Plastid phylogenomics improves resolution of phylogenetic relationship in the Cheirostylis and Goodyera clades of Goodyerinae (Orchidoideae, Orchidaceae)

Tu, Xiong-De; Liu, Ding-Kun; Xu, Shiping; Zhou, Cheng-Yuan; Gao, Xu-Yong; Zeng, Meng-Yao; Zhang, Sai; Chen, Jinliao; Ma, Liang; Zhou, Zhuang; Huang, Ming-Zhong; Chen, Shi-Pin; Liu, Zhong‐Jian; Lan, Siren; Li, Minghe

doi:10.1016/j.ympev.2021.107269

Cited by 22 publications

(29 citation statements)

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“…In orchids such as Cypripedium formosanum and Uncifera acuminata , inversions of the plastid genome were verified (Lin et al, 2015 ; Liu et al, 2020 ). In this study, G. schlechtendaliana had one inversion ( rps 16— psb I), which is the unique feature found in the species ( Supplementary Figure S2 ), and this result corresponds with that of Tu et al ( 2021 ). We propose that AT-rich content of this inversion, which had weak hydrogen bonding, caused structural variations.…”

Section: Discussionsupporting

confidence: 90%

“…Clade D is composed of only one species, G. procera , which was a sister to the remainder of Goodyera with high support value (PBP = 100, MBP = 100, PP = 1 in Figure 3 ), which was corresponded with Tu et al ( 2021 ). Hu et al ( 2016 ) identified that G. procera formed a clade with high support, which has distinctive characters such as narrowly ovate-elliptic leaves or densely non-secund flowers.…”

Section: Discussionsupporting

confidence: 70%

“…Tu et al ( 2021 ) suggested the combination of clades A and B into one clade; however, Hu et al ( 2016 ) defined them as two sections, sect. Goodyera and sect.…”

Section: Discussionmentioning

confidence: 99%

“…For example, Apostasioideae have intact ndh genes whereas Vanilloideae lost ndh genes. However, some ndh genes are intact or lost in Cypripedioideae, Orchidoideae, and Epidendroideae (Wicke et al, 2011 ; Kim et al, 2015 ; Lin et al, 2015 ; Ruhlman et al, 2015 ; Liu et al, 2020 ; Tu et al, 2021 ). We identified that pseudogenization of ndh B is associated with a specific character of a clade including G. nankoensis, G. marginata, G. repens , and G. rosulacea , which is a potential molecular feature to distinguish members of Goodyera ( Figure 3 ).…”

Section: Discussionmentioning

confidence: 99%

“…Hu et al ( 2016 ) conducted the phylogenetic analysis of Goodyera using plastid and nuclear ribosomal DNA sequences and suggested the division into four sections of Goodyera associated with morphological characters and their distributions. Tu et al ( 2021 ) utilized the whole plastid genome to study the phylogeny of Goodyerinae, especially Cheirostylis and Goodyera clades, and analyzed the plastome structure of Goodyerinae. In this study, we analyzed North American species based on whole plastid protein-coding genes and identified their relationships within Goodyera .…”

Section: Discussionmentioning

confidence: 99%

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Molecular Phylogeny and Historical Biogeography of Goodyera R. Br. (Orchidaceae): A Case of the Vicariance Between East Asia and North America

Kim

2022

Front. Plant Sci.

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Understanding of intercontinental distribution in the Northern Hemisphere has attracted a lot of attention from botanists. However, although Orchidaceae is the largest group of angiosperms, biogeographical studies on the disjunctive pattern have not been sufficient for this family. Goodyera R. Br. (tribe Cranichideae, subfamily Orchidoideae, family Orchidaceae) is widely distributed in temperate and tropical regions. Although the phylogenetic relationship of Goodyera inferred from both morphological and molecular data has been conducted, the sampled taxa were mainly distributed in Asia regions that resulted in non-monophyly of this genus. In this study, the complete plastid genomes of Goodyera, generated by next-generation sequencing (NGS) technique and sampled in East Asia and North America, were used to reconstruct phylogeny and explore the historical biogeography. A total of 18 Goodyera species including seven newly sequenced species were analyzed. Based on 79 protein-coding genes, the phylogenetic analysis revealed that Goodyera could be subdivided into four subclades with high support values. The polyphyletic relationships among Goodyera taxa were confirmed, and the unclear position of G. foliosa was also resolved. The datasets that are composed of the 14 coding sequences (CDS) (matK, atpF, ndhK, accD, cemA, clpP, rpoA, rpl22, ndhF, ccsA, ndhD, ndhI, ndhA, and ycf 1) showed the same topology derived from 79 protein-coding genes. Molecular dating analyses revealed the origin of Goodyera in the mid-Miocene (15.75 Mya). Nearctic clade of Goodyera was diverged at 10.88 Mya from their most recent common ancestor (MRCA). The biogeographical reconstruction suggests that subtropical or tropical Asia is the origin of Goodyera and it has subsequently spread to temperate Asia during the Miocene. In addition, Nearctic clade is derived from East Asian species through Bering Land Bridge (BLB) during the Miocene. The speciation of Goodyera is most likely to have occurred during Miocene, and climatic and geological changes are thought to have had a part in this diversification. Our findings propose both origin and vicariance events of Goodyera for the first time and add an example for the biogeographical history of the Northern Hemisphere.

