Telomere-to-telomere and haplotype-resolved genome assembly of the Chinese cork oak (Quercus variabilis).

The Quercus variabilis, a deciduous broadleaved tree species, holds significant ecological and economical value. While a chromosome-level genome for this species has been made available, it remains riddled with unanchored sequences and gaps. In this study, we present a nearly complete comprehensive telomere-to-telomere (T2T) and haplotype-resolved reference genome for Q. variabilis. This was achieved through the integration of ONT ultra-long reads, PacBio HiFi long reads, and Hi-C data. The resultant two haplotype genomes measure 789 Mb and 768 Mb in length, with a contig N50 of 65 Mb and 56 Mb, and were anchored to 12 allelic chromosomes. Within this T2T haplotype-resolved assembly, we predicted 36,830 and 36,370 protein-coding genes, with 95.9% and 96.0% functional annotation for each haplotype genome. The availability of the T2T and haplotype-resolved reference genome lays a solid foundation, not only for illustrating genome structure and functional genomics studies but also to inform and facilitate genetic breeding and improvement of cultivated Quercus species.

Variations in genetic diversity in cultivated Pistacia chinensis.

Identification of the evolution history and genetic diversity of a species is important in the utilization of novel genetic variation in this species, as well as for its conservation. Pistacia chinensis is an important biodiesel tree crop in China, due to the high oil content of its fruit. The aim of this study was to uncover the genetic structure of P. chinensis and to investigate the influence of intraspecific gene flow on the process of domestication and the diversification of varieties. We investigated the genetic structure of P. chinensis, as well as evolution and introgression in the subpopulations, through analysis of the plastid and nuclear genomes of 39 P. chinensis individuals from across China. High levels of variation were detected in the P. chinensis plastome, and 460 intraspecific polymorphic sites, 104 indels and three small inversions were identified. Phylogenetic analysis and population structure using the plastome dataset supported five clades of P. chinensis. Population structure analysis based on the nuclear SNPs showed two groups, clearly clustered together, and more than a third of the total individuals were classified as hybrids. Discordance between the plastid and nuclear genomes suggested that hybridization events may have occurred between highly divergent samples in the P. chinensis subclades. Most of the species in the P. chinensis subclade diverged between the late Miocene and the mid-Pliocene. The processes of domestication and cultivation have decreased the genetic diversity of P. chinensis. The extensive variability and structuring of the P. chinensis plastid together with the nuclear genomic variation detected in this study suggests that much unexploited genetic diversity is available for improvement in this recently domesticated species.

A chromosome-level genome assembly of the Chinese cork oak (Quercus variabilis).

Quercus variabilis (Fagaceae) is an ecologically and economically important deciduous broadleaved tree species native to and widespread in East Asia. It is a valuable woody species and an indicator of local forest health, and occupies a dominant position in forest ecosystems in East Asia. However, genomic resources from Q. variabilis are still lacking. Here, we present a high-quality Q. variabilis genome generated by PacBio HiFi and Hi-C sequencing. The assembled genome size is 787 Mb, with a contig N50 of 26.04 Mb and scaffold N50 of 64.86 Mb, comprising 12 pseudo-chromosomes. The repetitive sequences constitute 67.6% of the genome, of which the majority are long terminal repeats, accounting for 46.62% of the genome. We used ab initio, RNA sequence-based and homology-based predictions to identify protein-coding genes. A total of 32,466 protein-coding genes were identified, of which 95.11% could be functionally annotated. Evolutionary analysis showed that Q. variabilis was more closely related to Q. suber than to Q. lobata or Q. robur. We found no evidence for species-specific whole genome duplications in Quercus after the species had diverged. This study provides the first genome assembly and the first gene annotation data for Q. variabilis. These resources will inform the design of further breeding strategies, and will be valuable in the study of genome editing and comparative genomics in oak species.

GPER and IGF-1R mediate the anti-inflammatory effect of genistein against lipopolysaccharide (LPS)-induced nigrostriatal injury in rats.

