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

Autor(es)

Loeuille, Benoit ^[1] ; Thode, Veronica ^[2] ; Siniscalchi, Carolina ^[3] ; Andrade, Sonia ^[4] ; Rossi, Magdalena ^[5] ; Pirani, Jose Rubens ^[5]

Afiliação do(s) autor(es)

^[1] Univ Fed Pernambuco, Dept Bot, Recife, PE - Brazil

^[2] Univ Fed Rio Grande do Sul, Inst Biociencias, Porto Alegre, RS - Brazil

^[3] Mississippi State Univ, Dept Biol Sci, Mississippi State, MS 39762 - USA

^[4] Univ Sao Paulo, Dept Genet & Biol Evolut, Sao Paulo, SP - Brazil

^[5] Univ Sao Paulo, Dept Bot, Sao Paulo, SP - Brazil

• Tipo de documento: Artigo Científico
• Fonte: PeerJ; v. 9, FEB 24 2021.
• Citações Web of Science: 0

Resumo

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 similar to 20 kb and a small similar to 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 Glade. Our results bring new understandings into the evolution and diversity of plastomes at the species level. (AU)

• Processo FAPESP: 11/19231-7 - Filogenia das espécies sul-americanas de Viguiera (Asteraceae: Heliantheae)
• Beneficiário: Benoît Francis Patrice Loeuille
• Modalidade de apoio: Bolsas no Brasil - Pós-Doutorado
• Processo FAPESP: 10/51454-3 - Estudos morfoanatômicos, metabolômicos e moleculares como subsídios à sistemática de espécies de Asteraceae e acesso ao seu potencial farmacológico
• Beneficiário: Beatriz Appezzato da Glória
• Modalidade de apoio: Auxílio à Pesquisa - Temático