Comparative study of the leaf transcriptomes and ionoms of Juglans regia and its wild relative species Juglans cathayensis

Zhou, Zhongli; Han, Muxian; Hou, Meifang; Deng, Xiaojing; Tian, Rui; Min, Shui-Fa; Zhang, Jinbo

doi:10.1007/s11738-017-2504-8

Cited by 9 publications

(10 citation statements)

References 41 publications

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“…Those studies are publicly available and can be compared with our study. The past seven studies had used Trinity alone and by default parameters so as to construct de novo assemblies [10,11,12,13,30,43,44]. In addition, none of the studies made use of BUSCOs to evaluate the quality of assemblies.…”

Section: Plos Onementioning

confidence: 99%

Combining independent de novo assemblies to optimize leaf transcriptome of Persian walnut

et al. 2020

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Transcriptome resources can facilitate to increase yield and quality of walnuts. Finding the best transcriptome assembly has not been the subject of walnuts research as yet. This research generated 240,179,782 reads from 11 walnut leaves according to cDNA libraries. The reads provided a complete de novo transcriptome assembly. Fifteen different transcriptome assemblies were constructed from five different well-known assemblers used in scientific literature with different k-mer lengths (Bridger, BinPacker, SOAPdenovo-Trans, Trinity and SPAdes) as well as two merging approaches (EvidentialGene and Transfuse). Based on the four quality metrics of assembly, the results indicated an efficiency in the process of merging the assemblies after being generated by de novo assemblers. Finally, Evidential-Gene was recognized as the best assembler for the de novo assembly of the leaf transcriptome in walnut. Among a total number of 183,191 transcripts which were generated by EvidentialGene, there were 109,413 transcripts capable of protein potential (59.72%) and 104,926 were recognized as ORFs (57.27%). In addition, 79,185 transcripts were predicted to exist with at least one hit to the Pfam database. A number of 3,931 transcription factors were identified by BLAST searching against PlnTFDB. Furthermore, 6,591 of the predicted peptide sequences contained signaling peptides, while 92,704 contained transmembrane domains. Comparison of the assembled transcripts with transcripts of the walnut and published genome assembly for the 'Chandler' cultivar using the BLAST algorithm led to identify a total number of 27,304 and 19,178 homologue transcripts, respectively. De novo transcriptomes in walnut leaves can be developed for the future studies in functional genomics and genetic studies of walnuts.

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Section: Plos Onementioning

confidence: 99%

Combining independent de novo assemblies to optimize leaf transcriptome of Persian walnut

et al. 2020

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“…The population genetics, morphology, and diversity of J. mandshurica have been described (Aradhya et al, 2007;Dang et al, 2015;Hu et al, 2017;Liu et al, 2020;Manning, 1978;Zhang et al, 2019), but in general, interest in J. mandshurica based on its potential as a tertiary germplasm pool for improvement of J. regia (Chen et al, 2015;Hu et al, 2016;Ji et al, 2020;Trouern-Trend et al, 2020;Zhou et al, 2017). Wild populations of J. mandshurica and cultivated orchards of Persian walnut (J. regia) grow sympatrically (Dang et al, 2019) but hybridization between these two walnut species is reportedly rare (Shu et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

“…J. mandshurica is less valuable as a commodity than its close relative J. regia (Dang et al, 2016;Feng et al, 2018;Han et al, 2016). However, J. mandshurica expresses horticultural traits such as cluster bearing habit (6-13 fruits per terminal) that make it attractive to J. regia breeders, and disease tolerance/resistance to lesion nematodes (Pratylenchus vulnus) that recommend it as a rootstock for J. regia (Chen et al, 2015;Hu et al, 2016;Ji et al, 2020;Trouern-Trend et al, 2020;Zhou et al, 2017). J. mandshurica is also a potential medicinal crop because of its flavonoids (Bi et al, 2016;Sun et al, 2012;Yu et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Improved de novo chromosome‐level genome assembly of the vulnerable walnut tree Juglans mandshurica reveals gene family evolution and possible genome basis of resistance to lesion nematode