Neuroinflammation plays an important role in the pathogenesis of Parkinson's disease (PD). Genistein is an estrogen-like phytoestrogen that can exert biological effects via the crosstalk of estrogen receptor and insulin-like growth factor 1 receptor (IGF-1R). The present study aimed to evaluate the involvement of G protein-coupled estrogen receptor (GPER) and IGF-1R in the anti-inflammatory effects of genistein against lipopolysaccharide (LPS)-induced nigrostriatal injury in ovariectomized rats. Our results showed that genistein treatment could ameliorate the apomorphine-induced rotational behavior in LPS-induced inflammatory PD rat model. Genistein attenuated LPS-induced decrease of the contents of dopamine (DA) and its metabolites in striatum as well as the loss of tyrosine hydroxylase-immunoreactive (TH-IR) neurons in the substantia nigra (SN) of the lesioned side, which could be blocked by GPER antagonist G15 or IGF-1R antagonist JB1. Meanwhile, G15 or JB1 could attenuate the anti-inflammatory effects of genistein in LPS-induced microglial activation and production of tumor necrosis factor-α (TNF-α), interleukin 1ß (IL-1ß), inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2). Moreover, genistein could inhibit the LPS-induced phosphorylation of p38, JNK, ERK and IκB in the lesioned side of SN and these effects could also be blocked by G15 or JB1. Taken together, our data provide the first evidence that genistein can inhibit the increase of microglia and protect dopaminergic neurons at least in part via GPER and IGF-1R signaling pathways in ovariectomized PD rat model.

Characterization of the complete chloroplast genome of Quercus virginiana Mill. (Fagaceae).

The complete chloroplast genome of Quercus virginiana was sequenced with Illumina HiSeq 2000 platform. It was a typical quadruple structure as other plants of Quercus with 161,221 bp in length, including a large single-copy (LSC: 90,553 bp) region and a small single-copy (SSC: 19,016 bp) which were separated by a pair of inverted repeats (IRa, b: 25,826 bp) region. The overall GC content is 36.9%. A total of 131 genes was annotated which contained 86 protein-coding genes including the Trans splicing gene of rps12, 37 tRNA genes, and 8 rRNA genes. ML phylogenetic analysis compared with 17 expressed chloroplast genomes revealed that Q. virginiana was a sister to other species of Quercus, which were grouped together with five species of Section Quercus and another 12 species of Quercus were divided into another group.

The first complete chloroplast genome of Hovenia dulcis Thunb. (Rhamnaceae).

The complete chloroplast genome of Hovenia dulcis was sequenced with Illumina HiSeq 2000 platform. It was a typical quadruple structure as other plants of Hovenia with 162,962 bp in length, including a large single-copy (LSC: 90,900 bp) region and a small single-copy (SSC: 18,920 bp) which were separated by a pair of inverted repeats (IRa, b: 26,571 bp) region. The overall GC content is 36.6%. A total of 130 genes was annotated which contained 85 protein-coding genes including the Trans splicing gene of rps12, 37 tRNA genes, and 8 rRNA genes. ML phylogenetic analysis compared with 6 expressed chloroplast genomes of Rhamnaceae revealed that H. dulcis was closely related to the species of Zizyphus, and which were clustered into a group with Z. jujuba, Z. mauritiana and Z. spina-christi. Hovenia dulcis was relatively distant to other species of Berchemiella and Rhamnus, which were clustered into another group.

Chloroplast genome features and phylogenomic placement of Sorbus hupehensis var. paucijuga (Rosaceae).

