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Applications of High Throughput Sequencing Technologies in Forest and Other Species

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (25 November 2022) | Viewed by 10914

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Special Issue Editor

Prof. Dr. Lianfeng Gu

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Guest Editor

Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Interests: forest; long-read sequencing; genome; epitranscriptome; bioinformatics; Populus trichocarpa; Phyllostachys edulis; Dendrocalamus latiflorus Munro; post-transcriptional regulation
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Special Issue Information

Dear Colleagues,

Long-read sequencing technologies including PacBio and Oxford Nanopore sequencing provide unprecedented opportunities for forestry to overcome the disadvantage of short reads, especially for gymnosperm genome. At genome-wide level, PacBio or Nanopore has far superior contiguity for forestry genome assembly due to the long reads. At transcriptome level, both PacBio and Oxford Nanopore Technologies sequence single molecules can detect post-transcriptional regulation, including complex alternative splicing (AS), full-length splice variants, fusion transcripts, and alternative polyadenylation (APA) events, which contribute to transcriptome diversity. In addition, direct RNA-Seq based on an Oxford Nanopore Technologies sequence provides valuable information about RNA modifications, which are lost during PCR amplification in other methods.

However, the analysis of PacBio and Oxford Nanopore long-read data comes with new technical challenges, such as lack of genomic reference and high-quality gene annotations for non-model forestry species, such as gymnosperm. Both new experimental and bioinformatics method are needed to fully utilize the advantage of long-read sequencing for forestry genomics and transcriptomics research. In this SI, we welcome submission on reviews or original research that uses high throughput sequencing technology to address biological question in forestry and other species, or bioinformatics methods/computational tools or database for sequence data analysis in plant genomics and transcriptomics areas.

Prof. Dr. Lianfeng Gu
Guest Editor

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Keywords

forest
high-throughput sequencing
genome
epitranscriptome
bioinformatics
database
post-transcriptional regulation

Published Papers (6 papers)

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Research

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21 pages, 3185 KiB

Open AccessArticle

Characterization of the Genetic Variability within Ziziphus nummularia Genotypes by Phenotypic Traits and SSR Markers with Special Reference to Geographic Distribution

by Nisar Uddin, Noor Muhammad, Sameh Samir Ali, Riaz Ullah, Ahmed Bari, Hidayat Hussain and Daochen Zhu

Genes 2023, 14(1), 155; https://doi.org/10.3390/genes14010155 - 6 Jan 2023

Cited by 4 | Viewed by 1499

Abstract

Understanding the impacts and constraints of climate change on Ziziphus nummularia′s geographical distribution is crucial for its future sustainability. In this study, we analyze information obtained from the field investigation, the distribution and response of climatic changes of Ziziphus nummularia by the use of ArcGIS analysis. The genetic diversity of 180 genotypes from three populations was studied by morphological attributes and simple sequence repeat (SSR). The results showed that the significant bioclimatic variable limiting the distribution of Z. nummularia was the mean temperature (bio 10_18.tif and bio19). Under the current climatic change, the suitable growth region of Z. nummularia is Swat (35.22° N, 72.42° E), while the future distribution would be Buner (34.39° N, 72.61° E), respectively. A total of 11 phenotypic traits were noted and had significant phenotypic variation among the traits. A total of 120 alleles were amplified. The alleles per locus ranged from 2 to 6, averaging 4.42, whereas PIC ranged from 0.33 to 0.79. Within a mean value of 0.67 per locus, expected heterozygosity was 0.57, observed heterozygosity was 0.661, and average gene diversity was 0.49. Flow estimates (6.41) indicated frequent gene flow within genotypes. The clustering, STRUCTURE, and PCoA analysis indicated Swat and Buner migration routes and evolution as well. The results indicated the prevalence of genetic variability and relationships among Z. nummularia across geographical boundaries had retained unique alleles. This may facilitate the development of agronomically desirable cultivars. However, climate change has impacted species distributions, requiring strategies to conserve genetic resources in different areas. Full article

(This article belongs to the Special Issue Applications of High Throughput Sequencing Technologies in Forest and Other Species)

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11 pages, 2706 KiB

Open AccessArticle

Genome-Wide Identification of MIKCc-Type MADS-Box Family Gene and Floral Organ Transcriptome Characterization in Ma Bamboo (Dendrocalamus latiflorus Munro)

by Deming Yang, Jing Yang, Jiayi Wan, Yanping Xu, Lei Li, Jundong Rong, Lingyan Chen, Tianyou He and Yushan Zheng

