Transcriptional dynamics reveals the asymmetrical events underlying graft union formation in pecan (Carya illinoinensis).

Grafting is a widely used technique for pecan propagation; however, the background molecular events underlying grafting are still poorly understood. In our study, the graft partners during pecan [Carya illinoinensis (Wangenh.) K. Koch] graft union formation were separately sampled for RNA-seq, and the transcriptional dynamics were described via weighted gene co-expression network analysis. To reveal the main events underlying grafting, the correlations between modules and grafting traits were analyzed. Functional annotation showed that during the entire graft process, signal transduction was activated in the scion, while messenger RNA splicing was induced in the rootstock. At 2 days after grafting, the main processes occurring in the scion were associated with protein synthesis and processing, while the primary processes occurring in the rootstock were energy release-related. During the period of 7-14 days after grafting, defense response was a critical process taking place in the scion; however, the main process functioning in the rootstock was photosynthesis. From 22 to 32 days after grafting, the principal processes taking place in the scion were jasmonic acid biosynthesis and defense response, whereas the highly activated processes associated with the rootstock were auxin biosynthesis and plant-type secondary cell wall biogenesis. To further prove that the graft partners responded asymmetrically to stress, hydrogen peroxide contents as well as peroxidase and ß-1,3-glucanase activities were detected, and the results showed that their levels were increased in the scion not the rootstock at certain time points after grafting. Our study reveals that the scion and rootstock might respond asymmetrically to grafting in pecan, and the scion was likely associated with stress response, while the rootstock was probably involved in energy supply and xylem bridge differentiation during graft union formation.

Targeted metabolomics reveals key phenolic changes in pecan nut quality deterioration under different storage conditions.

Pecan nuts are highly enriched in phenolic compounds, which contribute to the health benefits of pecans. Phenolic compounds represent the main oxidation reaction substrates, thus leading to quality deterioration, namely pellicle browning or a decrease in beneficial effects during pecan storage. Hence, four different storage conditions were performed for 180 d to simulate real production situations. Targeted metabolomics was chosen to identify the specific phenolic compounds involved in quality deterioration under different storage conditions in 0, 90, and 180 d samples. A total of 118 phenolic compounds were detected, nine of which were identified for the first time in pecan. The total phenolic content (TPC) and antioxidant capacities initially demonstrated high scores, after which they tended to decrease during the storage process. The significantly modified phenolic compounds during storage were selected as the metabolite markers of pecan quality deterioration, including catechin, procyanidin (PA) trimer, PA tetramer, trigalloyl hexahydroxydiphenoyl (HHDP) glucose, and tetragalloyl hexoside. Fresh pecan kernels resulted in more pronounced changes in hydrolysable tannins (HTs), whereas dry kernels resulted in the most accentuated changes in condensed tannins (CTs). To the best of our knowledge, this is the first attempt to study individual phenolic changes during storage of pecan in such massive amounts. The results can offer a valuable theoretical basis for future control of pecan quality deterioration through phenolics during storage.

Stem rot on Adenia globosa caused by Lasiodiplodia theobromae in Jiangsu.

