Abstract Detail

Annonaceae evolution: integrating molecules, biogeography and ecology

Brandão, Rita D. [1], Staats, Martijn [2], Chatrou, Lars W. [3], Maas, Jan W. [4], Insupp, Bjorn [5], Arias, Tatiana [6], Erkens, Roy H.J. [7].

Annonaceae whole-plastome sequencing study: Improving next-generation sequencing strategies of non-model tropical trees (Guatteria).

The neotropical plant-family Annonaceae is one of the largest within the order Magnoliales (around 2400 species in 108 genera currently accepted) and, therefore, is a very interesting target for phylogenetic studies aiming at understanding the factors responsable for evolution and speciation of basal Angiosperms. Nowadays, with the advances in genetics, more specifically in sequencing capacity, it has become possible to sequence whole genomes and plastomes of non-model organisms with relative ease. For Annonaceae whole-plastomes sequences have not been reported in the literature yet. In this study, four Annonaceae plastids were sequenced through next-generation sequencing technology.
Fresh leave material from Annona muricata, Mkilua fragrans, Uvaria afzelii and Xylopia peruviana was collected from green-house grown trees. Upon chloroplast DNA extraction, paired-end libraries were prepared for DNA sequencing in an Illumina Hi-Seq instrument. Each sample was analysed and assembled separately. Quality control was performed with FastQC and Fastq Screen scripts to ensure that there were no problems with the sequencing process and that there are no contamination of the samples. Geneious software was used to filter bad quality bases and/or reads and iterative mapping steps. In the first mapping step, reads were mapped to the sequence of a chloroplast of Miliusa cuneate, an Asian Annonaceae species, to have a draft of the plastome for each species. In the following steps, consecutive rounds of mapping to the obtained sequences were performed. Remaining gaps were resolved with PCRs and automated sanger sequencing.
To our knowledge, these are the first non-asian Annonaceae plastomes to be reported. The percentage of reads used for the assembly varied between 0.71% (145,931/20,636,570) and 4.35% (44,0568/10,119,226). Most reads are most likely from the nuclear genome, as they did not map to other possible species, such as Human, if contamination of the samples had occured. The resulting plastid genome sizes were all around 153-157 Kbp. These sequences are relevant for the design and development of home-made baits for targetting-enrichment and subsequent sequencing of about 90 different South American Guatteria species. The analysis of the relationships of these species will lead to an improved hypothesis of their relationship needed to investigate biogeographic scenaria’s and hypotheses on the genus diversification. Preliminary data obtained on this genus will be discussed.

Related Links:
Annonaceae website

1 - Maastricht University, Maastricht Science Programme, P.O. Box 616, Maastricht, 6200 MD, The Netherlands
2 - Wageningen University, Wageningen, the Netherlands
3 - Wageningen University, Droevendaalsesteeg 1, WAGENINGEN, N/A, 6708 PB, Netherlands
4 - Utrecht University, Biology: Ecology and Biodiversity Group , Utrecht, the Netherlands
5 - Maastricht University, Maastricht, the Netherlands
6 - The University Of Hong Kong, School Of Biological Sciences, Potfulam Rd., Hong Kong, N/A, Hong Kong SAR
7 - Maastricht University, the Netherlands

Keywords:
Annonaceae
Guatteria
next-generation sequencing
target enrichment
chloroplast
plastid genome.

Presentation Type: Symposium or Colloquium Presentation
Session: SY04
Location: Pines South/Boise Centre
Date: Tuesday, July 29th, 2014
Time: 8:00 AM
Number: SY04001
Abstract ID:551
Candidate for Awards:None