Genes 2023, 14(1), 78; https://doi.org/10.3390/genes14010078 - 27 Dec 2022

Cited by 1 | Viewed by 1461

Abstract

Most bamboos die after flowering, and the molecular mechanisms responsible for flowering is poorly understood. The MIKCc-type MADS-box family gene is involved in the flowering process. To explore the mechanism of the MIKCc-type MADS-box gene and phytohormone regulation in the flowering of Dendrocalamus latiflorus Munro (D. latiflorus), characterized by extremely rapid growth and widely cultivated woody bamboo, we initially did a genome-wide analysis of the MIKCc-type MADS-box gene in D. latiflorus. In the meantime, transcriptome analysis was performed using the floral organs. A total of 170 MIKCc-Type MADS-Box genes were identified and divided into 15 categories. The cis-acting element analysis in promoters regions revealed that MIKC-type MADS-box family genes were associated with hormones, including auxin, abscisic acid (ABA), gibberellin (GA) and jasmonic acid (JA), which was found at 79, 476, 96, 486 sites and cover 61, 103, 73, 128 genes. Genome synteny analysis showed subgenome AA and BB were better than CC and obtained 49, 40, 39 synteny genes compared with Oryza sativa (O. sativa). In transcriptome analysis of floral organs, the enriched pathway from DEGs included circadian, vernalization and gibberellin pathways associated with the flowering process. We found that the jasmonic acid synthesis gene is highly expressed in the pistil, which may be the cause of Ma bamboo pollen abortion. The expression profile showed that most MIKC-type MADS-box genes exhibited high expression in flower organs. The consequences of this study will provide insight into the irregular flowering and low pollen counts of Ma bamboo. Full article

(This article belongs to the Special Issue Applications of High Throughput Sequencing Technologies in Forest and Other Species)

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11 pages, 2200 KiB

Open AccessArticle

A Novel Strategy for Constructing an Integrated Linkage Map in an F₁ Hybrid Population of Populus deltoides and Populus simonii

by Zhiting Li, Jinpeng Zhang, Zhiliang Pan, Shengjun Bai and Chunfa Tong

Genes 2022, 13(10), 1731; https://doi.org/10.3390/genes13101731 - 26 Sep 2022

Viewed by 1220

Abstract

The genetic linkage maps of the traditional F₂ population in inbred lines were estimated from the frequency of recombination events in both parents, providing full genetic information for genetic and genomic studies. However, in outbred forest trees, it is almost impossible to generate the F₂ population because of their high heterozygosity and long generation times. We proposed a novel strategy to construct an integrated genetic linkage map that contained both parental recombination information, with restriction-site-associated DNA sequencing (RADSeq) data in an F1 hybrid population of Populus deltoides and Populus simonii. We selected a large number of specific RAD tags to construct the linkage map, each of which contained two SNPs, one heterozygous only in the female parent and the other heterozygous only in the male. Consequently, the integrated map contained a total of 1154 RAD tags and 19 linkage groups, with a total length of 5255.49 cM and an average genetic distance of 4.63 cM. Meanwhile, the two parent-specific linkage maps were also constructed with SNPs that were heterozygous in one parent and homozygous in the other. We found that the integrated linkage map was more consensus with the genomic sequences of P. simonii and P. deltoides. Additionally, the likelihood of the marker order in each linkage group of the integrated map was greater than that in both parental maps. The integrated linkage map was more accurate than the parent-specific linkage maps constructed in the same F₁ hybrid population, providing a powerful genetic resource for identifying the quantitative trait loci (QTLs) with dominant effects, assembling genomic sequences, and performing comparative genomics in related Populus species. More importantly, this novel strategy can be used in other outbred species to build an integrated linkage map. Full article

(This article belongs to the Special Issue Applications of High Throughput Sequencing Technologies in Forest and Other Species)

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21 pages, 6754 KiB

Open AccessArticle

Integrative Investigation of Root-Related mRNAs, lncRNAs and circRNAs of “Muscat Hamburg” (Vitis vinifera L.) Grapevine in Response to Root Restriction through Transcriptomic Analyses

by Jingjing Liu, Hui Li, Lipeng Zhang, Yue Song, Juan He, Wenping Xu, Chao Ma, Yi Ren and Huaifeng Liu