The complete chloroplast genome of Sorbus hupehensis var. paucijuga was sequenced with Illumina HiSeq 2000 platform. It was a typical quadruple structure as other plants of Sorbus with 160,050 bp in length, including a large single-copy (LSC: 87,905 bp) region and a small single-copy (SSC: 19,325 bp) which were separated by a pair of inverted repeats (IRa, b: 26,410 bp) region. The overall GC content is 36.5%. A total of 130 genes was annotated which contained 85 protein-coding genes including the Trans splicing gene of rps12, 37 tRNA genes, and 8 rRNA genes. ML phylogenetic analysis compared with 7 expressed chloroplast genomes of Rosaceae revealed that S. hupehensis var. paucijuga was a sister to other Sorbus species. Six species of Sorbus were divided into two groups, the species of group one is distributed in Asia and the species of group two distributed in Europe. Among group one, S. hupehensis var. paucijuga had the closest genetic relationship with S. ulleungensis which is a New Endemic Species on Ulleung Island of Korea, and followed by S. setschwanensis which is only distributed in Sichuan and Guizhou of China. Sorbus hupehensis var. paucijuga has a relatively close relationship with the other three species of Sorbus in the group two. And, it has a relatively distant from other genera of Prunus mongolica and Rosa rugosa.

The complete chloroplast genome sequence of Stephanandra incisa.

Stephanandra incisa is a typical discontinuous distribution species in the eastern part of the subspecies with a high economic and ecological value. In this study, we have obtained the complete chloroplast genome of S. incisa using high-throughput sequencing. The chloroplast genome length was 159,583 bp, the AT content was 63.7%, while the large single copy and a small single copy area were 88,018 bp and 18,817 bp, respectively. It contains 131 genes, including 86 protein-coding genes, 37 transfer RNA genes, and eight ribosomal RNA genes. A maximum-likelihood phylogenetic tree supported the fact that S. incisa is closely related to Pyracantha fortuneana and Amelanchier sinica, which is consistent with the taxonomic view.

Characterization of the complete chloroplast genome of Tilia taishanensis S. B. Liang (Tiliaceae).

The complete chloroplast genome of an endangered endemic species in China Tilia taishanensis was sequenced with Illumina HiSeq 2000 platform. It was a typical quadruple structure as other plants of Tilia with 162,803 bp in length, including a large single copy (LSC: 91,114 bp) region and a small single copy (SSC: 20,379 bp) which were separated by a pair of inverted repeats (IRa, b: 25,655 bp) region. The overall GC content is 36.5%. A total of 129 genes was annotated which contained 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. ML Phylogenetic analysis compared with 33 expressed chloroplast genomes revealed that T. taishanensis was a sister to other Tilia species.

The complete chloroplast genome of Catalpa 'Bairihua', a hybrid variety with multi season flowering.

The complete chloroplast genome of Catalpa 'Bairihua' a hybrid variety with multi season flowering obtained from hybrid progeny of C. bungei 'Luoqiu Sihao' (C. bungei '01' × C. bungei 'Changguo Qiu') and C. fargesii f. duclouxii was first sequenced with the Illumina HiSeq 2000 platform. Which was 158,210 bp in length with a typical quadruple structure and contained a large single copy (LSC: 84,928 bp) region and a small single copy (SSC: 12,664 bp) region that were separated by a pair of inverted repeats (IRa, b: 30,309 bp) region. The GC content of the whole chloroplast genome is 38.1%. A total of 130 genes was annotated in the complete chloroplast genome, including 85 protein-coding genes, 37 tRNA genes and 8rRNA genes. ML phylogenetic analysis by comparing with 39 chloroplast genomes of the Bignoniaceae indicated that Catalpa 'Bairihua' was close to Tecomaria capensis.

The complete chloroplast genome of Cotoneaster schantungensis.

Cotoneaster schantungensis is an endangered vulnerable species restricted to Shandong Province. In this study, we report the sequencing of the C. schantungensis chloroplast (cp) genome using the Illumina Novaseq platform for the first time. The complete C. schantungensis cp genome is 159,883 bp in length and contains two inverted repeats (IRs), separated by a large single-copy region (LSC) and a small single-copy region (SSC). A total of 132 unique coding genes, including 85 protein-coding genes, 39 tRNA genes, and 8 rRNA genes were identified. The maximum likelihood phylogenetic analysis revealed that C. schantungensis is closely related to Eriobotrya japonica.