Genomics of the critically endangered monotypic genus Sinopora: the plastome of S. hongkongensis (Lauraceae).

Sinopora hongkongensis is a critically endangered endemic tree species restricted to Hong Kong. Here we report its plastome sequence. The S. hongkongensis plastome was 158,612 bp in length, with a large single-copy (LSC) region of 89,405 bp and a small single-copy (SSC) region of 18,205 bp, separated by two inverted repeat (IR) regions of 25,498 bp. It contained 126 genes, including 89 coding genes, 29 tRNA genes, and 8 rRNA genes. The overall GC content was 39.0%, and 43.0%, 37.7%, and 34.0%, in the IRs, LSC, and SSC regions, respectively. A phylogenetic analysis combining a subset of Lauraceae plastomes with closely related outgroup families confirms the placement of S. hongkongensis in Lauraceae and explores relationships with other genera in the family.

Plastome of Quercus xanthoclada and comparison of genomic diversity amongst selected Quercus species using genome skimming.

The genus Quercus L. contains several of the most economically important species for timber production in the Northern Hemisphere. It was one of the first genera described, but genetic diversity at a global scale within and amongst oak species remains unclear, despite numerous regional or species-specific assessments. To evaluate global plastid diversity in oaks, we sequenced the complete chloroplast of Quercus xanthoclada and compared its sequence with those available from other main taxonomic groups in Quercus. We quantify genomic divergence amongst oaks and performed a sliding window analysis to detect the most variable regions amongst members of the various clades, as well as divergent regions occurring in specific pairs of species. We identified private and shared SNPs amongst oaks species and sections and stress the need for a large global assessment of genetic diversity in this economically and ecologically important genus.

Exploring evolution and diversity of Chinese Dipterocarpaceae using next-generation sequencing.

Tropical forests, a key-category of land ecosystems, are faced with the world's highest levels of habitat conversion and associated biodiversity loss. In tropical Asia, Dipterocarpaceae are one of the economically and ecologically most important tree families, but their genomic diversity and evolution remain understudied, hampered by a lack of available genetic resources. Southern China represents the northern limit for Dipterocarpaceae, and thus changes in habitat ecology, community composition and adaptability to climatic conditions are of particular interest in this group. Phylogenomics is a tool for exploring both biodiversity and evolutionary relationships through space and time using plastome, nuclear and mitochondrial genome. We generated full plastome and Nuclear Ribosomal Cistron (NRC) data for Chinese Dipterocarpaceae species as a first step to improve our understanding of their ecology and evolutionary relationships. We generated the plastome of Dipterocarpus turbinatus, the species with the widest distribution using it as a baseline for comparisons with other taxa. Results showed low level of genomic diversity among analysed range-edge species, and different evolutionary history of the incongruent NRC and plastome data. Genomic resources provided in this study will serve as a starting point for future studies on conservation and sustainable use of these dominant forest taxa, phylogenomics and evolutionary studies.

The first complete chloroplast genome of a major mangrove species Sonneratia alba Sm. and its implications on conservation efforts.

Sonneratia alba Sm. is one of the most widely distributed mangrove species worldwide. In this study, the whole chloroplast genome of S. alba was assembled for the first time not only in Sonneratia, but also for a member of the mangrove plant community. The total chloroplast genome was 153,061 bp in length, with a large single copy (LSC) region of 87,226 bp and a small single copy (SSC) region of 18,033 bp, separated by two inverted repeats (IRs) regions of 23,901 bp. The overall GC content was 37.3%, and 43.1%, 35.4%, and 31.1% in the IRs, LSC, and SSC regions, respectively. It contained 106 genes, including 79 coding genes, 24 tRNA genes, and four rRNA genes. A phylogenetic analysis confirmed that S. alba was clustered with Trapa maximowiczii within the family Lythraceae.

Characterization of the complete chloroplast genome of endangered Cycads Zamia fischeri Miq. ex Lem.

