Integral Phylogenomic Approach over Ilex L. Species from Southern South America

Abstract

The use of molecular markers with inadequate variation levels has resulted in poorly resolved phylogenetic relationships within Ilex. Focusing on southern South American and Asian species, we aimed at contributing informative plastid markers. Also, we intended to gain insights into the nature of morphological and physiological characters used to identify species. We obtained the chloroplast genomes of I. paraguariensis and I. dumosa, and combined these with all the congeneric plastomes currently available to accomplish interspecific comparisons and multilocus analyses. We selected seven introns and nine IGSs as variable non-coding markers that were used in phylogenomic analyses. Eight extra IGSs were proposed as candidate markers. Southern South American species formed one lineage, except for I. paraguariensis, I. dumosa and I. argentina, which occupied intermediate positions among sampled taxa; Euroasiatic species formed two lineages. Some concordant relationships were retrieved from nuclear sequence data. We also conducted integral analyses, involving a supernetwork of molecular data, and a simultaneous analysis of quantitative and qualitative morphological and phytochemical characters, together with molecular data. The total evidence tree was used to study the evolution of non-molecular data, evidencing fifteen non-ambiguous synapomorphic character states and consolidating the relationships among southern South American species. More South American representatives should be incorporated to elucidate their origin.

The complete chloroplast genome of horned holly, Ilex cornuta Lindl. & Paxton (Aquifoliaceae)

“…Till now, nine complete chloroplast genomes of Ilex were sequenced: Seven of nine species are from China (Yao et al 2016) and two are from South America (Cascales et al 2017). Chloroplast genome of I. cornuta was also analyzed one time; however, they could not complete its chloroplast genome due to lack of sample (Cascales et al 2017).…”

“…Genome was sequenced using HiSeqX at Macrogen Inc., Korea, and de novo assembly and confirmation were performed by Velvet 1.2.10 (Zerbino and Birney 2008), SOAPGapCloser 1.12 (Zhao et al 2011), BWA 0.7.17 (Li 2013), and SAMtools 1.9 (Li et al 2009). Geneious R11 11.0.5 (Biomatters Ltd., Auckland, New Zealand) was used for annotation based on Ilex paraguariensis chloroplast, complete genome (KP016928; Cascales et al 2017).…”

The complete chloroplast genome of Nepal Holly, Ilex integra Thunb. (Aquifoliaceae)

“…Genome sequencing was performed using HiSeq4000 at Macrogen Inc., Korea and de novo assembly and conformation were done by Velvet 1.2.10 (Zerbino and Birney 2008), SOAPGapCloser 1.12 (Zhao et al 2011), BWA 0.7.17 (Li 2013), and SAMtools 1.9 (Li et al 2009). Geneious R11 11.0.5 (Biomatters Ltd., Auckland, New Zealand) was used for chloroplast genome annotation based on Ilex paraguariensis voucher Yerba mate chloroplast, complete genome (KP016928; Cascales et al 2017).…”

Unraveling the genetic complexity of a cultivated breeding population of “yerba mate” (Ilex paraguariensis St. Hil.)

“…This technique is particularly useful for non-model crop species, revealing variation at various levels (Al-Turki & Basahi 2015, Gaiero et al 2011, Kiani et al 2012, Kumar et al 2016, Seyedimoradi & Talebi 2014. To assess variation of chloroplastidic genome, we capitalize a panel of microsatellite markers recently designed for Ilex paraguariensis (J Cascales, unpublished data) from massive sequencing plastomic data (Cascales et al 2017).…”