Plastome Phylogenomic and Biogeographical Study on <i>Thuja</i> (Cupressaceae)

Adelalu, Kole F.; Zhang, Xu; Qu, Xiaolu; Landis, Jacob B.; Shen, Jun; Sun, Yanxia; Meng, Anming; Sun, Hang; Wang, Hengchang

doi:10.1155/2020/8426287

Cited by 6 publications

(5 citation statements)

References 77 publications

(149 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…3B) and the concatenation‐based tree from RAD‐seq data (Fig. 3A) were also found in previous studies (Hao et al, 2008; Leslie et al, 2012, 2020; Wang et al, 2019; Zhang et al, 2019), and the conflict is difficult to explain. It could be a result of differential lineage sorting of a dimorphic ancestral chloroplast genome among species and clades of Torreya or the result of chloroplast capture by T. jackii from Amentotaxus (Fig.…”

Section: Discussionsupporting

confidence: 80%

Phylogenomics and biogeography of Torreya (Taxaceae)—Integrating data from three organelle genomes, morphology, and fossils and a practical method for reducing missing data from RAD‐seq

Zhou

Harris

Xiang

2022

J of Systematics Evolution

View full text Add to dashboard Cite

Restriction site-associated DNA sequencing (RAD-seq) enables obtaining thousands of genetic markers for phylogenomic studies. However, RAD-seq data are subject to allele dropout (ADO) due to polymorphisms at enzyme cutting sites. We developed a new pipeline, RAD-seq Allele Dropout Remedy in our study of the gymnosperm genus, Torreya, to mitigate ADO in outgroups by recovering missing loci from previously published transcriptomes. By using RADADOR to supplement Rad-seq data in combination with plastome and mitochondrial gene sequences, morphology, and fossil records, we reconstructed the phylogenetic and biogeographic histories of the genus and tested hypotheses on anomalies of biodiversity of the eastern Asian-North American floristic disjunction. Our results showed that our pipeline recovered many loci missing from the outgroup, and the improved data yielded a more robust phylogeny for Torreya. Using the fossilized birth-death model and divergence-extinction-cladogenesis method, we resolved a detailed biogeographic history of Torreya that suggested a Jurassic origin spanning Laurasia and differential speciation and extinction among continents accounting for modern diversity, which is biased toward eastern Asia (EA). The biogeographic results also supported a vicariance origin of modern Torreya from a widespread ancestor in EA and North America (NA) in the mid-Eocene, and cross Beringian exchange in the early Paleogene before the vicariant isolation, in contrast to the "out of NA" pattern common to gymnosperms and to the "out of EA" hypothesis previously proposed for the genus. Furthermore, we observed phylogenetic discordance between the nuclear and plastid phylogenies for Torreya jackii, suggesting differential lineage sorting of plastid genomes among species of Torreya or plastid genome capture in T. jackii.

show abstract

Section: Discussionsupporting

confidence: 80%

Phylogenomics and biogeography of Torreya (Taxaceae)—Integrating data from three organelle genomes, morphology, and fossils and a practical method for reducing missing data from RAD‐seq

Zhou

Harris

Xiang

2022

J of Systematics Evolution

View full text Add to dashboard Cite

show abstract

“…However, compared with the genetic diversity metrics obtained with nSSRs, those obtained with cpSSRs for the ancient populations of P. orientalis were lower. The chloroplast genome of conifers has no inverted repeat (IR) region [54], which has a significant impact on the evolution rate of the plastid genome compared with that in angiosperms.…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity and Population Genetic Structure of Ancient Platycladus orientalis L. (Cupressaceae) in the Middle Reaches of the Yellow River by Chloroplast Microsatellite Markers

Cui

Deng

Sheng

et al. 2021

Forests

View full text Add to dashboard Cite

Ancient trees are famous for their life spans of hundreds or even thousands of years. These trees are rare, a testament to history and are important for scientific research. Platycladus orientalis, with the longest life span and a beautiful trunk, has become the most widely planted tree species and is believed to be sacred in China. Extensive declines in habitat area and quality pose the greatest threats to the loss of genetic diversity of ancient P. orientalis trees in the middle reaches of the Yellow River. Strengthening the protection of P. orientalis genetic resources is of great significance for the long-term development of reasonable conservation and breeding strategies. To better understand the genetic diversity and population structure of P. orientalis, we successfully analyzed four polymorphic chloroplast simple sequence repeat (cpSSR) loci and applied them to diversity and population structure analyses of 202 individuals from 13 populations in the middle reaches of the Yellow River. Based on the cpSSR data, 16 alleles were detected across 202 individuals, and a moderate level of genetic diversity was inferred from the genetic diversity parameters (H = 0.367 and AR = 1.964). The mean pairwise genetic differentiation coefficient (Fst) between populations was 0.153, indicating relatively high genetic population differentiations. Analysis of molecular variance (AMOVA) showed that only 8% of the variation occurred among populations. Structure analysis divided the 13 P. orientalis populations into two groups with no significant geographic population structure, which was consistent with the unweighted pair group method with arithmetic mean (UPGMA) and Mantel test results. These results may indicate that transplanting and cultivation by ancient human activities are the main factors responsible for the revealed pattern of genetic differentiation of ancient P. orientalis populations. Our research is of great significance for the future establishment of protection schemes and scientific breeding of P. orientalis.