Yan

She

et al. 2021

Molecular Ecology Resources

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Manchurian walnut (Juglans mandshurica Maxim.) is a synonym of J. cathayensis, a diploid, vulnerable, temperate deciduous tree valued for its wood and nut. It is also valued as a rootstock for Juglans regia because of its reported tolerance of lesion nematode.Reference genomes are available for several Juglans species, our goal was to produce a de novo, chromosome-level assembly of the J. mandshurica genome. Here, we reported an improved assembly of J. mandshurica with a contig N50 size of 6.49 Mb and a scaffold N50 size of 36.1 Mb. The total genome size was 548 Mb encoding 29,032 protein coding genes which were annotated. The collinearity analysis showed that J. mandshurica and J. regia originated from a common ancestor, with both species undergoing two WGD events. A genomic comparison showed that J. mandshurica was missing 1657 genes found in J. regia, and J. mandshurica includes 2827 genes not found in of the J. regia genome. The J. mandshurica contained 1440 unique paralogues that were highly enriched for flavonoid biosynthesis, phenylpropanoid biosynthesis, and plant-pathogen interaction. Four gene families related to disease resistance notable contraction (rapidly evolving; LEA, WAK, PPR, and PR) in J. mandshurica compared to eight species. JmaPR10 and JmaPR8 contained three orthologous gene pairs with J. regia that were highly expressed in root bark. JmaPR10 is a strong candidate gene for lesion nematodes resistance in J. mandshurica. The J. mandshurica genome should be a useful resource for study of the evolution, breeding, and genetic variation in walnuts (Juglans).

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“…Lupeol wound healing pharmacological effects, which shows anti-cancer activity in pancreatic cancer, breast cancer, prostate cancer, melanoma and other tumors [21]. Phytol is the basic raw material for the production of vitamin K1 and vitamin E [22]. The phenols compounds mainly include dl-.alpha.-tocopherol (10.94%) and eugenol (0.80%).…”

Section: The Gc-ms Analysis Of the Fresh Walnut Leaf Extractmentioning

confidence: 99%

Characterization of bioactive and bioenergy components from fresh walnut (Juglans regia) leaf

et al. 2020

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Walnut (Juglans regia) is an important economic tree specie, and has unique aroma in its leaf. In order to investigate the bioactive and bioenergy characteristic of compounds in ethanol and benzene extracts from fresh walnut leaf by gas chromatography/mass spectrometry (GC-MS). The results indicated that ethanol and benzene extracst fresh walnut leaf contain abundant alcohols, aromatic hydrocarbons, quinones, phenols, aldehydes, acids, ketones, alkanes, esterscompounds, especially including dl-.alpha.-Tocopherol, juglone, squalene andlupeol, which are important bioactive components. The functional analytic result suggested that compounds from fresh walnut leaf extracts can be developed into raw materials for industries of biofuel, biomedicine, cosmetic, spices and food additive. The ethanol extract of fresh walnut leaf is more rich in biomedicine and food additives components, such as ketones, alkanes, aldehydes, amines, and acides compounds. The benzene extract of fresh walnut leaf is more rich in biofuels, spices, and cosmetic components, such as phenols, aromatic hydrocarbons, olefines and quinones compounds.

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Comparative study of the leaf transcriptomes and ionoms of Juglans regia and its wild relative species Juglans cathayensis

Cited by 9 publications

References 41 publications

Combining independent de novo assemblies to optimize leaf transcriptome of Persian walnut

Combining independent de novo assemblies to optimize leaf transcriptome of Persian walnut

Improved de novo chromosome‐level genome assembly of the vulnerable walnut tree Juglans mandshurica reveals gene family evolution and possible genome basis of resistance to lesion nematode

Characterization of bioactive and bioenergy components from fresh walnut (Juglans regia) leaf

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