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

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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.

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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.

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    Authors and Affiliations

    1. Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA

      Jill L. Wegrzyn, Jeanne Whalen & Daniel Gonzalez-Ibeas

    2. TerViva, Oakland, CA, USA

      Claire S. Kinlaw & David E. Harry

    3. Department of Ecosystem Science and Management, Texas A&M University, College Station, TX, USA

      Jeffrey Puryear & Carol A. Loopstra

    4. Department of Plant Sciences, University of California, Davis, CA, USA

      Hans A. Vasquez-Gross, Randi A. Famula & David B. Neale

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    1. Jill L. Wegrzyn
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    2. Jeanne Whalen
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    Corresponding author

    Correspondence to David B. Neale.

    Additional information

    Communicated by W. Ratnam

    Jill L. Wegrzyn and Jeanne Whalen contributed equally to this work.

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    Wegrzyn, J.L., Whalen, J., Kinlaw, C.S. et al. Transcriptomic profile of leaf tissue from the leguminous tree, Millettia pinnata . Tree Genetics & Genomes 12, 44 (2016). https://doi.org/10.1007/s11295-016-0986-y

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