Adenia globosa, as an excellent indoor ornamental plant, is planted in Tropical Botanical Museum, Nanjing Zhongshan Botanical Garden, Jiangsu Province, China. In September 2022, a new stem basal rot disease was observed on A. globosa seedlings, being planted here. Stem basal rot were observed on approximately 80% of A. globosa seedlings. The basal stem of cutting seedlings appeared decayed, and stem tip eventually turned dry due to water loss (Figure S1A). To isolate the pathogen, three diseased stems were collected from three cuttings planted in different pots of the Tropical Botanical Museum. The stem sections (3 to 4 mm) were excised from the margins between healthy and diseased tissues, surface sterilized in 75% ethanol for 30 s and 1.5% NaClO for 90 s, rinsed three times in sterilized distilled water, plated on potato dextrose agar (PDA) and incubated at 25℃ in the dark. Pure cultures were obtained by monosporic isolation. Eight isolates were obtained, and all identified as Lasiodiplodia sp.. The colonies morphology of cultures, growing on PDA were cotton-like, the primary mycelia were black gray after 7 days, and the reverse sides of PDA plates were similar to front sides in color (Figure S1B). A representative isolate, QXM1-2 was selected for the further study. Conidia of QXM1-2 were oval or elliptic, with a mean size of 11.6 µm×6.6 µm (n=35). The conidia are colorless and transparent in the early stage, and become dark brown with one-septum in the later stage (Figure S1C). The conidiophores produced conidia after nearly four weeks of cultivation on PDA plate (Figure S1D). The conidiophore was a transparent cylindrical structure, with a size of (6.4-18.2) µm × (2.3-4.5) µm ( n = 35). These characteristics were consistent with the description of Lasiodiplodia sp. (Alves et al. 2008). The internal transcribed spacer regions (ITS), translation elongation factor 1-alpha (TEF1α) and ß-tubulin (TUB) genes (GenBank Accession No.OP905639, No.OP921005, and No.OP921006, respectively) were amplified and sequenced with the primer pairs ITS1/ITS4 (White et al. 1990), EF1-728F/EF1-986R (Alves et al. 2008) and Bt2a/Bt2b (Glass and Donaldson 1995), respectively. They had 99.8-100% homology to the ITS (504/505 bp) of Lasiodiplodia theobromae strain NH-1 (MK696029), TEF1α (316/316 bp) of strain PaP-3 (MN840491), and TUB (459/459 bp) of isolate J4-1 (MN172230). A neighbor-joining phylogenetic tree was generated by combining all sequenced loci in MEGA7. The isolate QXM1-2 clustered in the L. theobromae clade with 100% bootstrap support (Figure S2). To test pathogenicity, three A. globosa cutting seedlings that previously had been wounded with a sterile needle were inoculated with 20 µL conidia suspension (1×106 conidia/mL) on the stem base. The seedlings inoculated with 20 µL sterile water was used as the control. All plants were covered with clear polyethylene bags to keep moisture in a greenhouse (25℃, 80% relative humidity). The experiment was repeated three times. After 7 days post-inoculation, typical stem rot were found on the treated cutting seedlings and the control seedlings did not have any symptoms (Figure S1E-F). The same fungus, identified by morphological characteristics and sequencing using ITS, TEF1α and TUB genes, was isolated from the diseased tissues of the inoculated stems to complete Koch's postulates. This pathogen has been reported infecting the branch of castor bean (Tang et al. 2021) and root of Citrus (Al-Sadi et al. 2014). For our knowledge, this is the first report of L. theobromae infecting A. globosa in China. This study provides an important reference for the biology, epidemiology of L. theobromae.

First report of leaf spot on pecan (Carya illinoinensis) caused by Stemphylium eturmiunum in China.

