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Title: Exploring the loblolly pine ( Pinus taeda L.) genome by BAC sequencing and Cot analysis

Abstract

Loblolly pine (LP; Pinus taeda L.) is an economically and ecologically important tree in the southeastern U.S. To advance understanding of the loblolly pine (LP; Pinus taeda L.) genome, we sequenced and analyzed 100 BAC clones and performed a Cot analysis. The Cot analysis indicates that the genome is composed of 57, 24, and 10% highly-repetitive, moderately-repetitive, and single/low-copy sequences, respectively (the remaining 9% of the genome is a combination of fold back and damaged DNA). Although single/low-copy DNA only accounts for 10% of the LP genome, the amount of single/low-copy DNA in LP is still 14 times the size of the Arabidopsis genome. Since gene numbers in LP are similar to those in Arabidopsis, much of the single/low-copy DNA of LP would appear to be composed of DNA that is both gene- and repeat-poor. Macroarrays prepared from a LP bacterial artificial chromosome (BAC) library were hybridized with probes designed from cell wall synthesis/wood development cDNAs, and 50 of the “targeted” clones were selected for further analysis. An additional 25 clones were selected because they contained few repeats, while 25 more clones were selected at random. The 100 BAC clones were Sanger sequenced and assembled. Of the targeted BACs, 80%more » contained all or part of the cDNA used to target them. One targeted BAC was found to contain fungal DNA and was eliminated from further analysis. Combinations of similarity-based and ab initio gene prediction approaches were utilized to identify and characterize potential coding regions in the 99 BACs containing LP DNA. From this analysis, we identified 154 gene models (GMs) representing both putative protein-coding genes and likely pseudogenes. Ten of the GMs (all of which were specifically targeted) had enough support to be classified as intact genes. Interestingly, the 154 GMs had statistically indistinguishable (α = 0.05) distributions in the targeted and random BAC clones (15.18 and 12.61 GM/Mb, respectively), whereas the low-repeat BACs contained significantly fewer GMs (7.08 GM/Mb). However, when GM length was considered, the targeted BACs had a significantly greater percentage of their length in GMs (3.26%) when compared to random (1.63%) and low-repeat (0.62%) BACs. The results of our study provide insight into LP evolution and inform ongoing efforts to produce a reference genome sequence for LP, while characterization of genes involved in cell wall production highlights carbon metabolism pathways that can be leveraged for increasing wood production.« less

Authors:
 [1];  [2];  [3];  [1];  [1];  [4]; ORCiD logo [5];  [6];  [6];  [1];  [1]
  1. Mississippi State Univ., Mississippi State, MS (United States)
  2. Univ. of the Philippines, Quezon City (Philippines)
  3. Naresuan Univ., Phitsanulok (Thailand)
  4. Baylor College of Medicine, Houston, TX (United States)
  5. Univ. of Georgia, Athens, GA (United States)
  6. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1543545
Grant/Contract Number:  
[AC02-05CH11231]
Resource Type:
Accepted Manuscript
Journal Name:
Gene
Additional Journal Information:
[ Journal Volume: 663; Journal Issue: C]; Journal ID: ISSN 0378-1119
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Genetics & Heredity; Pinus taeda; Loblolly pine; Bacterial artificial chromosome; BAC; Cot analysis; Carbon metabolism

