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Diversity
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Genetic Diversity and Conservation of Economic Plants
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Genetic Diversity and Conservation of Economic Plants

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Plant Diversity".

Deadline for manuscript submissions: closed (30 June 2022) | Viewed by 12146

Special Issue Editors

Dr. Hong-Xiang Zhang

E-Mail Website
Guest Editor
State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
Interests: phylogeography; conservation genetics; genetic diversity; Central Asian plants
Dr. Xiao-Long Jiang

E-Mail Website
Guest Editor
The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha 410004, China
Interests: population genetics; landscape genetics; genomics; oaks
Dr. Bei Gao

E-Mail Website1 Website2
Guest Editor
State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
Interests: evolutionary genomics; bioinformatics; early land plants; desiccation tolerance
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Economic plants are beneficial to our life from foods to housing. They include fruit trees, medicinal plants, flower plants, woods and so on. Rich genetic resources of economic plants are the basic for varieties breeding and improvements. However, due to climatic changes and human activities, they meet the challenge of genetic diversity losses during the recent years. Economic plants and their wild relatives have undergone genetic erosions, distribution fragmentations, population declines and even extinct. Therefore, understanding the phylogenetic relationships, genetic diversity and genetic structure of these plants and their wild relatives is not only useful for cultivate new varieties, but also important for developing species conservation strategies. With the development of DNA sequencing technology, details species phylogenetic relationships and species spatial genetic patterns can detected even species have complex evolutionary history.

This special issue welcomes papers to improve the knowledge on phylogeography, landscape genetics, conservation genetics and barcoding of economic plants and their wild relatives. We look forward to receive your manuscript (both review and research articles) regarding to the above topics. When you want to know more information or have any questions, please do not hesitate to contact us.

Dr. Hong-Xiang Zhang
Dr. Xiao-Long Jiang
Dr. Bei Gao 
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diversity is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2100 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • genetic diversity
  • phylogeography
  • phylogenetics
  • landscape genetics
  • conservation genetics
  • barcoding
  • evolutionary genomics

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Published Papers (4 papers)

