Diversity, genetic structure, and population genomics of the tropical tree Centrolobium tomentosum in remnant and restored Atlantic forests

Cordeiro, Erick M. G.; Macrini, Camila Menezes Trindade; Sujii, Patrícia Sanae; Schwarcz, Kaiser Dias; Pinheiro, José Baldin; Rodrigues, Ricardo Ribeiro; Brancalion, Pedro Henrique Santin; Zucchi, Maria Imaculada

doi:10.1007/s10592-019-01195-z

Cited by 14 publications

(9 citation statements)

References 67 publications

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“…The reads from nuclear and mitochondrial DNA obtained from the sequencing were used in this first-time comparison of the genetic diversity and genomic divergence among the three species from the Euterpe genus. The advances in next-generation sequencing (NGS) is allowing the discovery of a large number of single nucleotide polymorphism (SNPs), even for nonmodel species [85][86][87][88]. This generates a valuable source of bi-allelic genetic markers that are appropriate to evaluate the genetic diversity even when sample sizes are small [89].…”

Section: A Comparison Using Nuclear and Mitochondrial Genome Sequence...mentioning

confidence: 99%

Complete chloroplast genomes and phylogeny in three Euterpe palms (E. edulis, E. oleracea and E. precatoria) from different Brazilian biomes

et al. 2022

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The Brazilian palm fruits and hearts-of-palm of Euterpe edulis, E. oleracea and E. precatoria are an important source for agro-industrial production, due to overexploitation, conservation strategies are required to maintain genetic diversity. Chloroplast genomes have conserved sequences, which are useful to explore evolutionary questions. Besides the plastid DNA, genome skimming allows the identification of other genomic resources, such as single nucleotide polymorphisms (SNPs), providing information about the genetic diversity of species. We sequenced the chloroplast genome and identified gene content in the three Euterpe species. We performed comparative analyses, described the polymorphisms among the chloroplast genome sequences (repeats, indels and SNPs) and performed a phylogenomic inference based on 55 palm species chloroplast genomes. Finally, using the remaining data from genome skimming, the nuclear and mitochondrial reads, we identified SNPs and estimated the genetic diversity among these Euterpe species. The Euterpe chloroplast genomes varied from 159,232 to 159,275 bp and presented a conserved quadripartite structure with high synteny with other palms. In a pairwise comparison, we found a greater number of insertions/deletions (indels = 93 and 103) and SNPs (284 and 254) between E. edulis/E. oleracea and E. edulis/E. precatoria when compared to E. oleracea/E. precatoria (58 indels and 114 SNPs). Also, the phylogeny indicated a closer relationship between E. oleracea/E. precatoria. The nuclear and mitochondrial genome analyses identified 1,077 SNPs and high divergence among species (FST = 0.77), especially between E. edulis and E. precatoria (FST = 0.86). These results showed that, despite the few structural differences among the chloroplast genomes of these Euterpe palms, a differentiation between E. edulis and the other Euterpe species can be identified by point mutations. This study not only brings new knowledge about the evolution of Euterpe chloroplast genomes, but also these new resources open the way for future phylogenomic inferences and comparative analyses within Arecaceae.

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Section: A Comparison Using Nuclear and Mitochondrial Genome Sequence...mentioning

confidence: 99%

Complete chloroplast genomes and phylogeny in three Euterpe palms (E. edulis, E. oleracea and E. precatoria) from different Brazilian biomes

et al. 2022

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“…While we detected strong gene flow from natural to restored populations, we did not find any signs of gene flow in the opposite direction. This is surprising because gene flow from restored to natural populations was detected in other restoration projects (Aavik et al., 2013; Cordeiro et al., 2019; Gemeinholzer et al., 2020). A possible reason could be the smaller size of the restored compared to the natural populations resulting in lower propagule pressure from restored gene pools.…”

Section: Discussionmentioning

confidence: 95%

Populations restored using regional seed are genetically diverse and similar to natural populations in the region

