Generation of a large-scale genomic resource for functional and comparative genomics in Liriodendron tulipifera L.

Haiying Liang, Saravanaraj Ayyampalayam, Norman Wickett, Abdelali Barakat, Yi Xu, Lena Landherr, Paula E. Ralph, Yuannian Jiao, Tao Xu, Scott E. Schlarbaum, Hong Ma, James H. Leebens-Mack, Claude W. dePamphilis

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Liriodendron tulipifera L., a member of Magnoliaceae in the order Magnoliales, has been used extensively as a reference species in studies on plant evolution. However, genomic resources for this tree species are limited. We constructed cDNA libraries from ten different types of tissues: premeiotic flower buds, postmeiotic flower buds, open flowers, developing fruit, terminal buds, leaves, cambium, xylem, roots, and seedlings. EST sequences were generated either by 454 GS FLX or Sanger methods. Assembly of almost 2. 4 million sequencing reads from all libraries resulted in 137,923 unigenes (132,905 contigs and 4,599 singletons). About 50% of the unigenes had significant matches to publically available plant protein sequences, representing a wide variety of putative functions. Approximately 30,000 simple sequence repeats were identified. More than 97% of the cell wall formation genes in the Cell Wall Navigator and the MAIZEWALL databases are represented. The cinnamyl alcohol dehydrogenase (CAD) homologs identified in the L. tulipifera EST dataset showed different expression levels in the ten tissue types included in this study. In particular, the LtuCAD1 was found to partially recover the stiffness of the floral stems in the Arabidopsis thaliana CAD4 and CAD5 double mutant plants, of the LtuCAD1 in lignin biosynthesis. L. tulipifera genes have greater sequence similarity to homologs from other woody angiosperm species than to non-woody model plants. This large-scale genomic resour"HistryDatesce will be instrumental for gene discovery, cDNA microarray production, and marker-assisted breeding in L. tulipifera, and strengthen this species' role in comparative studies.

Original languageEnglish (US)
Pages (from-to)941-954
Number of pages14
JournalTree Genetics and Genomes
Volume7
Issue number5
DOIs
StatePublished - Oct 1 2011

Fingerprint

Liriodendron
Liriodendron tulipifera
Genomics
genomics
bud
flower
unigenes
buds
Expressed Sequence Tags
resource
Cell Wall
gene
Magnoliaceae
Cambium
Magnoliales
cell walls
cinnamyl alcohol dehydrogenase
Angiosperms
Xylem
Plant Proteins

All Science Journal Classification (ASJC) codes

  • Forestry
  • Molecular Biology
  • Genetics
  • Horticulture

Cite this

Liang, Haiying ; Ayyampalayam, Saravanaraj ; Wickett, Norman ; Barakat, Abdelali ; Xu, Yi ; Landherr, Lena ; Ralph, Paula E. ; Jiao, Yuannian ; Xu, Tao ; Schlarbaum, Scott E. ; Ma, Hong ; Leebens-Mack, James H. ; dePamphilis, Claude W. / Generation of a large-scale genomic resource for functional and comparative genomics in Liriodendron tulipifera L. In: Tree Genetics and Genomes. 2011 ; Vol. 7, No. 5. pp. 941-954.
@article{79dcfd396a2c482ba82d52104fd6bb1d,
title = "Generation of a large-scale genomic resource for functional and comparative genomics in Liriodendron tulipifera L.",
abstract = "Liriodendron tulipifera L., a member of Magnoliaceae in the order Magnoliales, has been used extensively as a reference species in studies on plant evolution. However, genomic resources for this tree species are limited. We constructed cDNA libraries from ten different types of tissues: premeiotic flower buds, postmeiotic flower buds, open flowers, developing fruit, terminal buds, leaves, cambium, xylem, roots, and seedlings. EST sequences were generated either by 454 GS FLX or Sanger methods. Assembly of almost 2. 4 million sequencing reads from all libraries resulted in 137,923 unigenes (132,905 contigs and 4,599 singletons). About 50{\%} of the unigenes had significant matches to publically available plant protein sequences, representing a wide variety of putative functions. Approximately 30,000 simple sequence repeats were identified. More than 97{\%} of the cell wall formation genes in the Cell Wall Navigator and the MAIZEWALL databases are represented. The cinnamyl alcohol dehydrogenase (CAD) homologs identified in the L. tulipifera EST dataset showed different expression levels in the ten tissue types included in this study. In particular, the LtuCAD1 was found to partially recover the stiffness of the floral stems in the Arabidopsis thaliana CAD4 and CAD5 double mutant plants, of the LtuCAD1 in lignin biosynthesis. L. tulipifera genes have greater sequence similarity to homologs from other woody angiosperm species than to non-woody model plants. This large-scale genomic resour{"}HistryDatesce will be instrumental for gene discovery, cDNA microarray production, and marker-assisted breeding in L. tulipifera, and strengthen this species' role in comparative studies.",
author = "Haiying Liang and Saravanaraj Ayyampalayam and Norman Wickett and Abdelali Barakat and Yi Xu and Lena Landherr and Ralph, {Paula E.} and Yuannian Jiao and Tao Xu and Schlarbaum, {Scott E.} and Hong Ma and Leebens-Mack, {James H.} and dePamphilis, {Claude W.}",
year = "2011",
month = "10",
day = "1",
doi = "10.1007/s11295-011-0386-2",
language = "English (US)",
volume = "7",
pages = "941--954",
journal = "Tree Genetics and Genomes",
issn = "1614-2942",
publisher = "Springer Verlag",
number = "5",