Pecan [Carya illinoinensis (Wangenh.) K. Koch] is an important nut tree species, which has been widely planted in Jiangsu and Anhui Provinces of China in recent years (Mo et al. 2018). In May 2022, a new leaf spot disease was observed on both young and old leaves of pecan trees in the Luhe area, Nanjing, Jiangsu Province. Approximately 30% of pecan trees suffered from the disease, which affected the growth of young trees and nut production to cause economic loss. Initially, the leaf spots were grayish black and round. Then, disease spots enlarged and joined together, forming irregular lesions with uneven edges. In the last stage, the leaflets were withered. To isolate the pathogen, three symptomatic leaves were collected from each of three different pecan trees. Leaf sections (3 to 4 mm) were excised from the margin of spots, surface sterilized in 75% alcohol for 30 s, then sterilized in 1.5% NaClO for 90 s. After rinsing three times with sterile distilled water, leaf sections were placed on potato dextrose agar (PDA) medium and incubated at 25 °C in a dark environment for 5 days. Pure cultures were obtained by monosporic isolation. A total of 20 isolates were obtained, and 12 isolates were identified as Stemphylium sp. with the same morphological features and ITS sequences. A representative isolate, named LH3-3, was selected for further study. Colonies on PDA were light yellow with dense mycelium and were brownish yellow on the reverse side. Conidia were 16.3 to 34.4 × 8.1 to 16.3 µm) (n=35), muriform, brown, with transverse and longitudinal septa, lightly deformed at the transverse septa. Ascomata were not observed. The morphological characteristics were consistent with the description of Stemphylium eturmiunum (Simmons 2001). The internal transcribed spacer region (ITS) and portions of genes for calmodulin (cmdA) and glyceraldehyde-3-phosphate dehydrogenase (gpd) were amplified and sequenced with the primers ITS1/ITS4 (White et al. 1990), CALDF1/CALDR2 (Xu et al. 2022) and GPD-F/R (Xie et al. 2019), respectively. Sequences were deposited in GenBank under accessions OP482492 (ITS), OP495734 (cmdA), and OP495735 (gpd). BLAST analysis showed that the sequences had 99.67-100% homology to ITS (525/525 bp) of S. eturmiunum strain ST14 (MH843733), cmdA (694/694 bp) of strain CBS122124 (KU850832), and gpd (299/300 bp) of isolate UMSe0030 (MK336876). MEGA 7.0 was used to construct a phylogenetic analysis based on concatenated sequences of ITS, cmdA, and gpd using the neighbor-joining method. The results showed that LH3-3 clustered on the branch of S. eturmiunum, and the support rate was 100%. A spore suspension in sterile water was made from strain LH3-3 grown on PDA, and adjusted to 1×106 spores/mL with a hemocytometer. To test pathogenicity, 20 µl drops of the spore suspension were placed on the left sides of four healthy detached leaflets of mature pecan trees and leaves of three 3-month-old seedlings. The right side of each leaflet was inoculated with 20 µl drops of sterile distilled water as the control. All inoculated seedlings and detached leaflets were covered with a transparent plastic bag and cultured in a greenhouse at 25 °C, 80% relative humidity, and a 12 h light cycle until symptom appeared. The experiment was repeated three times. After 7 days of inoculation, grayish black lesions appeared on all inoculation sites with the spore suspension but not in the controls. The leaf spot symptoms were similar to those observed in orchards. The same fungus, identified by morphological characteristics and sequencing of ITS, cmdA, and gpd, was re-isolated from the diseased spots of the inoculated leaflets to complete Koch's postulates. S. eturmiunum has been reported to infect garlic (Dumin et al. 2022) and tomato (Prencipee et al. 2021), but this is the first report of S. eturmiunum causing leaf spot of C. illinoinensis. This study provides a basis for further study on the biology, epidemiology, and management of the disease.

Transcriptomic Analysis to Unravel Potential Pathways and Genes Involved in Pecan (Carya illinoinensis) Resistance to Pestalotiopsis microspora.

Fruit black spot (FBS), a fungal disease of pecan (Carya illinoinensis (Wangenh) K. Koch) caused by the pathogen Pestalotiopsis microspora, is a serious disease and poses a critical threat to pecan yield and quality. However, the details of pecan responses to FBS infection at the transcriptional level remain to be elucidated. In present study, we used RNA-Seq to analyze differential gene expression in three pecan cultivars with varied resistance to FBS infection: Xinxuan-4 (X4), Mahan (M), and Wichita (W), which were categorized as having low, mild, and high susceptibility to FBS, respectively. Nine RNA-Seq libraries were constructed, comprising a total of 58.56 Gb of high-quality bases, and 2420, 4380, and 8754 differentially expressed genes (DEGs) with |log2Fold change| ≥ 1 and p-value < 0.05 were identified between M vs. X4, W vs. M, and W vs. X4, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analyses were performed to further annotate DEGs that were part of specific pathways, which revealed that out of 134 total pathways, MAPK signaling pathway, plant−pathogen interaction, and plant hormone signal transduction were highly enriched. Transcriptomic profiling analysis revealed that 1681 pathogen-related genes (PRGs), including 24 genes encoding WRKY transcription factors, potentially participate in the process of defense against Pestalotiopsis microspora infection in pecan. The correlation of WRKY TFs and PRGs was also performed to reveal the potential interaction networks among disease-resistance/pathogenesis-related genes and WRKY TFs. Expression profiling of nine genes annotated as TIFY, WRKY TF, and disease-resistance protein-related genes was performed using qRT-PCR, and the results were correlated with RNA-Seq data. This study provides valuable information on the molecular basis of pecan−Pestalotiopsis microspora interaction mechanisms and offers a repertoire of candidate genes related to pecan fruit response to FBS infection.