Citation Formats

Perera, Dinum, Magbanua, Zenaida V., Thummasuwan, Supaphan, Mukherjee, Dipaloke, Arick, II, Mark, Chouvarine, Philippe, Nairn, Campbell J., Schmutz, Jeremy, Grimwood, Jane, Dean, Jeffrey F. D., and Peterson, Daniel G. Exploring the loblolly pine (Pinus taeda L.) genome by BAC sequencing and Cot analysis. United States: N. p., 2018. Web. doi:10.1016/j.gene.2018.04.024.
Perera, Dinum, Magbanua, Zenaida V., Thummasuwan, Supaphan, Mukherjee, Dipaloke, Arick, II, Mark, Chouvarine, Philippe, Nairn, Campbell J., Schmutz, Jeremy, Grimwood, Jane, Dean, Jeffrey F. D., & Peterson, Daniel G. Exploring the loblolly pine (Pinus taeda L.) genome by BAC sequencing and Cot analysis. United States. doi:10.1016/j.gene.2018.04.024.
Perera, Dinum, Magbanua, Zenaida V., Thummasuwan, Supaphan, Mukherjee, Dipaloke, Arick, II, Mark, Chouvarine, Philippe, Nairn, Campbell J., Schmutz, Jeremy, Grimwood, Jane, Dean, Jeffrey F. D., and Peterson, Daniel G. Thu . "Exploring the loblolly pine (Pinus taeda L.) genome by BAC sequencing and Cot analysis". United States. doi:10.1016/j.gene.2018.04.024. https://www.osti.gov/servlets/purl/1543545.
@article{osti_1543545,
title = {Exploring the loblolly pine (Pinus taeda L.) genome by BAC sequencing and Cot analysis},
author = {Perera, Dinum and Magbanua, Zenaida V. and Thummasuwan, Supaphan and Mukherjee, Dipaloke and Arick, II, Mark and Chouvarine, Philippe and Nairn, Campbell J. and Schmutz, Jeremy and Grimwood, Jane and Dean, Jeffrey F. D. and Peterson, Daniel G.},
abstractNote = {Loblolly pine (LP; Pinus taeda L.) is an economically and ecologically important tree in the southeastern U.S. To advance understanding of the loblolly pine (LP; Pinus taeda L.) genome, we sequenced and analyzed 100 BAC clones and performed a Cot analysis. The Cot analysis indicates that the genome is composed of 57, 24, and 10% highly-repetitive, moderately-repetitive, and single/low-copy sequences, respectively (the remaining 9% of the genome is a combination of fold back and damaged DNA). Although single/low-copy DNA only accounts for 10% of the LP genome, the amount of single/low-copy DNA in LP is still 14 times the size of the Arabidopsis genome. Since gene numbers in LP are similar to those in Arabidopsis, much of the single/low-copy DNA of LP would appear to be composed of DNA that is both gene- and repeat-poor. Macroarrays prepared from a LP bacterial artificial chromosome (BAC) library were hybridized with probes designed from cell wall synthesis/wood development cDNAs, and 50 of the “targeted” clones were selected for further analysis. An additional 25 clones were selected because they contained few repeats, while 25 more clones were selected at random. The 100 BAC clones were Sanger sequenced and assembled. Of the targeted BACs, 80% contained all or part of the cDNA used to target them. One targeted BAC was found to contain fungal DNA and was eliminated from further analysis. Combinations of similarity-based and ab initio gene prediction approaches were utilized to identify and characterize potential coding regions in the 99 BACs containing LP DNA. From this analysis, we identified 154 gene models (GMs) representing both putative protein-coding genes and likely pseudogenes. Ten of the GMs (all of which were specifically targeted) had enough support to be classified as intact genes. Interestingly, the 154 GMs had statistically indistinguishable (α = 0.05) distributions in the targeted and random BAC clones (15.18 and 12.61 GM/Mb, respectively), whereas the low-repeat BACs contained significantly fewer GMs (7.08 GM/Mb). However, when GM length was considered, the targeted BACs had a significantly greater percentage of their length in GMs (3.26%) when compared to random (1.63%) and low-repeat (0.62%) BACs. The results of our study provide insight into LP evolution and inform ongoing efforts to produce a reference genome sequence for LP, while characterization of genes involved in cell wall production highlights carbon metabolism pathways that can be leveraged for increasing wood production.},
doi = {10.1016/j.gene.2018.04.024},
journal = {Gene},
number = [C],
volume = [663],
place = {United States},
year = {2018},
month = {4}
}

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