}

Liang, H, Ayyampalayam, S, Wickett, N, Barakat, A, Xu, Y, Landherr, L, Ralph, PE, Jiao, Y, Xu, T, Schlarbaum, SE, Ma, H, Leebens-Mack, JH & dePamphilis, CW 2011, 'Generation of a large-scale genomic resource for functional and comparative genomics in Liriodendron tulipifera L.', Tree Genetics and Genomes, vol. 7, no. 5, pp. 941-954. https://doi.org/10.1007/s11295-011-0386-2

Generation of a large-scale genomic resource for functional and comparative genomics in Liriodendron tulipifera L. / Liang, Haiying; Ayyampalayam, Saravanaraj; Wickett, Norman; Barakat, Abdelali; Xu, Yi; Landherr, Lena; Ralph, Paula E.; Jiao, Yuannian; Xu, Tao; Schlarbaum, Scott E.; Ma, Hong; Leebens-Mack, James H.; dePamphilis, Claude W.

In: Tree Genetics and Genomes, Vol. 7, No. 5, 01.10.2011, p. 941-954.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Generation of a large-scale genomic resource for functional and comparative genomics in Liriodendron tulipifera L.

AU - Liang, Haiying

AU - Ayyampalayam, Saravanaraj

AU - Wickett, Norman

AU - Barakat, Abdelali

AU - Xu, Yi

AU - Landherr, Lena

AU - Ralph, Paula E.

AU - Jiao, Yuannian

AU - Xu, Tao

AU - Schlarbaum, Scott E.

AU - Ma, Hong

AU - Leebens-Mack, James H.

AU - dePamphilis, Claude W.

PY - 2011/10/1

Y1 - 2011/10/1

N2 - Liriodendron tulipifera L., a member of Magnoliaceae in the order Magnoliales, has been used extensively as a reference species in studies on plant evolution. However, genomic resources for this tree species are limited. We constructed cDNA libraries from ten different types of tissues: premeiotic flower buds, postmeiotic flower buds, open flowers, developing fruit, terminal buds, leaves, cambium, xylem, roots, and seedlings. EST sequences were generated either by 454 GS FLX or Sanger methods. Assembly of almost 2. 4 million sequencing reads from all libraries resulted in 137,923 unigenes (132,905 contigs and 4,599 singletons). About 50% of the unigenes had significant matches to publically available plant protein sequences, representing a wide variety of putative functions. Approximately 30,000 simple sequence repeats were identified. More than 97% of the cell wall formation genes in the Cell Wall Navigator and the MAIZEWALL databases are represented. The cinnamyl alcohol dehydrogenase (CAD) homologs identified in the L. tulipifera EST dataset showed different expression levels in the ten tissue types included in this study. In particular, the LtuCAD1 was found to partially recover the stiffness of the floral stems in the Arabidopsis thaliana CAD4 and CAD5 double mutant plants, of the LtuCAD1 in lignin biosynthesis. L. tulipifera genes have greater sequence similarity to homologs from other woody angiosperm species than to non-woody model plants. This large-scale genomic resour"HistryDatesce will be instrumental for gene discovery, cDNA microarray production, and marker-assisted breeding in L. tulipifera, and strengthen this species' role in comparative studies.

AB - Liriodendron tulipifera L., a member of Magnoliaceae in the order Magnoliales, has been used extensively as a reference species in studies on plant evolution. However, genomic resources for this tree species are limited. We constructed cDNA libraries from ten different types of tissues: premeiotic flower buds, postmeiotic flower buds, open flowers, developing fruit, terminal buds, leaves, cambium, xylem, roots, and seedlings. EST sequences were generated either by 454 GS FLX or Sanger methods. Assembly of almost 2. 4 million sequencing reads from all libraries resulted in 137,923 unigenes (132,905 contigs and 4,599 singletons). About 50% of the unigenes had significant matches to publically available plant protein sequences, representing a wide variety of putative functions. Approximately 30,000 simple sequence repeats were identified. More than 97% of the cell wall formation genes in the Cell Wall Navigator and the MAIZEWALL databases are represented. The cinnamyl alcohol dehydrogenase (CAD) homologs identified in the L. tulipifera EST dataset showed different expression levels in the ten tissue types included in this study. In particular, the LtuCAD1 was found to partially recover the stiffness of the floral stems in the Arabidopsis thaliana CAD4 and CAD5 double mutant plants, of the LtuCAD1 in lignin biosynthesis. L. tulipifera genes have greater sequence similarity to homologs from other woody angiosperm species than to non-woody model plants. This large-scale genomic resour"HistryDatesce will be instrumental for gene discovery, cDNA microarray production, and marker-assisted breeding in L. tulipifera, and strengthen this species' role in comparative studies.

UR - http://www.scopus.com/inward/record.url?scp=80052758396&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=80052758396&partnerID=8YFLogxK

U2 - 10.1007/s11295-011-0386-2

DO - 10.1007/s11295-011-0386-2

M3 - Article

AN - SCOPUS:80052758396

VL - 7

SP - 941

EP - 954

JO - Tree Genetics and Genomes

JF - Tree Genetics and Genomes

SN - 1614-2942

IS - 5

ER -