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Research

12 pages, 1853 KiB  
Article
A High-Quality Genome Assembly of the Mitochondrial Genome of the Oil-Tea Tree Camellia gigantocarpa (Theaceae)
by Cui Lu, Li-Zhi Gao and Qun-Jie Zhang
Diversity 2022, 14(10), 850; https://doi.org/10.3390/d14100850 - 8 Oct 2022
Cited by 8 | Viewed by 2166
Abstract
Camellia gigantocarpa is one of the oil-tea trees whose seeds can be used to extract high-quality vegetable oil. To date, there are no data on the mitochondrial genome of the oil-tea tree, in contrast to the tea-tree C. sinensis, which belongs to [...] Read more.
Camellia gigantocarpa is one of the oil-tea trees whose seeds can be used to extract high-quality vegetable oil. To date, there are no data on the mitochondrial genome of the oil-tea tree, in contrast to the tea-tree C. sinensis, which belongs to the same genus. In this paper, we present the first complete mitochondrial genomes of C. gigantocarpa obtained using PacBio Hi-Fi (high-fidelity) and Hi-C sequencing technologies to anchor the 970,410 bp genome assembly into a single sequence. A set of 44 protein-coding genes, 22 non-coding genes, 746 simple sequence repeats (SSRs), and more than 201 kb of repetitive sequences were annotated in the genome assembly. The high percentage of repetitive sequences in the mitochondrial genome of C. gigantocarpa (20.81%) and C.sinensis (22.15%, tea tree) compared to Arabidopsis thaliana (4.96%) significantly increased the mitogenome size in the genus Camellia. The comparison of the mitochondrial genomes between C. gigantocarpa and C. sinensis revealed genes exhibit high variance in gene order and low substitution rate within the genus Camellia. Information on the mitochondrial genome provides a better understanding of the structure and evolution of the genome in Camellia and may contribute to further study of the after-ripening process of oil-tea trees. Full article
(This article belongs to the Special Issue Genetic Diversity and Conservation of Economic Plants)
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15 pages, 3257 KiB  
Article
Wild Apples Are Not That Wild: Conservation Status and Potential Threats of Malus sieversii in the Mountains of Central Asia Biodiversity Hotspot
by Zhongping Tian, Houjuan Song, Yuzhuo Wang, Jin Li, Mierkamili Maimaiti, Zhongquan Liu, Hongxiang Zhang and Jian Zhang
Diversity 2022, 14(6), 489; https://doi.org/10.3390/d14060489 - 15 Jun 2022
Cited by 12 | Viewed by 3783
Abstract
As one of the global biodiversity hotspots, the mountains of Central Asia are home to a large number of wild fruit species. Although the hotspots are constantly being seriously affected by climate and land-use changes, effective assessments of the impacts of these changes [...] Read more.
As one of the global biodiversity hotspots, the mountains of Central Asia are home to a large number of wild fruit species. Although the hotspots are constantly being seriously affected by climate and land-use changes, effective assessments of the impacts of these changes for the dominant species of wild fruit forests, wild apple (Malus sieversii), have been limited. We compiled 8344 occurrence records for wild apple across its whole distribution ranges from field surveys and herbarium and literature records. After data thinning to reduce sampling bias, we used ensemble niche models to project current and future suitable habitats, examined the importance of environmental factors, and assessed whether current national protected areas (PAs) are effective in protecting the suitable habitats. We found that the distribution of wild apple is currently fragmented. Under future scenarios, it would shift 118–227 km towards high latitudes and ~200 m towards high elevations, losing nearly 27–56% of suitable habitats in the south, and gaining some habitats in the north. The increased temperature and expansion of cropland contributed to these shifts. Nevertheless, about 13% of the suitable habitats are covered by existing PAs and less than 25% of suitable habitats will be protected in the future. The cold spots for protecting intact wild fruit forests are located in Xinjiang, China and Kyrgyzstan. Overall, we provide a detailed evaluation of the impacts of climate and land-use changes on current and future distributions of wild apple in Central Asia. Considering that this species faces a greater risk of habitat loss in the south of Central Asia, we advocate developing effective in situ conservation strategies with long-term monitoring that will provide deep insights into the fate of wild fruit forests. Full article
(This article belongs to the Special Issue Genetic Diversity and Conservation of Economic Plants)
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12 pages, 1623 KiB  
Article
Characterization and Phylogenetic Analyses of the Complete Mitochondrial Genome of Sugarcane (Saccharum spp. Hybrids) Line A1
by Dinggang Zhou, Ying Liu, Jingzuo Yao, Ze Yin, Xinwen Wang, Liping Xu, Youxiong Que, Ping Mo and Xiaolan Liu
Diversity 2022, 14(5), 333; https://doi.org/10.3390/d14050333 - 25 Apr 2022
Cited by 8 | Viewed by 2629
Abstract
Modern sugarcane cultivars are highly polyploid with complex nuclear genomic genetic background, while their mitochondrion (mt) genomes are much simpler, smaller and more manageable and could provide useful phylogenetic information. In this study, the mt genome of a modern commercial cultivar A1 was [...] Read more.