Genes 2022, 13(9), 1547; https://doi.org/10.3390/genes13091547 - 27 Aug 2022

Cited by 2 | Viewed by 1239

Abstract

Root restriction is a physical and ecological cultivation mode which restricts plant roots into a limited container to regulate vegetative and reproduction growth by reshaping root architecture. However, little is known about related molecular mechanisms. To uncover the root-related regulatory network of endogenous RNAs under root restriction cultivation (referred to RR), transcriptome-wide analyses of mRNAs, long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) involved in root development were performed. During root development, RR treatment had a positive effect on root weight, typically, young roots were significantly higher than conventional cultivation (referred to NR) treatment, suggesting that root architecture reconstruction under RR was attributed to the vigorous induction into lateral roots. Furthermore, a total of 26,588 mRNAs, 1971 lncRNAs, and 2615 circRNAs were identified in root of annual “Muscat Hamburg” grapevine by the transcriptomic analyses. The expression profile of mRNAs, lncRNAs and circRNA were further confirmed by the quantitative real-time PCR (RT-qPCR). Gene ontology enrichment analysis showed that a majority of the differentially expressed mRNAs, lncRNAs and circRNAs were enriched into the categories of cellular process, metabolic process, cell part, binding, and catalytic activity. In addition, the regulatory network of endogenous RNAs was then constructed by the prediction of lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA network, implying that these RNAs play significant regulatory roles for root architecture shaping in response to root restriction. Our results, for the first time, the regulatory network of competitive endogenous RNAs (ceRNAs) functions of lncRNA and circRNA was integrated, and a basis for studying the potential functions of non-coding RNAs (ncRNAs) during root development of grapevine was provided. Full article

(This article belongs to the Special Issue Applications of High Throughput Sequencing Technologies in Forest and Other Species)

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28 pages, 5146 KiB

Open AccessArticle

Transcriptomic Profile Analysis of Populus talassica × Populus euphratica Response and Tolerance under Salt Stress Conditions

by Ying Liu, Zhan Jiang Han, Meng Xu Su and Min Zhang

Genes 2022, 13(6), 1032; https://doi.org/10.3390/genes13061032 - 8 Jun 2022

Cited by 5 | Viewed by 2135

Abstract

A new Populus variety with a strong salt tolerance was obtained from cross breeding P. talassica as the female parent and P. euphratica as the male parent. In order to elucidate the molecular mechanism and find out the major differentially expressed genes of salt tolerance of P. talassica × P. euphratica, after being subjected to salt stress, at 0, 200, and 400 mmol/L NaCl, the root, stem, and leaf transcriptomes (denoted as R0, S0, and L0; R200, S200, and L200; and R400, S400, and L400, respectively) of P. talassica × P. euphratica were sequenced. In total, 41,617 differentially expressed genes (DEGs) were identified in all the comparison groups with 21,603 differentially upregulated genes and 20,014 differentially downregulated genes. Gene Ontology analysis showed that DEGs were significantly enriched in biological processes that may be involved in salt stress, such as ‘cell communication’, ‘ion transport’, ‘signaling’, and signal ‘transmission’. Kyoto Encyclopedia of Genes and Genomes analysis showed that DEGs were mainly enriched in pathways of ‘plant–pathogen interaction’, ‘carbon metabolism’, and ‘plant hormone signal transmission’. The pathways and related gene information formed a basis for future research on the mechanisms of salt stress, the development of molecular markers, and the cloning of key genes in P. talassica × P. euphratica. Full article

(This article belongs to the Special Issue Applications of High Throughput Sequencing Technologies in Forest and Other Species)

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Review

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11 pages, 1304 KiB

Open AccessReview

Mechanism of Stone (Hardened Endocarp) Formation in Fruits: An Attempt toward Pitless Fruits, and Its Advantages and Disadvantages

by Muhammad Khalil Ullah Khan, Noor Muhammad, Zhuolong Jia, Jianying Peng and Mengjun Liu

Genes 2022, 13(11), 2123; https://doi.org/10.3390/genes13112123 - 15 Nov 2022

Cited by 1 | Viewed by 2520

Abstract

Stone (hardened endocarp) has a very important role in the continuity of plant life. Nature has gifted plants with various seed protection and dispersal strategies. Stone-fruit-bearing species have evolved a unique adaptation in which the seed is encased in an extremely hard wood-like shell called the stone. The lignification of the fruit endocarp layer produces the stone, a feature that separates drupes from other plants. Stone cells emerge from parenchyma cells after programmed cell death and the deposition of cellulose and lignin in the secondary cell wall. Generally, the deposition of lignin in primary cell walls is followed by secondary thickening of cell walls to form stone cells. This review article describes the molecular mechanisms and factors that influence the production of stone in the fruit. This is the first review article that describes the molecular mechanisms regulating stone (harden endocarp) formation in fruits. This article will help breeders understand the molecular and genetic basis for the stone formation in fruit, and this could lead to new and innovative directions to breed stoneless fruit cultivars in the future. Full article

(This article belongs to the Special Issue Applications of High Throughput Sequencing Technologies in Forest and Other Species)

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