Search

The Chinese chestnut (Castanea mollissima Bl.) is a woody nut crop with a high ecological value. Although many cultivars have been selected from natural seedlings, elite lines with comprehensive agronomic traits and characters remain rare. To explore genetic resources with aid of whole genome sequence will play important roles in modern breeding programs for chestnut. In this study, we generated a high-quality C. mollissima genome assembly by combining 90× Pacific Biosciences long read and 170× high-throughput chromosome conformation capture data. The assembly was 688.93 Mb in total, with a contig N50 of 2.83 Mb. Most of the assembled sequences (99.75%) were anchored onto 12 chromosomes, and 97.07% of the assemblies were accurately anchored and oriented. A total of 33,638 protein-coding genes were predicted in the C. mollissima genome. Comparative genomic and transcriptomic analyses provided insights into the genes expressed in specific tissues, as well as those associated with burr development in the Chinese chestnut. This highly contiguous assembly of the C. mollissima genome provides a valuable resource for studies aiming at identifying and characterizing agronomical-important traits, and will aid the design of breeding strategies to develop more focused, faster, and predictable improvement programs.

To fully protect and utilize Acer truncatum resources, the phenotypic variation and genetic diversity of A. truncatum in different regions should be understood. In this study, leaves of A. truncatum trees from 15 provenances were used as experimental materials to analyze leaf morphological variation and genetic diversity at the molecular level. The results showed that the sizes of leaves of A. truncatum trees from different provenances were significantly different, and there was a certain correlation with the geographical environment: leaf size gradually decreased with increasing longitude, latitude and elevation. According to principal component analysis (PCA), the variation in leaf morphology among provenances concerned mainly the petioles, leaf width, and leaf length; there was no correlation between leaf morphological variation and geographic distance. From 240 pairs of sequence-related amplified polymorphism (SRAP) primer combinations, 12 pairs that met the conditions were identified, and a total of 267 bands were amplified; 252 of the bands were polymorphic, with a polymorphism percentage of 94.38%, and an average of 22.25 bands and 21 polymorphic bands were amplified from each pair of primers. Ne, H and I indicated that A. truncatum has relatively high genetic variation and a rich genetic diversity at the species level. Among the provenances, H and I were 0.1754 and 0.2707 respectively, indicating that the genetic diversity among the provenances of A. truncatum was low. There were differences in genetic diversity parameters among the various sources. Yongji, Shanxi (6) had the highest genetic diversity, and Huixian, Gansu (15) had the lowest genetic diversity. The genetic similarity coefficients among the various sources ranged from 0.8404 to 0.9558, the range of variation was 0.1154, and the average coefficient was 0.9006. The provenance of Taian, Shandong (4) and Yongji, Shanxi (6) had the closest genetic relationship, with a genetic similarity coefficient of 0.9558 and a D of 0.0824; Pingquan, Hebei (2) and Huixian, Gansu (15) were the most distantly related, with the largest D, and a genetic similarity coefficient of 0.8404. Cluster analysis based on the genetic similarity coefficient also showed that the Ds and geographic distances of A. truncatum from different provenances were not correlated. These results provide a reference for research on A. truncatum germplasm management and ecological adaptability.

Malus spectabilis ‘Guanghui’ is an important ornamental plant, which complete chloroplast genome (Accession: MT501657) was sequenced, assembled and annotated. The genome size is 1601,230 bp and the overall GC content is 36.50%, with large single-copy (LSC, 89,310bp) regions, small single-copy (SSC, 19,196 bp) regions, and two inverted repeat regions (IRs, 23,632bp each). A total of 129 genes are successfully annotated, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic relationships showed that Malus spectabilis ‘Guanghui’ is closely related to the species of Malus sieversii.

Punica granatum ‘Luqing1’ is an important d fruit tree with high quality and strong cold-resistance. The complete chloroplast genome (Accession: MN630638) was sequenced, assembled, and annotated. The size of chloroplast genome was 158,638 bp with large single-copy (LSC, 89,021 bp) regions, small single-copy (SSC, 18,685 bp) regions, and two inverted repeat regions (IRs, 25,466 bp each). A total of 130 genes were successfully annotated, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The phylogenetic relationships showed that P. granatum ‘Luqing1’ was closely related with different pomegranate cultivars.

Cercis canadensis ‘Forest Pansy’ is a tree species with high ornamental value, which complete chloroplast (cp) genome was sequenced, assembled, and annotated. The genome size is 158,960 bp with a total GC content of 36.17%. The cp genome is made up of a large single-copy region (88,114 bp), a small single-copy region (19,590 bp), and two inverted repeat regions (25,628 bp each). It contains 128 genes, including 84 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Eighteen genes were duplicated in IRs. The maximum-likelihood (ML) phylogenetic analysis indicated that the Leguminosae species are grouped together, and C. canadensis ‘Forest Pansy’ is closely related to C. canadensis. The result would provide valuable information for genetic studies on Cercis genus.

