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25 February 2021, Volume 43 Issue 01
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  • Articles
    Molecular phylogeny, biogeography and character evolution of the montane genus Incarvillea Juss. (Bignoniaceae)
    Santosh Kumar Rana, Dong Luo, Hum Kala Rana, Shaotian Chen, Hang Sun
    2021, 43(01):  1-14.  doi:10.1016/j.pld.2020.09.002
    Abstract ( 193 )   HTML ( )   PDF (22573KB) ( 53 )   Save
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    The complex orogeny of the Himalaya and the Qinghai-Tibet Plateau (QTP) fosters habitat fragmentation that drives morphological differentiation of mountain plant species. Consequently, determining phylogenetic relationships between plant subgenera using morphological characters is unreliable. Therefore, we used both molecular phylogeny and historical biogeographic analysis to infer the ancestral states of several vegetative and reproductive characters of the montane genus Incarvillea. We determined the taxonomic position of the genus Incarvillea within its family and inferred the biogeographical origin of taxa through Bayesian inference (BI), maximum likelihood (ML) and maximum parsimony (MP) analyses using three molecular data sets (trnL-trnF sequences, nr ITS sequences, and a data set of combined sequences) derived from 81% of the total species of the genus Incarvillea. Within the genus-level phylogenetic framework, we examined the character evolution of 10 key morphological characters, and inferred the ancestral area and biogeographical history of the genus. Our analyses revealed that the genus Incarvillea is monophyletic and originated in Central Asia during mid-Oligocene ca. 29.42 Ma. The earliest diverging lineages were subsequently split into the Western Himalaya and Sino-Himalaya during the early Miocene ca. 21.12 Ma. These lineages resulted in five re-circumscribed subgenera (Amphicome, Olgaea, Niedzwedzkia, Incarvillea, and Pteroscleris). Moreover, character mapping revealed the ancestral character states of the genus Incarvillea (e.g., suffruticose habit, cylindrical capsule shape, subligneous capsule texture, absence of capsule wing, and loculicidal capsule dehiscence) that are retained at the earliest diverging ancestral nodes across the genus. Our phylogenetic tree of the genus Incarvillea differs from previously proposed phylogenies, thereby recommending the placement of the subgenus Niedzwedzkia close to the subgenus Incarvillea and maintaining two main divergent lineages.
    Comparative plastomic analysis and insights into the phylogeny of Salvia (Lamiaceae)
    Hong Wu, Peng-Fei Ma, Hong-Tao Li, Guo-Xiong Hu, De-Zhu Li
    2021, 43(01):  15-26.  doi:10.1016/j.pld.2020.07.004
    Abstract ( 136 )   HTML ( )   PDF (12360KB) ( 44 )   Save
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    Salvia is the largest genus of Lamiaceae, with almost 1000 species, and has been divided into 11 subgenera. Salvia subg. Glutinaria, native to East Asia, is particularly important because of its potential medicinal value. However, the interspecific relationships of this subgenus have not been resolved and the plastomes of Salvia have rarely been studied. In the current study, we compared plastid genome structure and organization of 19 species of Salvia (14 newly sequenced and 5 previously published). Our comparative analysis showed that all Salvia plastomes examined have a quadripartite structure typical of most angiosperms and contain an identical set of 114 unique genes (80 protein-coding genes, 4 rRNA genes, and 30 tRNA genes). The plastome structure of all Salvia species is highly conserved like other Lamiaceae plastomes. Gene content, gene order, and GC content were highly similar in these plastomes. The inverted repeats/single copy region (IR/SC) boundaries of Salvia are highly conserved, and IR contraction only occurred in two species (Salvia mekongensis and S. rosmarinus). In Salvia, sequence divergence was higher in non-coding regions than in coding regions. We found that using large single copy (LSC) and small single copy regions (SSC) with exclusion of the rapidly evolving sites produced the highest resolution in phylogenetic analysis of Salvia, suggesting that using suitable informative sites to build trees is more conducive in phylogenetic research. This study assembled a powerful matrix data set for studying the phylogeny of Salvia, resolving the interspecific relationship of Salvia subg. Glutinaria. The newly sequenced plastid genomes will also enrich the plastome database of Salvia, providing the scientific basis for the development and utilization of germplasm resources of this large and important genus.
