Comparative Chloroplast Genomics Reveals a Unique Gene Inversion in Two Cordia Trees (Cordiaceae)

Alawfi, Mohammad S.; Albokhari, Enas J.

doi:10.3390/f14091778

Cited by 3 publications

(3 citation statements)

References 88 publications

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“…However, due to the rapid evolutionary divergence within the Boraginaceae family, the phylogenetic relationships in the family remain elusive [19]. The Cordiaceae subfamily, in addition to Cordia, may also include the Varronia and Patagonula genera [19,20], which means the species in these two genera are the most genetically close to Cordia. Cohen [18] conducted both morphological and molecular phylogenetic studies on the Boraginaceae family.…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, his results using only molecular markers (including matk, ndhF, and trnL-trnF markers of cpDNA, and ITS markers of nrDNA) indicated that Cordiaceae is the most closed to Heliotropiaceae. Nevertheless, further studies using rbcL, ndhF, and trnL-trnF markers of cpDNA [19] and whole cpDNA genomes [20] indicated that Cordiaceae is sister to Ehretiaceae. Since no Varronia, Patagonula, Ehretiaceae, or Heliotropiaceae genomes are available currently, we could not include them in our phylogeny analysis.…”

Section: Discussionmentioning

confidence: 99%

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Genome Assembly of Cordia subcordata, a Coastal Protection Species in Tropical Coral Islands

Chen,

Wang,

Jian

et al. 2023

IJMS

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Cordia subcordata trees or shrubs, belonging to the Boraginaceae family, have strong resistance and have adapted to their habitat on a tropical coral island in China, but the lack of genome information regarding its genetic background is unclear. In this study, the genome was assembled using both short/long whole genome sequencing reads and Hi–C reads. The assembled genome was 475.3 Mb, with 468.7 Mb (99.22%) of the sequences assembled into 16 chromosomes. Repeat sequences accounted for 54.41% of the assembled genome. A total of 26,615 genes were predicted, and 25,730 genes were functionally annotated using different annotation databases. Based on its genome and the other 17 species, phylogenetic analysis using 336 single-copy genes obtained from ortholog analysis showed that C. subcordata was a sister to Coffea eugenioides, and the divergence time was estimated to be 77 MYA between the two species. Gene family evolution analysis indicated that the significantly expanded gene families were functionally related to chemical defenses against diseases. These results can provide a reference to a deeper understanding of the genetic background of C. subcordata and can be helpful in exploring its adaptation mechanism on tropical coral islands in the future.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Genome Assembly of Cordia subcordata, a Coastal Protection Species in Tropical Coral Islands

Chen,

Wang,

Jian

et al. 2023

IJMS

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“…A haplotype tree was constructed to investigate the genetic structure and diversity of Phoebe chekiangensis populations [19]. Geographical grouping of the Phoebe chekiangensis populations was conducted by estimating the phylogeny and evolutionary time of cpDNA haplotypes [20]. Historical and dynamic analysis was utilized to determine potential spatial and population expansions in various geographical clusters, along with the timing of such events [21].…”

Section: Introductionmentioning

confidence: 99%

Chloroplast Spacer DNA Analysis Revealed Insights into Phylogeographical Structure of Phoebe chekiangensis

Wu,

Chen,

Nan

et al. 2024

Forests

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Research studies on the conservation genetics of endangered plants play a crucial role in establishing management plans for biodiversity conservation. Phoebe chekiangensis is a precious and scarce tree species resource in the East China region. To comprehend the origin, evolutionary history, geographical, and historical factors that has contributed to the current distribution pattern of Phoebe chekiangensis in the East China region, we conducted a phylogeographic analysis that utilized intergenic spacers of chloroplast DNA (cpDNA). We amplified and sequenced three spacer regions of cpDNA (psbC-trnS, trnL-Intro, and Ycf3) intergenic spacer regions of 306 individuals from 11 populations, encompassing the majority of its geographical range in China. Our analysis revealed a total of 11 haplotypes. The research findings show that the spacer regions of the cpDNA genetic diversity of Phoebe chekiangensis was Hd = 0.423, and the nucleotide diversity was Pi × 10−3 = 0.400. At the species level, the population differentiation index Fst = 0.25610 (p < 0.05), and the gene flow Nm = 0.73. The genetic variation between populations was 29.14%, while within populations, it was 70.86%, with the inter-population genetic variation much lower than the within-population variation. The divergence time between the genera Phoebe and Machilus was estimated to be approximately 37.87 mya (PP = 1; 95%HPD: 25.63–44.54 mya), and the crown group time of the genus Phoebe was estimated to be 21.30 mya (PP = 1; 95%HPD: 9.76–34.94 mya). The common ancestor of the 11 Phoebe chekiangensis haplotypes was 7.85 mya, while the H7, H8, and H10 haplotypes of Phoebe chekiangensis (northern region) differentiated relatively late, with a divergence time of 1.90 mya. Neutrality tests (NTs) and mismatch distribution analysis (MDA) suggest that the time frame for Phoebe chekiangensis to expand southwestward along Wuyishan was relatively short and its adaptability to the environment was low, thereby limiting the formation of new haplotypes. These results suggest that Phoebe chekiangensis exhibited greater adaptation to the northern subtropics than to the central subtropics, offering valuable insights for the conservation and utilization of germplasm resources.

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Intraspecific and Intrageneric Genomic Variation across Three Sedum Species (Crassulaceae): A Plastomic Perspective

Zhang,

Han,

et al. 2024

Genes

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Sedum is the largest succulent genus in Crassulaceae. Because of predominant maternal inheritance, little recombination, and slow evolution, plastomes can serve as powerful super barcodes for inter- or intra-species phylogenetic analyses. While previous research has focused on plastomes between Sedum species, intra-species studies are scarce. Here, we sequenced plastomes from three Sedum species (Sedum alfredii, Sedum plumbizincicola, and Sedum japonicum) to understand their evolutionary relationships and plastome structural evolution. Our analyses revealed minimal size and GC content variation across species. However, gene distribution at IR boundaries, repeat structures, and codon usage patterns showed diversity at both inter-specific and intra-specific levels. Notably, an rps19 gene expansion and a bias toward A/T-ending codons were observed. Codon aversion motifs also varied, potentially serving as markers for future studies. Phylogenetic analyses confirmed the non-monophyly of Sedum and divided the Acre clade into two groups. Individuals from the same species clustered together, with strong support for the relationships between S. alfredii, S. tricarpum, and S. plumbizincicola. Additionally, S. japonicum clearly affiliates with the Acre clade. This study provides valuable insights into both intra-specific and intra-generic plastome variation in Sedum, as well as overall plastome evolution within the genus.

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Comparative Chloroplast Genomics Reveals a Unique Gene Inversion in Two Cordia Trees (Cordiaceae)

Cited by 3 publications

References 88 publications

Genome Assembly of Cordia subcordata, a Coastal Protection Species in Tropical Coral Islands

Genome Assembly of Cordia subcordata, a Coastal Protection Species in Tropical Coral Islands

Chloroplast Spacer DNA Analysis Revealed Insights into Phylogeographical Structure of Phoebe chekiangensis

Intraspecific and Intrageneric Genomic Variation across Three Sedum Species (Crassulaceae): A Plastomic Perspective

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