Höfner

Klein-Raufhake

Lampei

et al. 2021

Journal of Applied Ecology

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Ecological restoration and plant re‐introductions aim to create plant populations that are genetically similar to natural populations to preserve the regional gene pool, yet genetically diverse to allow adaptation to a changing environment. For this purpose, seeds for restoration are increasingly sourced from multiple populations in the target region. However, it has only rarely been tested whether using regional seed indeed leads to genetically diverse restored populations which are genetically similar to natural populations. We used single nucleotide polymorphism (SNP) markers to investigate genetic diversity within and differentiation among populations of Centaurea jacea and Betonica officinalis on restored and natural meadows in the White Carpathians, Czech Republic. The restoration took place 20 years ago using regional seeds propagated from a mix of multiple regional source populations. We included original regional seeds in our analysis to compare the restored populations with their origin (only in C. jacea). Additionally, we analysed conventional seeds without certified origin because these would have constituted a common alternative for restoration seeding in the absence of regional seeds. The differentiation between restored and natural populations (mean pairwise FST = 0.018 in Centaurea and 0.021 in Betonica) was similar to the differentiation among natural populations (FST = 0.023 and 0.021), and the restored populations were slightly more genetically diverse than the natural populations. In addition, restored populations were relatively similar to their origin, the regional seeds (FST = 0.015). In contrast, conventional seeds were strongly differentiated from all regional populations (FST = 0.100 and 0.059, in Centaurea and Betonica respectively) and harboured substantially lower genetic diversity. We also found signs of gene flow via pollen or seed dispersal from natural to restored populations but not vice versa. Policy implications. Regionally sourced seeds can produce genetically diverse populations at natural levels of genetic differentiation.

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“…The reads from nuclear and mitochondrial DNA obtained from the sequencing were used in this first-time comparison of the genetic diversity and genomic divergence among the three species from the Euterpe genus. The advances in next-generation sequencing (NGS) is allowing the discovery of a large number of single nucleotide polymorphism (SNPs), even for non-model species [85][86][87][88]. This generates a valuable source of bi-allelic genetic markers that are appropriate to evaluate the genetic diversity even when sample sizes are small [89].…”

Section: A Comparison Using Nuclear and Mitochondrial Genome Sequence...mentioning

confidence: 99%

Complete chloroplast genomes and phylogeny in three Euterpe palms (E. edulis, E. oleraceae and E. precatoria) from different Brazilian biomes

Francisconi

Cauz-Santos

Marroquín

et al. 2022

Preprint

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The Brazilian palm fruits and hearts-of-palm of Euterpe edulis, E. oleracea and E. precatoria are an important source for agro-industrial production, but overexploitation requires conservation strategies to maintain genetic diversity. Chloroplast genomes have conserved sequences, which are useful to explore evolutionary questions. Besides the plastid DNA, genome skimming allows the identification of other genomic resources, such as single nucleotide polymorphisms (SNPs), providing information about the genetic diversity of species. We sequenced the chloroplast genome and identified gene content in the three Euterpe species. We performed comparative analyses, described the polymorphisms among the chloroplast genome sequences (repeats, indels and SNPs) and performed a phylogenomic inference based on 55 palm species chloroplast genomes. Finally, using the remaining data from genome skimming, the nuclear and mitochondrial reads, we identified SNPs and estimated the genetic diversity among these Euterpe species. The Euterpe chloroplast genomes varied from 159,232 to 159,275 bp and presented a conserved quadripartite structure with high synteny with other palms. In a pairwise comparison, we found a greater number of insertions/deletions (indels = 93 and 103) and SNPs (284 and 254) between E. edulis/E. oleracea and E. edulis/E. precatoria when compared to E. oleracea/E. precatoria (58 indels and 114 SNPs). Also, the phylogeny indicated a closer relationship between E. oleracea/E. precatoria. The nuclear and mitochondrial genome analyses identified 1,077 SNPs and high divergence among species (FST = 0.77), especially between E. edulis and E. precatoria (FST = 0.86). These results showed that, despite the few structural differences among the chloroplast genomes of these Euterpe palms, a differentiation between E. edulis and the other Euterpe species can be identified by point mutations. This study not only brings new knowledge about the evolution of Euterpe chloroplast genomes, but also these new resources open the way for future phylogenomic inferences and comparative analyses within Arecaceae.

show abstract

Diversity, genetic structure, and population genomics of the tropical tree Centrolobium tomentosum in remnant and restored Atlantic forests

Cited by 14 publications

References 67 publications

Complete chloroplast genomes and phylogeny in three Euterpe palms (E. edulis, E. oleracea and E. precatoria) from different Brazilian biomes

Complete chloroplast genomes and phylogeny in three Euterpe palms (E. edulis, E. oleracea and E. precatoria) from different Brazilian biomes

Populations restored using regional seed are genetically diverse and similar to natural populations in the region

Complete chloroplast genomes and phylogeny in three Euterpe palms (E. edulis, E. oleraceae and E. precatoria) from different Brazilian biomes

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