First report of leaf spot on Deutzia crenata caused by Neopestalotiopsis ellipsospora in China.

Deutzia crenata Sieb. et Zucc, native to Japan, with white flowers in early summer, is a high quality ornamental shrub widely planted in China. In October 2021, a new leaf spot disease was observed on approximately 70% of the 320 D. crenata trees growing in Nanjing Botanical Garden, Jiangsu Province, China. The disease started as irregular small gray spots on the leaf of D. crenata that coalesced into larger lesions. Infected leaves turned yellow (Figure S1A) and leaves with multiple spots withered. To isolate the pathogen, leaf sections (3 to 4 mm) were excised from the lesion margin, surface sterilized in 75% alcohol for 30 s and then in 1.5% NaClO for 90 s, rinsed three times in sterilized distilled water, plated on potato dextrose agar (PDA) and incubated at 25℃in the darkness. Pure cultures were obtained by monosporic isolation. The colony of a representative isolate (L-1), growing on PDA was circular, white, and cottony, and the surface undulate and pale luteous (Figure S1B). The reverse was similar in color (Figure S1C). The conidial masses were black and appeared over PDA plates after 12 days (Figure S1D). Conidia [18.3 to 28.4×5.4 to 8.5 µm (mean 24.5×6.7 µm)] (n=35) were fusiform to ellipsoid and four-septate (one basal and one apical cell hyaline, and three brown median cells), with two to three apical appendages (Figure S1E). These characteristics were consistent with the description of Neopestalotiopsis sp. (Maharachchikumbura et al. 2014). Three regions of the internal transcribed spacer (ITS), translation elongation factor 1-alpha (TEF1α), and ß-tubulin (TUB) genes (GenBank Accession No. OM663738, No. OM687134 and No. OM687133, respectively) were amplified and sequenced with the primers pairs ITS1/ITS4 (Innis et al. 1990), EF1-526F/EF1-1567R (Maharachchikumbura et al. 2014) and Bt2a/Bt2b (Glass and Donaldson 1995), respectively. The obtained sequences were 95.4-99.8% similar to those from Neopestalotiopsis sp. accessions in GenBank. A neighbor-joining phylogenetic tree was generated by combining all sequenced loci in MEGA7. The isolate L-1 clustered in the N. ellipsospora clade with 98% bootstrap support (Figure S2). To test pathogenicity, three detached healthy leaves and three one-year-old D. crenata seedlings were inoculated with 20 µL conidia suspension (1×106 spores/mL) on the left sides of leaves. The right side of each leaf was inoculation with 20 µL of sterile water as the experimental control. All plants were covered with clear polyethylene bags and incubated in a greenhouse (Institute of Botany, Jiangsu Province and Chinese Academy of Sciences) at 25℃, 80% relative humidity, and a 12-h light/dark cycle. The experiment was repeated three times. After 5 days of inoculation, leaf spots typical of those observed in the orchards were observed on the left sides of all inoculated leaves and the right sides did not have any leaf spot symptoms (Figure S1F-G). The same fungus was isolated from the diseased spots of the inoculated leaves to complete Koch,s postulates (Figure S1H). N. ellipsospora is known to cause leaf spots on Camellia sinensis and sweet potato, infects fruits of Ardisia crenata in China (Maharachchikumbura et al. 2014; Maharachchikumbura et al. 2016; Wang et al. 2019), and causes stem spots on Acanthopanax divaricatus in Korea (Yun et al. 2015). This is the first report of N. ellipsospora causing leaf spot on D. crenata in the world. The occurrence of this disease needs to be monitored, because it can reduce the ornamental value of D. crenata. This finding provides the foundation to further investigate the biology and epidemiology of this disease so that effective strategies can be developed to manage this disease.

