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Transcriptomic profile of leaf tissue from the leguminous tree, Millettia pinnata

  • Jill L. Wegrzyn
  • Jeanne Whalen
  • Claire S. Kinlaw
  • David E. Harry
  • Jeffrey Puryear
  • Carol A. Loopstra
  • Daniel Gonzalez-Ibeas
  • Hans A. Vasquez-Gross
  • Randi A. Famula
  • David B. NealeEmail author
Original Article
Part of the following topical collections:
  1. Genome Biology

Abstract

Millettia pinnata (formerly Pongamia pinnata) is a fast-growing leguminous tree indigenous to the Indian subcontinent, Southeast Asia, and Australia. This species has been introduced to subtropical and arid regions of Africa, India, the Philippines, Malaysia, Australia, and the USA for commercial growth. Exhibiting saline and drought tolerance, as well as nitrogen-fixing properties, M. pinnata has been used extensively for traditional medicine and agriculture and, more recently, for the production of a biofuel feedstock. The large size, high oil content, and fatty acid profile of the seeds are well suited for biofuel production. In this study, we characterized the leaf transcriptome that was assembled de novo from 72 seedlings pooled into eight libraries. Deep paired-end short-read sequencing was performed on individual libraries using the Illumina HiSeq 2000 platform. The Trinity-assembled transcriptome of 25,146 unique genes was annotated with a combination of open-source tools. Functional annotation was facilitated through sequence homology searches, Gene Ontology term assignment, and protein domain identification. A total of 11,873 genes were classified as full-length, and 22,603 sequences were functionally annotated. Predominate Gene Ontology biological process categories included phosphorylation, metabolic processes, and oxidation-reduction processes. Orthologous gene family analysis identified 19,640 families among the 11 sequenced plant species compared. A total of 4280 were conserved across all species, and 103 were unique to the M. pinnata leaf transcriptome. The unique M. pinnata gene families included transcripts with an array of functions including ubiquitin-like modifier proteins and BED zinc finger proteins with membership in pathways related to salt tolerance and disease resistance.

Keywords

Biofuel Leguminous tree Millettia pinnata Transcriptome 

Notes

Acknowledgments

This study was funded by the SBIR Award no. IIP-1112926 from the National Science Foundation.

Data Archiving Statement

The short-read data are available publicly through the NCBI SRA database under the accession numbers SAMN02982713, SAMN02982708, SAMN02982707, and SAMN02982706. These are leaf tissue samples, paired-end data. The BioProject is available under accession number PRJNA258017.

Supplementary material

11295_2016_986_MOESM1_ESM.doc (32 kb)
Table S1 (DOC 32 kb)
11295_2016_986_MOESM2_ESM.doc (34 kb)
Table S2 (DOC 34 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Jill L. Wegrzyn
    • 1
  • Jeanne Whalen
    • 1
  • Claire S. Kinlaw
    • 2
  • David E. Harry
    • 2
  • Jeffrey Puryear
    • 3
  • Carol A. Loopstra
    • 3
  • Daniel Gonzalez-Ibeas
    • 1
  • Hans A. Vasquez-Gross
    • 4
  • Randi A. Famula
    • 4
  • David B. Neale
    • 4
    Email author
  1. 1.Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsUSA
  2. 2.TerVivaOaklandUSA
  3. 3.Department of Ecosystem Science and ManagementTexas A&M UniversityCollege StationUSA
  4. 4.Department of Plant SciencesUniversity of CaliforniaDavisUSA

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