The whole chloroplast (cp) genome sequence of Zamia fischeri has been characterized. The cp genome length was 164,767 bp in length, with a GC content of 39.7%, containing a large single copy (LSC) of 90,226 bp, a small single copy (SSC) of 23,223 bp, and a pair of inverted repeats (IRs) of 25,659 bp. The genome contained 127 genes, including 88 protein-coding genes, 31 tRNA genes, and 8 rRNA genes. A phylogenetic analysis based on complete chloroplast genomes in Cycads indicates that Z. fischeri clustered with another Zamia (Z. furfuracea). This complete chloroplast sequence offers a promising tool for further species identification, population genetic conservation, and evolutionary studies of Zamiaceae, as well as for Cycadales.

The complete mitochondrial genome of the Basidiomycete fungus Pleurotus cornucopiae (Paulet) Rolland.

Pleurotus cornucopiae is a commercial edible and medicinal fungus. Herein, we determined and analyzed its complete mitochondrial genome. The mitogenome length was 72,134 bp with a GC content of 26.7%, contained 14 conserved protein coding genes, two rRNA genes (rnl and rns), ribosomal protein gene rps3 and 24 tRNA genes. Pleurotus cornucopiae has a similar gene content and gene order of the mitogenome as P. ostreatus and P. eryngii. A phylogenetic analysis based on complete mitogenome in related fungi showed that P. cornucopiae is a member of the order Agaricales, forming a clade with P. ostreatus and P. eryngii, with P. ostreatus as a sister taxa. The mitochondrial genome sequence of P. cornucopiae appeared a promising tool for further studies of the taxonomy and evolution of Pleurotaceae and Agaricales.

The chloroplast genome sequence of Michelia alba (Magnoliaceae), an ornamental tree species.

Magnoliaceae are both economically and ornamentally important trees. Despite extensive studies in this family, the taxonomy of Michelia L. remains unclear, as well as the taxonomical status of Michelia alba. Herein, we report the complete chloroplast genome of M. alba DC. The chloroplast genome was 159,789 bp in length, with a large single-copy (LSC) region of 87,951 bp and a small single-copy (SSC) region of 18,798 bp, separated by two inverted repeat (IRs) regions of 26,570 bp. It contained 156 genes, including 83 coding genes, 68 tRNA genes, and 8 rRNA genes. The overall GC content was 39.3%, and 43.2%, 38.0%, 34.3%, in the IRs, LSC, and SSC regions, respectively. A phylogenetic analysis showed that M. alba is closely related to M. odora, with the genus Michelia nested inside Magnolia.

The first complete chloroplast sequence of a major tropical timber tree in the Meranti family: Vatica odorata (Dipterocarpaceae).

Dipterocarpaceae are one of the economically most important native tree families for timber production in tropical Asia. We report the complete chloroplast genome of Vatica odorata (Griff.) Symington, the first in the family Dipterocarpaceae. The chloroplast genome was 151,465 bp in length, with a large single-copy (LSC) region of 83,538 bp and a small single-copy (SSC) region of 20,095 bp, separated by two inverted repeat (IRs) regions of 23,916 bp. It contained 126 genes, including 90 coding genes, 30 tRNA genes, and 8 rRNA genes. The overall GC content was 37.2%, and 43.1%, 35.2%, and 33.3% in the IRs, LSC and SSC regions, respectively. A phylogenetic tree showed Vatica accumulated more variation when compared with Tilia, and that internal relationships in Malvales need to be reassessed.

The complete mitochondrial genome of the Agrocybe aegerita, an edible mushroom.

Agrocybe aegerita is a medicinally and nutritionally important edible basidiomycete. Despite previous phylogenetic studies, the taxonomy of A. aegerita complex remains unclear due to lacking of resolutive data. Herein, the complete mitochondrial genome of A. aegerita is reported and analyzed. The mitogenome length was 116,329 bp, with a GC content of 27.6%, include 17 typical protein-coding genes, two ribosomal protein genes (rps3), two ribosomal RNA genes and a set of 32 transfer RNA genes. A phylogenetic analyses using complete mitogenome in Agaricales showed that A. aegerita is closely related to the genus Pleurotus and represents a clade clearly independent from other Agaricales species.

Comparison of intraspecific, interspecific and intergeneric chloroplast diversity in Cycads.