First report of leaf spot on Magnolia grandiflora caused by Lasiodiplodia theobromae in Jiangsu.

Magnolia grandiflora linn, with large and fragrant flowers, is widely planted in the south of Yangtze River valley in China. It is an excellent street tree and a beautiful ornamental tree for landscaping. In October 2021, a new leaf spot disease was observed on M. grandiflora seedlings and mature trees growing in Nanjing Botanical Garden, Jiangsu Province, China. According to statistics, about 300 M. grandiflora trees were planted here, and approximately 60% of M. grandiflora trees suffered from the disease. In the beginning, small black spots appeared on the leaf of M. grandiflora, and then the disease spots were connected into coalesced, and eventually lead to a large area of leaf dead (Figure S1A). To isolate the pathogen, ten diseased leaves were collected from ten plants distributed in different five areas of the botanical garden. The leaf sections (3 to 4 mm) were excised from the margins between healthy and diseased tissues, surface sterilized in 75% alcohol for 30 s and then in 1.5% NaClO for 90 s, rinsed three times in sterilized distilled water, plated on potato dextrose agar (PDA) and incubated at 25℃in the darkness. Pure cultures were obtained by monosporic isolation. Twenty-three isolates were obtained (the isolate rate of 72%), and identified as Lasiodiplodia sp.. A representative isolate, G-H-1 was used for the further study. The colony of G-H-1, growing on PDA was cotton-like. The primary mycelia was gray and white in the early stage of culture. It gradually turned black gray in the later stage, and the reverse was similar in color (Figure S1B). The pycnidia (fruiting body) was black and appeared over PDA plates after 15 days (Figure S1C). The hyphae of G-H-1 were dark brown, and the conidia were monospora, oval or elliptic, with a size of (9.6 ~ 13.3) µm× (5.7 ~ 8.0) µm (mean 11.7×6.6 µm, n=35) (Figure S1D). In the pycnidia, the conidiophores were inside and produced conidia (Figure S1E). In the early stage, the conidia of G-H-1 were colorless transparent, then gradually turned dark brown with a septum in the center (Figure S1F). These characteristics were consistent with the description of Lasiodiplodia sp. (Alves et al. 2008). The regions of ITS, translation elongation factor 1-alpha (TEF1α) and ß-tubulin (TUB) genes (GenBank Accession No.OM698339, No.OM942757, and No.OM942756, respectively) were amplified and sequenced with the primer pairs ITS1/ITS4 (White et al. 1990), EF1-728F/EF1-986R (Alves et al. 2008) and Bt2a/Bt2b (Glass and Donaldson 1995). The obtained sequences showed 99.05-99.81% similarity with those from L. theobromae accessions in GenBank. A neighbor-joining phylogenetic tree was generated by combining all sequenced loci in MEGA7. The isolate G-H-1 clustered in the L. theobromae clade with 96% bootstrap support (Figure S2). To test pathogenicity, three one-year-old M. grandiflora seedlings that previously had been wounded with a sterile needle were inoculated with 20 µL conidia suspension (1×106 spores/mL) on the left sides of leaves. Inoculation with 20 µL sterile water was treated as the control, which were inoculated on the right sides of leaves. All plants were covered with clear polyethylene bags to keep moisture. And inoculated detached leaves were incubated in a greenhouse (Institute of Botany, Jiangsu Province and Chinese Academy of Sciences) at 25℃, 80% relative humidity, and a 12-h light/dark cycle. The experiment was repeated three times. After 5 days of inoculation, typical black spots were found on the left sides of all inoculated leaves and the right sides did not have any leaf spot symptoms (Figure S1G-H). After 25 days of inoculation, perforation occurred at the black spots on the leaves of the inoculated plants, resulting in incomplete leaf (Figure S1I), which is identical disease symptoms to those observed in garden. The same fungus, identified by morphological characteristics and sequencing using ITS, TEF1α and TUB genes, was isolated from the diseased spots of the inoculated leaves to complete Koch,s postulates. The pathogen has a very wide host range. For example, it has been reported to cause dieback and sooty canker on Ficus trees (Abo Rehab et al. 2014), infected trunk of sultana seedless (Tang et al. 2021) and castor bean (Akgul et al. 2015), root of Citrus (Al-Sadi et al. 2014), date palm, and Mango (Al-Sadi et al. 2013) and Cassia fistula (Deng et al. 2015). But, according to nt.ars-grin.gov, there are no other reports of L. theobromae on M. grandiflora in the world. So, this would be the first one. This study provides an important reference for the biology, epidemiology.

