Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences from Aldama (Heliantheae, Asteraceae) and comparative chloroplast genomics analyses with closely related genera

Benoit Loeuille; Verônica Thode; Carolina Siniscalchi; Sonia Andrade; Magdalena Rossi; José Rubens Pirani

doi:10.7717/peerj.10886

Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences from Aldama (Heliantheae, Asteraceae) and comparative chloroplast genomics analyses with closely related genera

PeerJ. 2021 Feb 24:9:e10886. doi: 10.7717/peerj.10886. eCollection 2021.

Authors

Benoit Loeuille^#¹, Verônica Thode^#², Carolina Siniscalchi³, Sonia Andrade⁴, Magdalena Rossi⁵, José Rubens Pirani⁵

Affiliations

¹ Departamento de Botânica, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil.
² Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
³ Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States of America.
⁴ Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, São Paulo, Brazil.
⁵ Departamento de Botânica, Universidade de São Paulo, São Paulo, São Paulo, Brazil.

^# Contributed equally.

Abstract

Aldama (Heliantheae, Asteraceae) is a diverse genus in the sunflower family. To date, nearly 200 Asteraceae chloroplast genomes have been sequenced, but the plastomes of Aldama remain undescribed. Plastomes in Asteraceae usually show little sequence divergence, consequently, our hypothesis is that species of Aldama will be overall conserved. In this study, we newly sequenced 36 plastomes of Aldama and of five species belonging to other Heliantheae genera selected as outgroups (i.e., Dimerostemma asperatum, Helianthus tuberosus, Iostephane heterophylla, Pappobolus lanatus var. lanatus, and Tithonia diversifolia). We analyzed the structure and gene content of the assembled plastomes and performed comparative analyses within Aldama and with other closely related genera. As expected, Aldama plastomes are very conserved, with the overall gene content and orientation being similar in all studied species. The length of the plastome is also consistent and the junction between regions usually contain the same genes and have similar lengths. A large ∼20 kb and a small ∼3 kb inversion were detected in the Large Single Copy (LSC) regions of all assembled plastomes, similarly to other Asteraceae species. The nucleotide diversity is very low, with only 1,509 variable sites in 127,466 bp (i.e., 1.18% of the sites in the alignment of 36 Aldama plastomes, with one of the IRs removed, is variable). Only one gene, rbcL, shows signatures of positive selection. The plastomes of the selected outgroups feature a similar gene content and structure compared to Aldama and also present the two inversions in the LSC region. Deletions of different lengths were observed in the gene ycf2. Multiple SSRs were identified for the sequenced Aldama and outgroups. The phylogenetic analysis shows that Aldama is not monophyletic due to the position of the Mexican species A. dentata. All Brazilian species form a strongly supported clade. Our results bring new understandings into the evolution and diversity of plastomes at the species level.

Keywords: Complete plastome; Compositae; Species-level plastome evolution; rbcL positive selection; ycf2 gene.

Grants and funding

This work was supported by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP-Sp-Brazil) (Thematic Project: 2010/51454-3). Benoît Loeuille received a postdoctoral grant from FAPESP (2011/19231-7). Beatriz Appezatto-da-Glória provided financial support (through a FAPESP Thematic Project). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.