Development of a BAC library for yellow-poplar (Liriodendron tulipifera) and the identification of genes associated with flower development and lignin biosynthesis

Haiying Liang, Eric G. Fang, Jeffrey P. Tomkins, Meizhong Luo, David Kudrna, Hye Ran Kim, K. Arumuganathan, Shaying Zhao, James Leebens-Mack, Scott E. Schlarbaum, Jo Ann Banks, Claude W. Depamphilis, Dina F. Mandoli, Rod A. Wing, John E. Carlson

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

Liriodendron tulipifera L., a member of the Magnoliaceae, occupies an important phylogenetic position as a basal angiosperm that has retained numerous putatively ancestral morphological characters, and thus has often been used in studies of the evolution of flowering plants and of specific gene families. However, genomic resources for these early branching angiosperm lineages are very limited. In this study, we describe the construction of a large-insert bacterial artificial chromosome (BAC) library from L. tulipifera. Flow cytometry estimates that this nuclear genome is approximately 1,802 Mbp per haploid genome (±16 SD). The BAC library contains 73,728 clones, a 4.8-fold genome coverage, with an average insert size of 117 kb, a chloroplast DNA content of 0.2%, and little to no bacterial sequences nor empty vector content clones. As a test of the utility of this BAC library, we screened the library with six single/low-copy genic probes. We obtained at least two positive clones for each gene and confirmed the clones by DNA sequencing. A total of 182 paired end sequences were obtained from 96 of the BAC clones. Using BLAST searches, we found that 25% of the BAC end sequences were similar to DNA sequences in GenBank. Of these, 68% shared sequence with transposable elements and 25% with genes from other taxa. This result closely reflected the content of random sequences obtained from a small insert genomic library for L. tulipifera, indicating that the BAC library construction process was not biased. The first genomic DNA sequences for Liriodendron genes are also reported. All the Liriodendron genomic sequences described in this paper have been deposited in the GenBank data library. The end sequences from shotgun genomic clones and BAC clones are under accession DU169330-DU169684. Partial sequences of Gigantea, Frigida, LEAFY, cinnamyl alcohol dehydrogenase, 4-coumarate:CoA ligase, and phenylalanine ammonia-lyase genes are under accession DQ223429-DQ223434.

Original languageEnglish (US)
Pages (from-to)215-225
Number of pages11
JournalTree Genetics and Genomes
Volume3
Issue number3
DOIs
StatePublished - Jul 1 2007

Fingerprint

Liriodendron
Bacterial Artificial Chromosomes
Liriodendron tulipifera
bacterial artificial chromosomes
Lignin
lignin
clone
chromosome
flower
Clone Cells
biosynthesis
clones
flowering
genomics
gene
Genes
angiosperm
genes
DNA
Angiosperms

All Science Journal Classification (ASJC) codes

  • Forestry
  • Molecular Biology
  • Genetics
  • Horticulture

Cite this

Liang, Haiying ; Fang, Eric G. ; Tomkins, Jeffrey P. ; Luo, Meizhong ; Kudrna, David ; Kim, Hye Ran ; Arumuganathan, K. ; Zhao, Shaying ; Leebens-Mack, James ; Schlarbaum, Scott E. ; Banks, Jo Ann ; Depamphilis, Claude W. ; Mandoli, Dina F. ; Wing, Rod A. ; Carlson, John E. / Development of a BAC library for yellow-poplar (Liriodendron tulipifera) and the identification of genes associated with flower development and lignin biosynthesis. In: Tree Genetics and Genomes. 2007 ; Vol. 3, No. 3. pp. 215-225.
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abstract = "Liriodendron tulipifera L., a member of the Magnoliaceae, occupies an important phylogenetic position as a basal angiosperm that has retained numerous putatively ancestral morphological characters, and thus has often been used in studies of the evolution of flowering plants and of specific gene families. However, genomic resources for these early branching angiosperm lineages are very limited. In this study, we describe the construction of a large-insert bacterial artificial chromosome (BAC) library from L. tulipifera. Flow cytometry estimates that this nuclear genome is approximately 1,802 Mbp per haploid genome (±16 SD). The BAC library contains 73,728 clones, a 4.8-fold genome coverage, with an average insert size of 117 kb, a chloroplast DNA content of 0.2{\%}, and little to no bacterial sequences nor empty vector content clones. As a test of the utility of this BAC library, we screened the library with six single/low-copy genic probes. We obtained at least two positive clones for each gene and confirmed the clones by DNA sequencing. A total of 182 paired end sequences were obtained from 96 of the BAC clones. Using BLAST searches, we found that 25{\%} of the BAC end sequences were similar to DNA sequences in GenBank. Of these, 68{\%} shared sequence with transposable elements and 25{\%} with genes from other taxa. This result closely reflected the content of random sequences obtained from a small insert genomic library for L. tulipifera, indicating that the BAC library construction process was not biased. The first genomic DNA sequences for Liriodendron genes are also reported. All the Liriodendron genomic sequences described in this paper have been deposited in the GenBank data library. The end sequences from shotgun genomic clones and BAC clones are under accession DU169330-DU169684. Partial sequences of Gigantea, Frigida, LEAFY, cinnamyl alcohol dehydrogenase, 4-coumarate:CoA ligase, and phenylalanine ammonia-lyase genes are under accession DQ223429-DQ223434.",
author = "Haiying Liang and Fang, {Eric G.} and Tomkins, {Jeffrey P.} and Meizhong Luo and David Kudrna and Kim, {Hye Ran} and K. Arumuganathan and Shaying Zhao and James Leebens-Mack and Schlarbaum, {Scott E.} and Banks, {Jo Ann} and Depamphilis, {Claude W.} and Mandoli, {Dina F.} and Wing, {Rod A.} and Carlson, {John E.}",
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Liang, H, Fang, EG, Tomkins, JP, Luo, M, Kudrna, D, Kim, HR, Arumuganathan, K, Zhao, S, Leebens-Mack, J, Schlarbaum, SE, Banks, JA, Depamphilis, CW, Mandoli, DF, Wing, RA & Carlson, JE 2007, 'Development of a BAC library for yellow-poplar (Liriodendron tulipifera) and the identification of genes associated with flower development and lignin biosynthesis', Tree Genetics and Genomes, vol. 3, no. 3, pp. 215-225. https://doi.org/10.1007/s11295-006-0057-x