Complete chloroplast genome of Ilex dabieshanensis: Genome structure, comparative analyses with three traditional Ilex tea species, and its phylogenetic relationships within the family Aquifoliaceae.

Ilex dabieshanensis K. Yao & M. B. Deng is not only a highly valued tree species for landscaping, it is also a good material for making kuding tea due to its anti-inflammatory and lipid-lowering medicinal properties. Utilizing next-generation and long-read sequencing technologies, we assembled the whole chloroplast genome of I. dabieshanensis. The genome was 157,218 bp in length, exhibiting a typical quadripartite structure with a large single copy (LSC: 86,607 bp), a small single copy (SSC: 18,427 bp) and a pair of inverted repeat regions (IRA and IRB: each of 26,092 bp). A total of 121 predicted genes were encoded, including 113 distinctive (79 protein-coding genes, 30 tRNAs, and 4 rRNAs) and 8 duplicated (8 protein-coding genes) located in the IR regions. Overall, 132 SSRs and 43 long repeats were detected and could be used as potential molecular markers. Comparative analyses of four traditional Ilex tea species (I. dabieshanensis, I. paraguariensis, I. latifolia and I. cornuta) revealed seven divergent regions: matK-rps16, trnS-psbZ, trnT-trnL, atpB-rbcL, petB-petD, rpl14-rpl16, and rpl32-trnL. These variations might be applicable for distinguishing different species within the genus Ilex. Phylogenetic reconstruction strongly suggested that I. dabieshanensis formed a sister clade to I. cornuta and also showed a close relationship to I. latifolia. The generated chloroplast genome information in our study is significant for Ilex tea germplasm identification, phylogeny and genetic improvement.

Insight into the CBL and CIPK gene families in pecan (Carya illinoinensis): identification, evolution and expression patterns in drought response.

BACKGROUND: Calcium (Ca2+) serves as a ubiquitous second messenger and plays a pivotal role in signal transduction. Calcineurin B-like proteins (CBLs) are plant-specific Ca2+ sensors that interact with CBL-interacting protein kinases (CIPKs) to transmit Ca2+ signals. CBL-CIPK complexes have been reported to play pivotal roles in plant development and response to drought stress; however, limited information is available about the CBL and CIPK genes in pecan, an important nut crop. RESULTS: In the present study, a total of 9 CBL and 30 CIPK genes were identified from the pecan genome and divided into four and five clades based on phylogeny, respectively. Gene structure and distribution of conserved sequence motif analysis suggested that family members in the same clade commonly exhibited similar exon-intron structures and motif compositions. The segmental duplication events contributed largely to the expansion of pecan CBL and CIPK gene families, and Ka/Ks values revealed that all of them experienced strong negative selection. Phylogenetic analysis of CIPK proteins from 14 plant species revealed that CIPKs in the intron-poor clade originated in seed plants. Tissue-specific expression profiles of CiCBLs and CiCIPKs were analysed, presenting functional diversity. Expression profiles derived from RNA-Seq revealed distinct expression patterns of CiCBLs and CiCIPKs under drought treatment in pecan. Moreover, coexpression network analysis helped to elucidate the relationships between these genes and identify potential candidates for the regulation of drought response, which were verified by qRT-PCR analysis. CONCLUSIONS: The characterization and analysis of CBL and CIPK genes in pecan genome could provide a basis for further functional analysis of CiCBLs and CiCIPKs in the drought stress response of pecan.

