affecting leaf architecture; however, the evolutionary history of the
MIR319
gene family across Brassicaceae remains unknown and requires investigation. We therefore identified homologous and homeologous segments of ca. 100 kb, with or without
MIR319
, performed comparative synteny analysis and genome fractionation studies. We detected variable rates of gene retention across members of Brassicaceae when genomic blocks of
MIR319a
,
MIR319b
, and
MIR319c
were compared either between themselves or against
Arabidopsis thaliana
genome which was taken as the base genome. The highest levels of shared genes were found between
A. thaliana
and
Capsella rubella
in both
MIR319b
- and
MIR319c
-containing genomic segments, and with the closest species of
A. thaliana
,
A. lyrata
, only in
MIR319a
-containing segment. Synteny analysis across 12 genomes (with 30 sub-genomes) revealed
MIR319c
to be the most conserved
MIRNA
loci (present in 27 genomes/sub-genomes) followed by
MIR319a
(present in 23 genomes/sub-genomes);
MIR319b
was found to be frequently lost (present in 20 genomes/sub-genomes) and thus is under least selection pressure for retention. Genome fractionation revealed extensive and differential loss of
MIRNA
homeologous loci and flanking genes from various sub-genomes of
Brassica
species that is in accordance with their older history of polyploidy when compared to
Camelina sativa,
a recent neopolyploid, where the effect of genome fractionation was least. Finally, estimation of phylogenetic relationship using precursor sequences of
MIR319
reveals
MIR319a
and
MIR319b
form sister clades, with
MIR319c
forming a separate clade. An intra-species synteny analysis between
MIR319a
-,
MIR319b-
, and
MIR319c-
containing genomic segments suggests segmental duplications at the base of Brassicaceae to be responsible for the origin of
MIR319a
and
MIR319b
.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><pmid>30242472</pmid><doi>10.1007/s00427-018-0620-0</doi><tpages>16</tpages><orcidid>https://orcid.org/0000-0002-9241-2613</orcidid></addata></record> |
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language | eng |
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source | Springer Nature |
subjects | Animal Genetics and Genomics Biomedical and Life Sciences Brassicaceae Cell Biology Developmental Biology Evolutionary Biology Evolutionary genetics Gene families Genes Genomes Genomic analysis Leaves Life Sciences miRNA Original Article Pattern formation Phylogeny Plant Genetics and Genomics Polyploidy Regulatory sequences Seedlings Species Synteny Zoology |
title | Microsynteny analysis to understand evolution and impact of polyploidization on MIR319 family within Brassicaceae |
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