Characterization of mango (Mangifera indica L.) transcriptome and chloroplast genome

Characterization of mango (Mangifera indica L.) transcriptome and chloroplast genome We characterized mango leaf transcriptome and chloroplast genome using next generation DNA sequencing. The RNA-seq output of mango transcriptome generated >12 million reads (total nucleotides sequenced >1 Gb). De novo transcriptome assembly generated 30,509 unigenes with lengths in the range of 300 to ≥3,000 nt and 67× depth of coverage. Blast searching against nonredundant nucleotide databases and several Viridiplantae genomic datasets annotated 24,593 mango unigenes (80 % of total) and identified Citrus sinensis as closest neighbor of mango with 9,141 (37 %) matched sequences. The annotation with gene ontology and Clusters of Orthologous Group terms categorized unigene sequences into 57 and 25 classes, respectively. More than 13,500 unigenes were assigned to 293 KEGG pathways. Besides major plant biology related pathways, KEGG based gene annotation pointed out active presence of an array of biochemical pathways involved in (a) biosynthesis of bioactive flavonoids, flavones and flavonols, (b) biosynthesis of terpenoids and lignins and (c) plant hormone signal transduction. The mango transcriptome sequences revealed 235 proteases belonging to five catalytic classes of proteolytic enzymes. The draft genome of mango chloroplast (cp) was obtained by a combination of Sanger and next generation sequencing. The draft mango cp genome size is 151,173 bp with a pair of inverted repeats of 27,093 bp separated by small and large single copy regions, respectively. Out of 139 genes in mango cp genome, 91 found to be protein coding. Sequence analysis revealed cp genome of C. sinensis as closest neighbor of mango. We found 51 short repeats in mango cp genome supposed to be associated with extensive rearrangements. This is the first report of transcriptome and chloroplast genome analysis of any Anacardiaceae family member. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Plant Molecular Biology Springer Journals

Characterization of mango (Mangifera indica L.) transcriptome and chloroplast genome

Loading next page...
 
/lp/springer_journal/characterization-of-mango-mangifera-indica-l-transcriptome-and-98RJz2vywU
Publisher
Springer Journals
Copyright
Copyright © 2014 by Springer Science+Business Media Dordrecht
Subject
Life Sciences; Plant Sciences; Biochemistry, general; Plant Pathology
ISSN
0167-4412
eISSN
1573-5028
D.O.I.
10.1007/s11103-014-0179-8
Publisher site
See Article on Publisher Site

Abstract

We characterized mango leaf transcriptome and chloroplast genome using next generation DNA sequencing. The RNA-seq output of mango transcriptome generated >12 million reads (total nucleotides sequenced >1 Gb). De novo transcriptome assembly generated 30,509 unigenes with lengths in the range of 300 to ≥3,000 nt and 67× depth of coverage. Blast searching against nonredundant nucleotide databases and several Viridiplantae genomic datasets annotated 24,593 mango unigenes (80 % of total) and identified Citrus sinensis as closest neighbor of mango with 9,141 (37 %) matched sequences. The annotation with gene ontology and Clusters of Orthologous Group terms categorized unigene sequences into 57 and 25 classes, respectively. More than 13,500 unigenes were assigned to 293 KEGG pathways. Besides major plant biology related pathways, KEGG based gene annotation pointed out active presence of an array of biochemical pathways involved in (a) biosynthesis of bioactive flavonoids, flavones and flavonols, (b) biosynthesis of terpenoids and lignins and (c) plant hormone signal transduction. The mango transcriptome sequences revealed 235 proteases belonging to five catalytic classes of proteolytic enzymes. The draft genome of mango chloroplast (cp) was obtained by a combination of Sanger and next generation sequencing. The draft mango cp genome size is 151,173 bp with a pair of inverted repeats of 27,093 bp separated by small and large single copy regions, respectively. Out of 139 genes in mango cp genome, 91 found to be protein coding. Sequence analysis revealed cp genome of C. sinensis as closest neighbor of mango. We found 51 short repeats in mango cp genome supposed to be associated with extensive rearrangements. This is the first report of transcriptome and chloroplast genome analysis of any Anacardiaceae family member.

Journal

Plant Molecular BiologySpringer Journals

Published: Feb 11, 2014

References

  • 2D-DIGE analysis of mango (Mangifera indica L.) fruit reveals major proteomic changes associated with ripening
    Andrade Jde, M; Toledo, TT; Nogueira, SB; Cordenunsi, BR; Lajolo, FM; Nascimento, JR
  • The chloroplast genome sequence of Syzygium cumini (L.) and its relationship with other angiosperms
    Asif, H; Khan, A; Iqbal, A; Khan, IA; Heinze, B; Azim, MK
  • The complete chloroplast genome sequences of Solanum tuberosum and comparative analysis of with solanaceae species identified the presence of 241 bp deletion in cultivated potato chloroplast DNA sequence
    Chung, HJ; Jung, JD; Park, HW; Kim, JH; Cha, HW; Min, SR; Jeong, WJ; Liu, JR
  • GenomeVx: simple web-based creation of editable circular chromosome maps
    Conant, GC; Wolfe, KH
  • Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
    Conesa, A; Gotz, S
  • Transcriptome sequencing to produce SNP-based genetic maps of onion
    Duangjit, J; Bohanec, B; Chan, AP; Town, CD; Havey, MJ
  • Full-length transcriptome assembly from RNA-seq data without a reference genome
    Grabherr, MG; Haas, BJ; Yassour, M; Levin, JZ; Thompson, DA; Amit, I; Adiconis, X; Fan, L; Raychowdhury, R; Zeng, Q; Chen, Z; Mauceli, E; Hacohen, N; Gnirke, A; Rhind, N; Palma, F; Birren, BW; Nusbaum, C; Lindblad-Toh, K; Friedman, N; Regev, A
  • Advancing RNA-seq analysis
    Haas, BJ; Zody, MC
  • Biotechnological advances in mango (Mangifera indica L.) and their future implication in crop improvement: a review
    Krishna, H; Singh, SK
  • Enhanced levels of the aroma and flavor compound S-linalool by metabolic engineering of the terpenoid pathway in tomato fruits
    Lewinshon, E; Schalechet, F; Wilkinson, J; Matsui, K; Tadmor, Y; Nam, K; Amar, O; Lastochkin, E; Larkov, O; Ravid, U; Hiatt, W; Gepstein, S; Pichersky, E

You’re reading a free preview. Subscribe to read the entire article.


DeepDyve is your
personal research library

It’s your single place to instantly
discover and read the research
that matters to you.

Enjoy affordable access to
over 18 million articles from more than
15,000 peer-reviewed journals.

All for just $49/month

Explore the DeepDyve Library

Search

Query the DeepDyve database, plus search all of PubMed and Google Scholar seamlessly

Organize

Save any article or search result from DeepDyve, PubMed, and Google Scholar... all in one place.

Access

Get unlimited, online access to over 18 million full-text articles from more than 15,000 scientific journals.

Your journals are on DeepDyve

Read from thousands of the leading scholarly journals from SpringerNature, Elsevier, Wiley-Blackwell, Oxford University Press and more.

All the latest content is available, no embargo periods.

See the journals in your area

DeepDyve

Freelancer

DeepDyve

Pro

Price

FREE

$49/month
$360/year

Save searches from
Google Scholar,
PubMed

Create lists to
organize your research

Export lists, citations

Read DeepDyve articles

Abstract access only

Unlimited access to over
18 million full-text articles

Print

20 pages / month

PDF Discount

20% off