Hovenia acerba Lindl. is an important medicinal plant, for which complete chloroplast genome (Accession: MN782301) was sequenced, assembled and annotated. The genome size is 161,668 bp and the overall GC content is 36.69%, with large single-copy (LSC, 89,451bp) regions, small single-copy (SSC, 18,979 bp) regions, and two inverted repeat regions (IRs, 26,619 bp each). A total of 130 genes are successfully annotated, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic relationships showed that H. acerba is closely related to the species of Ziziphus genus.

‘Huangjinya’ is an excellent albino tea germplasm cultivated in China because of its bright color and high amino acid content. It is light sensitive, with yellow leaves under intense light while green leaves under weak light. As well, the flavonoid and carotenoid levels increased after moderate shading treatment. However, the mechanism underlying this interesting phenomenon remains unclear. In this study, the transcriptome of ‘Huangjinya’ plants exposed to sunlight and shade were analyzed by high-throughput sequencing followed by de novo assembly. Shading ‘Huangjinya’ made its leaf color turn green. De novo assembly showed that the transcriptome of ‘Huangjinya’ leaves comprises of 127,253 unigenes, with an average length of 914 nt. Among the 81,128 functionally annotated unigenes, 207 differentially expressed genes were identified, including 110 up-regulated and 97 down-regulated genes under moderate shading compared to full light. Gene ontology (GO) indicated that the differentially expressed genes are mainly involved in protein and ion binding and oxidoreductase activity. Antioxidation-related pathways, including flavonoid and carotenoid biosynthesis, were highly enriched in these functions. Shading inhibited the expression of flavonoid biosynthesis-associated genes and induced carotenoid biosynthesis-related genes. This would suggest that decreased flavonoid biosynthetic gene expression coincides with increased flavonoids (e.g., catechin) content upon moderate shading, while carotenoid levels and biosynthetic gene expression are positively correlated in ‘Huangjinya.’ In conclusion, the leaf color changes in ‘Huangjinya’ are largely determined by the combined effects of flavonoid and carotenoid biosynthesis.

'Huangjinya' is an excellent albino tea germplasm cultivated in China because of its bright color and high amino acid content. It is light sensitive, with yellow leaves under intense light while green leaves under weak light. As well, the flavonoid and carotenoid levels increased after moderate shading treatment. However, the mechanism underlying this interesting phenomenon remains unclear. In this study, the transcriptome of 'Huangjinya' plants exposed to sunlight and shade were analyzed by high-throughput sequencing followed by de novo assembly. Shading 'Huangjinya' made its leaf color turn green. De novo assembly showed that the transcriptome of 'Huangjinya' leaves comprises of 127,253 unigenes, with an average length of 914 nt. Among the 81,128 functionally annotated unigenes, 207 differentially expressed genes were identified, including 110 up-regulated and 97 down-regulated genes under moderate shading compared to full light. Gene ontology (GO) indicated that the differentially expressed genes are mainly involved in protein and ion binding and oxidoreductase activity. Antioxidation-related pathways, including flavonoid and carotenoid biosynthesis, were highly enriched in these functions. Shading inhibited the expression of flavonoid biosynthesis-associated genes and induced carotenoid biosynthesis-related genes. This would suggest that decreased flavonoid biosynthetic gene expression coincides with increased flavonoids (e.g., catechin) content upon moderate shading, while carotenoid levels and biosynthetic gene expression are positively correlated in 'Huangjinya.' In conclusion, the leaf color changes in 'Huangjinya' are largely determined by the combined effects of flavonoid and carotenoid biosynthesis. [ABSTRACT FROM AUTHOR]

The organogenesis potential is different among cultivars and must be optimized for individual genotype. Shoot organogenesis capacity from in vitro leaves and root organogenesis capacity of in vitro shoots in six clonal apple rootstock cultivars were compared. The shoot organogenesis capacity was highly genotype dependent. 'GM256' was found to be the most responsive genotype for shoot regeneration from leaf explants among the cultivars, showing high regeneration percentage on all tested media. The effects of basal medium composition and cytokinins on shoot regeneration were different depending on rootstock genotype. Optimum regeneration occurred on Murashige and Skoog (MS) basal medium for '71-3-150', and optimum regeneration occurred on Quoirin and Lepoivre (QL) basal medium for '60-160' and 'ПB'. Thidiazuron (TDZ) was more effective than 6-benzylaminopurine (BA) for Malus prunifolia (Y), whereas TDZ and BA were not significantly different for the other cultivars. All rootstock cultivars showed high root organogenic capacity. The percentage of rooting reached more than 90% and the mean root number per plantlet ranged from three to five. The optimum rooting medium was different for different rootstock cultivars. Optimum root organogenesis occurred on half-strength QL medium for 'GM256' and 'Y', and for 'ПB' and 'JM7' on one-quarter-strength MS medium. [ABSTRACT FROM AUTHOR]