Modern sugarcane cultivars are highly polyploid with complex nuclear genomic genetic background, while their mitochondrion (mt) genomes are much simpler, smaller and more manageable and could provide useful phylogenetic information. In this study, the mt genome of a modern commercial cultivar A1 was sequenced via Illumina Hiseq XTen and PacBio Sequel platform. The assembled and annotated mitochondrial genomes of A1 were composed of two circular DNA molecules, one large and one small, which were named Chromosome 1 and Chromosome 2. The two distinct circular chromosomes of mitogenome construct is consisted with other sugarcane cultivars i.e., Saccharum officinarum Khon Kaen 3 and Saccharum spp. hybrids ROC22 and FN15. The Chromosome 1 of A1 mitogenome is 300,822 bp in length with the GC content of 43.94%, and 7.14% of Chromosome 1 sequences (21,468 nucleotides) are protein coding genes (PCGs) while 92.86% (279,354 nucleotides) are intergenic region. The length of Chromosome 2 is 144,744 bp with the GC content of 43.57%, and 8.20% of Chromosome 2 sequences (11,865 nucleotides) are PCGs while 91.80% (132,879 nucleotides) are intergenic region. A total of 43 genes are located on Chromosome 1, which contains 22 PCGs (six nad genes, four rps genes, four atp genes, three ccm genes, three cox genes, one mat gene and one mtt gene) and 21 non-coding genes including 15 tRNAs and 6 rRNAs. Chromosome 2 includes 18 genes in total, which contains 13 PCGs (four nad genes, three rps genes, two atp genes, one ccm gene, one cob gene, one cox gene and one rpl gene) and five non-coding genes (tRNA genes). Analysis of codon usage of 35 PCGs showed that codon ending in A/U was preferred. Investigation of gene composition indicated that the types and copy numbers of CDS genes, tRNAs and rRNAs of A1 and FN15 were identical. The cox1 gene has two copies and the trnP gene has one copy in A1, FN15 and ROC22 three lines, while there is only one copy of cox1 and two copies of trnP in S. officinarum Khon Kaen 3. In addition, S. officinarum Khon Kaen 3 have no nad1 gene and rps7 gene. 100 sequence repeats, 38 SSRs and 444 RNA editing sites in A1 mt genome were detected. Moreover, the maximum likelihood phylogenetic analysis found that A1 were more closely related to S. spp. hybrid (ROC22 and FN15) and S. officinarum (Khon Kaen 3). Herein, the complete mt genome of A1 will provide essential DNA molecular information for further phylogenetic and evolutionary analysis for Saccharum and Poaceae. Full article
(This article belongs to the Special Issue Genetic Diversity and Conservation of Economic Plants)
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18 pages, 6660 KiB  
Article
Characterization of the Complete Chloroplast Genome of the Dragonhead Herb, Dracocephalumheterophyllum (Lamiaceae), and Comparative Analyses with Related Species
by Gui Fu, Yuping Liu, Marcos A. Caraballo-Ortiz, Changyuan Zheng, Tao Liu, Yujie Xu and Xu Su
Diversity 2022, 14(2), 110; https://doi.org/10.3390/d14020110 - 3 Feb 2022
Cited by 7 | Viewed by 2490
Abstract
Dracocephalum heterophyllum (Lamiaceae: tribe Mentheae) is an annual aromatic herb native to East Asia with a long record of human uses, including medicinal, alimentary, and ornamental values. However, no information is available about its molecular biology, and no genomic study has been performed [...] Read more.
Dracocephalum heterophyllum (Lamiaceae: tribe Mentheae) is an annual aromatic herb native to East Asia with a long record of human uses, including medicinal, alimentary, and ornamental values. However, no information is available about its molecular biology, and no genomic study has been performed on D. heterophyllum. Here, we report the complete chloroplast (cp) genome of D. heterophyllum and a series of comparative genomic analyses between this and closely related species of Lamiaceae. Results indicated that the cp genome has a typical circular structure of 150,869 bp in length, consisting of a long single-copy (LSC) region with 82,410 bp, a short single-copy (SSC) region with 17,098 bp, and two inverted repeat (IR) regions of 51,350 bp. A total of 133 genes were identified, including 37 tRNA genes, 8 rRNA genes and 88 protein-coding genes, with a GC content of 37.8%. The gene content, organization, and GC values observed here were similar to those of other Dracocephalum species. We detected 99 different simple sequence repeat loci, and the codon usage analysis revealed a preferential use of the Leu codon with an A/U ending. Comparative analysis of cp genome sequences revealed five highly variable regions with remarkably higher Pi values (>0.03). The mean Ka/Ks between D. heterophyllum and three other Dracocephalum species ranged from 0.01079 (psbB) to 1.0497 (ycf2). Two cp genes, ycf2 and rps11, were proven to have high ratios of Ka/Ks, implying that cp genes may had undergone positive selection in the evolutionary history. We performed multiple sequence alignments using the cp genome of 22 species and constructed maximum likelihood (ML) and Bayesian trees, and found that D. heterophyllum were more closely related to D. moldavica and D. palmatum. In addition, the phylogenetic relationships between Dracocephalum and other members of Lamiaceae were consistent with previous results. These results are valuable for further formulating effective strategies of conservation and management for species in Dracocephalum, as well as providing a foundation for future research on the genetic resources of Dracocephalum. Full article
(This article belongs to the Special Issue Genetic Diversity and Conservation of Economic Plants)
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