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Section: Discussionsupporting

confidence: 90%

Section: Discussionsupporting

confidence: 70%

“…Tu et al ( 2021 ) suggested the combination of clades A and B into one clade; however, Hu et al ( 2016 ) defined them as two sections, sect. Goodyera and sect.…”

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Molecular Phylogeny and Historical Biogeography of Goodyera R. Br. (Orchidaceae): A Case of the Vicariance Between East Asia and North America

Kim

2022

Front. Plant Sci.

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Plastid genome evolution in leafless members of the orchid subfamily Orchidoideae, with a focus on Degranvillea dermaptera

Barrett,

Pace,

Corbett

2024

American J of Botany

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PremiseLeafless, heterotrophic plants are prime examples of organismal modification, the genomic consequences of which have received considerable interest. In particular, plastid genomes (plastomes) are being sequenced at a high rate, allowing continual refinement of conceptual models of reductive evolution in heterotrophs. However, numerous sampling gaps exist, hindering the ability to conduct comprehensive phylogenomic analyses in these plants.MethodsUsing floral tissue from an herbarium specimen, we sequenced and analyzed the plastome of Degranvillea dermaptera, a rarely collected, leafless orchid species from South America about which little is known, including its phylogenetic affinities.ResultsThe plastome is the most reduced of those sequenced among the orchid subfamily Orchidoideae. In Degranvillea, it has lost the majority of genes found in leafy autotrophic species, is structurally rearranged, and has similar gene content to the most reduced plastomes among the orchids. We found strong evidence for the placement of Degranvillea within the subtribe Spiranthinae using models that explicitly account for heterotachy, or lineage‐specific evolutionary rate variation over time. We further found evidence of relaxed selection on several genes and of correlations among substitution rates and several other “traits” of the plastome among leafless members of orchid subfamily Orchidoideae.ConclusionsOur findings advance knowledge on the phylogenetic relationships and paths of plastid genome evolution among the orchids, which have experienced more independent transitions to heterotrophy than any other plant family. This study demonstrates the importance of herbarium collections in comparative genomics of poorly known species of conservation concern.

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New insights on the phylogeny, evolutionary history, and ecological adaptation mechanism in cycle‐cup oaks based on chloroplast genomes

Li,

Zheng,

Wang

et al. 2024

Ecology and Evolution

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Cycle‐cup oaks (Quercus section Cyclobalanopsis) are one of the principal components of forests in the tropical and subtropical climates of East and Southeast Asia. They have experienced relatively recent increases in the diversification rate, driven by changing climates and the Himalayan orogeny. However, the evolutionary history and adaptive mechanisms at the chloroplast genome level in cycle‐cup oaks remain largely unknown. Therefore, we studied this problem by conducting chloroplast genomics on 50 of the ca. 90 species. Comparative genomics and other analyses showed that Quercus section Cyclobalanopsis had a highly conserved chloroplast genome structure. Highly divergent regions, such as the ndhF and ycf1 gene regions and the petN—psbM and rpoB—trnC‐GCA intergenic spacer regions, provided potential molecular markers for subsequent analysis. The chloroplast phylogenomic tree indicated that Quercus section Cyclobalanopsis was not monophyletic, which mixed with the other two sections of subgenus Cerris. The reconstruction of ancestral aera inferred that Palaeotropics was the most likely ancestral range of Quercus section Cyclobalanopsis, and then dispersed to Sino‐Japan and Sino‐Himalaya. Positive selection analysis showed that the photosystem genes had the lowest ω values among the seven functional gene groups. And nine protein‐coding genes containing sites for positive selection: ndhA, ndhD, ndhF, ndhH, rbcL, rpl32, accD, ycf1, and ycf2. This series of analyses together revealed the phylogeny, evolutionary history, and ecological adaptation mechanism of the chloroplast genome of Quercus section Cyclobalanopsis in the long river of earth history. These chloroplast genome data provide valuable information for deep insights into phylogenetic relationships and intraspecific diversity in Quercus.

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Plastid phylogenomics improves resolution of phylogenetic relationship in the Cheirostylis and Goodyera clades of Goodyerinae (Orchidoideae, Orchidaceae)

Cited by 22 publications

References 54 publications

Molecular Phylogeny and Historical Biogeography of Goodyera R. Br. (Orchidaceae): A Case of the Vicariance Between East Asia and North America

Molecular Phylogeny and Historical Biogeography of Goodyera R. Br. (Orchidaceae): A Case of the Vicariance Between East Asia and North America

Plastid genome evolution in leafless members of the orchid subfamily Orchidoideae, with a focus on Degranvillea dermaptera

New insights on the phylogeny, evolutionary history, and ecological adaptation mechanism in cycle‐cup oaks based on chloroplast genomes

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