Cycads are among the most threatened plant species. Increasing the availability of genomic information by adding whole chloroplast data is a fundamental step in supporting phylogenetic studies and conservation efforts. Here, we assemble a dataset encompassing three taxonomic levels in cycads, including ten genera, three species in the genus Cycas and two individuals of C. debaoensis. Repeated sequences, SSRs and variations of the chloroplast were analyzed at the intraspecific, interspecific and intergeneric scale, and using our sequence data, we reconstruct a phylogenomic tree for cycads. The chloroplast was 162,094 bp in length, with 133 genes annotated, including 87 protein-coding, 37 tRNA and 8 rRNA genes. We found 7 repeated sequences and 39 SSRs. Seven loci showed promising levels of variations for application in DNA-barcoding. The chloroplast phylogeny confirmed the division of Cycadales in two suborders, each of them being monophyletic, revealing a contradiction with the current family circumscription and its evolution. Finally, 10 intraspecific SNPs were found. Our results showed that despite the extremely restricted distribution range of C. debaoensis, using complete chloroplast data is useful not only in intraspecific studies, but also to improve our understanding of cycad evolution and in defining conservation strategies for this emblematic group.

The phylogeny and biogeographic history of ashes (fraxinus, oleaceae) highlight the roles of migration and vicariance in the diversification of temperate trees.

The cosmopolitan genus Fraxinus, which comprises about 40 species of temperate trees and shrubs occupying various habitats in the Northern Hemisphere, represents a useful model to study speciation in long-lived angiosperms. We used nuclear external transcribed spacers (nETS), phantastica gene sequences, and two chloroplast loci (trnH-psbA and rpl32-trnL) in combination with previously published and newly obtained nITS sequences to produce a time-calibrated multi-locus phylogeny of the genus. We then inferred the biogeographic history and evolution of floral morphology. An early dispersal event could be inferred from North America to Asia during the Oligocene, leading to the diversification of the section Melioides sensus lato. Another intercontinental dispersal originating from the Eurasian section of Fraxinus could be dated from the Miocene and resulted in the speciation of F. nigra in North America. In addition, vicariance was inferred to account for the distribution of the other Old World species (sections Sciadanthus, Fraxinus and Ornus). Geographic speciation likely involving dispersal and vicariance could also be inferred from the phylogenetic grouping of geographically close taxa. Molecular dating suggested that the initial divergence of the taxonomical sections occurred during the middle and late Eocene and Oligocene periods, whereas diversification within sections occurred mostly during the late Oligocene and Miocene, which is consistent with the climate warming and accompanying large distributional changes observed during these periods. These various results underline the importance of dispersal and vicariance in promoting geographic speciation and diversification in Fraxinus. Similarities in life history, reproductive and demographic attributes as well as geographical distribution patterns suggest that many other temperate trees should exhibit similar speciation patterns. On the other hand, the observed parallel evolution and reversions in floral morphology would imply a major influence of environmental pressure. The phylogeny obtained and its biogeographical implications should facilitate future studies on the evolution of complex adaptive characters, such as habitat preference, and their possible roles in promoting divergent evolution in trees.

Deciduous trees and the application of universal DNA barcodes: a case study on the circumpolar Fraxinus.

The utility of DNA barcoding for identifying representative specimens of the circumpolar tree genus Fraxinus (56 species) was investigated. We examined the genetic variability of several loci suggested in chloroplast DNA barcode protocols such as matK, rpoB, rpoC1 and trnH-psbA in a large worldwide sample of Fraxinus species. The chloroplast intergenic spacer rpl32-trnL was further assessed in search for a potentially variable and useful locus. The results of the study suggest that the proposed cpDNA loci, alone or in combination, cannot fully discriminate among species because of the generally low rates of substitution in the chloroplast genome of Fraxinus. The intergenic spacer trnH-psbA was the best performing locus, but genetic distance-based discrimination was moderately successful and only resulted in the separation of the samples at the subgenus level. Use of the BLAST approach was better than the neighbor-joining tree reconstruction method with pairwise Kimura's two-parameter rates of substitution, but allowed for the correct identification of only less than half of the species sampled. Such rates are substantially lower than the success rate required for a standardised barcoding approach. Consequently, the current cpDNA barcodes are inadequate to fully discriminate Fraxinus species. Given that a low rate of substitution is common among the plastid genomes of trees, the use of the plant cpDNA "universal" barcode may not be suitable for the safe identification of tree species below a generic or sectional level. Supplementary barcoding loci of the nuclear genome and alternative solutions are proposed and discussed.