Development of a BAC library for yellow-poplar (Liriodendron tulipifera) and the identification of genes associated with flower development and lignin biosynthesis. / Liang, Haiying; Fang, Eric G.; Tomkins, Jeffrey P.; Luo, Meizhong; Kudrna, David; Kim, Hye Ran; Arumuganathan, K.; Zhao, Shaying; Leebens-Mack, James; Schlarbaum, Scott E.; Banks, Jo Ann; Depamphilis, Claude W.; Mandoli, Dina F.; Wing, Rod A.; Carlson, John E.

In: Tree Genetics and Genomes, Vol. 3, No. 3, 01.07.2007, p. 215-225.

Research output: Contribution to journalArticle

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T1 - Development of a BAC library for yellow-poplar (Liriodendron tulipifera) and the identification of genes associated with flower development and lignin biosynthesis

AU - Liang, Haiying

AU - Fang, Eric G.

AU - Tomkins, Jeffrey P.

AU - Luo, Meizhong

AU - Kudrna, David

AU - Kim, Hye Ran

AU - Arumuganathan, K.

AU - Zhao, Shaying

AU - Leebens-Mack, James

AU - Schlarbaum, Scott E.

AU - Banks, Jo Ann

AU - Depamphilis, Claude W.

AU - Mandoli, Dina F.

AU - Wing, Rod A.

AU - Carlson, John E.

PY - 2007/7/1

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N2 - Liriodendron tulipifera L., a member of the Magnoliaceae, occupies an important phylogenetic position as a basal angiosperm that has retained numerous putatively ancestral morphological characters, and thus has often been used in studies of the evolution of flowering plants and of specific gene families. However, genomic resources for these early branching angiosperm lineages are very limited. In this study, we describe the construction of a large-insert bacterial artificial chromosome (BAC) library from L. tulipifera. Flow cytometry estimates that this nuclear genome is approximately 1,802 Mbp per haploid genome (±16 SD). The BAC library contains 73,728 clones, a 4.8-fold genome coverage, with an average insert size of 117 kb, a chloroplast DNA content of 0.2%, and little to no bacterial sequences nor empty vector content clones. As a test of the utility of this BAC library, we screened the library with six single/low-copy genic probes. We obtained at least two positive clones for each gene and confirmed the clones by DNA sequencing. A total of 182 paired end sequences were obtained from 96 of the BAC clones. Using BLAST searches, we found that 25% of the BAC end sequences were similar to DNA sequences in GenBank. Of these, 68% shared sequence with transposable elements and 25% with genes from other taxa. This result closely reflected the content of random sequences obtained from a small insert genomic library for L. tulipifera, indicating that the BAC library construction process was not biased. The first genomic DNA sequences for Liriodendron genes are also reported. All the Liriodendron genomic sequences described in this paper have been deposited in the GenBank data library. The end sequences from shotgun genomic clones and BAC clones are under accession DU169330-DU169684. Partial sequences of Gigantea, Frigida, LEAFY, cinnamyl alcohol dehydrogenase, 4-coumarate:CoA ligase, and phenylalanine ammonia-lyase genes are under accession DQ223429-DQ223434.

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