Characterization and expression analysis of the SPL gene family during floral development and abiotic stress in pecan (Carya illinoinensis).

SQUAMOSA promoter binding protein-like (SPL) genes are a type of plant-specific transcription factors that play crucial roles in the regulation of phase transition, floral transformation, fruit development, and various stresses. Although SPLs have been characterized in several model species, no systematic analysis has been studied in pecans, an important woody oil tree species. In this study, a total of 32 SPL genes (CiSPLs) were identified in the pecan genome. After conducting phylogenetic analysis of the conserved SBP proteins from Arabidopsis, rice, and poplar, the CiSPLs were separated into eight subgroups. The CiSPL genes within the same subgroup contained very similar exon-intron structures and conserved motifs. Nine segmentally duplicated gene pairs in the pecan genome and 16 collinear gene pairs between the CiSPL and AtSPL genes were identified. Cis-element analysis showed that CiSPL genes may regulate plant meristem differentiation and seed development, participate in various biological processes, and respond to plant hormones and environmental stresses. Therefore, we focused our study on the expression profiles of CiSPL genes during flower and fruit development. Most of the CiSPL genes were predominantly expressed in buds and/or female flowers. Additionally, quantitative real time PCR (qRT-PCR) analyses confirmed that CiSPL genes showed distinct spatiotemporal expression patterns in response to drought and salt treatments. The study provides foundation for the further exploration of the function and evolution of SPL genes in pecan.

The complete chloroplast genome sequence of Carya illinoinensis cv. wichita and its phylogenetic analysis.

Carya illinoinensis is an important nut tree with high economic and ecological values. Here, we presented the complete chloroplast (cp) genome sequence of C. illinoinensis cv. wichita. The whole cp genome is 160,532 bp in length, displaying a typical quadripartite structure with a large single-copy (LSC) of 897,99 bp, a small single-copy (SSC) region of 18,751 bp, and a pair of inverted repeats (IRs) of 25,991 bp. A total of 128 genes were predicted to contain in the whole cp genome, including 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The GC contents of the cp genome is 36.19%. Phylogenomic analysis suggested Carya illinoinensis as a sister species of C. cathayensis, C. kweichowensis, and Annamocarya sinensis.

Characterization and phylogenetic relationships analysis of the complete chloroplast genome of Carya ovata.

Carya ovata is a slow-growing, long-lived deciduous species that belongs to section Carya of genus Carya. In this study, we de novo assembled the complete chloroplast genome of C. ovata, and analyzed its phylogenetic relationship. The circular genome was 160,765 bp in length, comprising a large single-copy region (89,975 bp), a small single-copy region (18,788 bp), and a pair of inverted repeat regions (26,001 bp each). The chloroplast genome was predicted to contain 131 genes, including 83 protein-coding genes, 40 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Overall, the GC content of the chloroplast genome was 36.16%. Phylogenetic analysis suggested that C. ovata was closely related to C. illinoinensis, a representative of section Apocarya within the genus Carya.

Transcriptomic Analysis Provides Insights into Grafting Union Development in Pecan (Carya illinoinensis).

Pecan (Carya illinoinensis), as a popular nut tree, has been widely planted in China in recent years. Grafting is an important technique for its cultivation. For a successful grafting, graft union development generally involves the formation of callus and vascular bundles at the graft union. To explore the molecular mechanism of graft union development, we applied high throughput RNA sequencing to investigate the transcriptomic profiles of graft union at four timepoints (0 days, 8 days, 15 days, and 30 days) during the pecan grafting process. After de novo assembly, 83,693 unigenes were obtained, and 40,069 of them were annotated. A total of 12,180 differentially expressed genes were identified between by grafting. Genes involved in hormone signaling, cell proliferation, xylem differentiation, cell elongation, secondary cell wall deposition, programmed cell death, and reactive oxygen species (ROS) scavenging showed significant differential expression during the graft union developmental process. In addition, we found that the content of auxin, cytokinin, and gibberellin were accumulated at the graft unions during the grafting process. These results will aid in our understanding of successful grafting in the future.