show abstract

“…We used the GetOrganelle v 1.7.4.1 (Jin et al, 2020) to get contigs for plastid genomes using six plastomes of Thuja and Thujopsis from NCBI GenBank (Adelalu et al, 2019(Adelalu et al, , 2020Qu et al, 2017; Table S1) as the seed. Bowtie2 v 2.4.2 (Langmead & Salzberg, 2012) was used to map quality-filtered reads to the seed and recruit plastid-associated reads, and de novo assemblies were performed in SPAdes v 3.13.0 (Bankevich et al, 2012).…”

Section: Phylogeny Reconstruction Of Plastid Genomesmentioning

confidence: 99%

“…In a phylogeny of fossil and extant species based on seed cone morphology, T. sutchuenensis was grouped in a clade with T. ehrenswaerdii, a fossil species known from the Paleocene sediments of Greenland (Schweitzer, 1974); this clade was sister to all other Thuja (McIver & Basinger, 1989). However, molecular studies did not suggest an ancestral position of T. sutchuenensis (Adelalu et al, 2020;Li & Xiang, 2005;Peng & Wang, 2008). We reconstructed the reticular evolutionary history of Thuja in PhyloNet, allowing for the existence of missing taxa due to incomplete sampling and/or extinction.…”

Section: "Ghost Introgression" Into T Sutchuenensismentioning

confidence: 99%

“…Using both plastid and nuclear markers, Peng and Wang (2008) found considerable discordance among the plastid and nuclear gene trees, indicating the possibility of reticulate evolution in Thuja. Adelalu et al (2020) inferred the interspecific phylogeny of Thuja using complete plastid genomes and obtained a different result with a (T. standishii, T. koraiensis) clade which was sister to a (T. plicata, (T. occidentalis, T. sutchuenensis)) clade. Overall, previous studies suggested that Thuja had a complex evolutionary history, and resolving the phylogenetic uncertainty among Thuja species and inferring their biogeographical history are challenging using limited data.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Seeing through the hedge: Phylogenomics of Thuja (Cupressaceae) reveals prominent incomplete lineage sorting and ancient introgression for Tertiary relict flora

Zhang

Ruhsam

et al. 2021

Cladistics

View full text Add to dashboard Cite

The Eastern Asia (EA) -North America (NA) disjunction is a well-known biogeographic pattern of the Tertiary relict flora; however, few studies have investigated the evolutionary history of this disjunction using a phylogenomic approach. Here, we used 2369 single copy nuclear genes and nearly full plastomes to reconstruct the evolutionary history of the small Tertiary relict genus Thuja, which consists of five disjunctly distributed species. The nuclear species tree strongly supported an EA clade Thuja standishii-Thuja sutchuenensis and a "disjunct clade", where western NA species T. plicata is sister to an EA-eastern NA disjunct Thuja occidentalis-Thuja koraiensis group. Our results suggested that the observed topological discordance among the gene trees as well as the cytonuclear discordance is mainly due to incomplete lineage sorting, probably facilitated by the fast diversification of Thuja around the Early Miocene and the large effective population sizes of ancestral lineages. Furthermore, approximately 20% of the T. sutchuenensis nuclear genome is derived from an unknown ancestral lineage of Thuja, which might explain the close resemblance of its cone morphology to that of an ancient fossil species. Overall, our study demonstrates that single genes may not resolve interspecific relationships for disjunct taxa, and that more reliable results will come from hundreds or thousands of loci, revealing a more complex evolutionary history. This will steadily improve our understanding of their origin and evolution.

show abstract

Plastome Phylogenomic and Biogeographical Study on Thuja (Cupressaceae)

Cited by 6 publications

References 77 publications

Phylogenomics and biogeography of Torreya (Taxaceae)—Integrating data from three organelle genomes, morphology, and fossils and a practical method for reducing missing data from RAD‐seq

Phylogenomics and biogeography of Torreya (Taxaceae)—Integrating data from three organelle genomes, morphology, and fossils and a practical method for reducing missing data from RAD‐seq

Genetic Diversity and Population Genetic Structure of Ancient Platycladus orientalis L. (Cupressaceae) in the Middle Reaches of the Yellow River by Chloroplast Microsatellite Markers

Seeing through the hedge: Phylogenomics of Thuja (Cupressaceae) reveals prominent incomplete lineage sorting and ancient introgression for Tertiary relict flora

Contact Info

Product

Resources

About