    Plastid phylogenomic insights into the evolution of subfamily Dialioideae (Leguminosae)
    Han-Rui Bai, Oyetola Oyebanji, Rong Zhang, Ting-Shuang Yi
    2021, 43(01):  27-34.  doi:10.1016/j.pld.2020.06.008
    Abstract ( 101 )   HTML ( )   PDF (13339KB) ( 19 )   Save
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    The subfamily Dialioideae (Leguminosae) consists of 17 genera and about 85 species. Previous studies have detected significant plastid genome (plastome) structure variations in legumes, particularly in subfamilies Papilionoideae and Caesalpinioideae. Hence it is important to investigate plastomes from the newly recognized Dialioideae to better understand the plastome variation across the whole family. Here, we used nine plastomes representing nine genera of Dialioideae to explore plastome structural variation and intergeneric relationships in this subfamily. All plastomes of Dialioideae exhibited a typical quadripartite structure, and had relatively conserved structure compared with other legume subfamilies. However, the genome size ranged from 154,124 bp to 165,973 bp and gene numbers ranged from 129 to 132, mainly due to the expansion and contraction of the inverted repeat (IR) regions. The IR of Distemonanthus benthamianus has experienced two separate expansions into the large single copy (LSC) region and the small single copy (SSC) region, and one contraction from SSC. Poeppigia procera has experienced two separate IR expansions into LSC, while Dicorynia paraensis has experienced an IR contraction from LSC. Highly divergent regions or genes (ndhC-trnVUAC,psbK-trnQUUG,rps19-rps3, rpl33-rps18,accD-psaI,trnGUCC-trnSGCU,psbI-trnSGCU,5'rps16-trnQUUG and ycf1) were identified as potential molecular markers for further species delimitation and population genetics analysis in legumes. Phylogenetic analysis based on 77 protein-coding sequences fully resolved the intergeneric relationships among nine genera except a moderately supported sister relationship between Petalostylis labicheoides and Labichea lanceolata. Our study reveals new insights into the structural variations of plastomes in subfamily Dialioideae and advances our understanding of the evolutionary trajectories of legume plastomes.
    Plastome phylogenomics of the East Asian endemic genus Dobinea
    Changkun Liu, Jin Yang, Lei Jin, Shuying Wang, Zhenyan Yang, Yunheng Ji
    2021, 43(01):  35-42.  doi:10.1016/j.pld.2020.05.002
    Abstract ( 79 )   HTML ( )   PDF (11525KB) ( 20 )   Save
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    Dobinea is a dioecious genus endemic to East Asia that consists of two extant species: Dobinea delavayi and Dobinea vulgaris. Although the genus is morphologically distinct, its phylogenetic position remains controversial. In this study, we investigated the phylogenetic relationships between Dobinea and related taxa by sequencing the whole plastome DNA sequences for both extant species of Dobinea and comparing them to published plastomes within Sapindales. The complete plastomes of D. vulgaris and D. delavayi were 160,683 and 160, 154 base pairs (bp) in length, including a pair of inverted repeat regions (IRs, 26,889 and 26,759 bp) divided by the large single-copy region (LSC, 87,962 and 87,555 bp) and small single-copy region (SSC, 18,943 and 19,081 bp), and identically encoded 113 unique genes (79 protein-coding genes, 30 tRNAs, and 4 rRNA genes). Plastid phylogenomic analyses showed that Dobinea was a well-supported monophyletic unit and sister to the clade including tribes Anacardieae and Rhoideae, which suggests that Dobinea is a member of Anacardiaceae. In addition, molecular dating inferred D. delavayi and D. vulgaris diverged approximately 10.76 Ma, suggesting the divergence between these two species may have been driven by the intensification of the Asian summer monsoon and the establishment of distinct monsoon regimes in East Asia.
    Development of genomic resources for the genus Celtis (Cannabaceae) based on genome skimming data
    Luxian Liu, Yonghua Zhang, Pan Li
    2021, 43(01):  43-53.  doi:10.1016/j.pld.2020.09.005
    Abstract ( 111 )   HTML ( )   PDF (15724KB) ( 22 )   Save
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    Celtis is a Cannabaceae genus of 60-70 species of trees, or rarely shrubs, commonly known as hack-berries. This woody genus consists of very valuable forest plants that provide important wildlife habitat for birds and mammals. Although previous studies have identified its phylogenetic position, interspecific relationships within Celtis remain unclear. In this study, we generated genome skimming data from five Celtis species to analyze phylogenetic relationships within the genus and develop genome resources. The plastomes of Celtis ranged in length from 158,989 bp to 159,082 bp, with a typical angiosperm quadripartite structure, and encoded a total of 132 genes with 20 duplicated in the IRs. Comparative analyses showed that plastome content and structure were relatively conserved. Whole plastomes showed no signs of gene loss, translocations, inversions, or genome rearrangement. Six plastid hotspot regions (trnH-psbA, psbA-trnK, trnG-trnR, psbC-trnS, cemA-petA and rps8-rpl14), 4097 polymorphic nuclear SSRs, as well as 62 low or single-copy gene fragments were identified within Celtis. Moreover, the phylogenetic relationships based on the complete plastome sequences strongly endorse the placement of C. biondii as sister to the ((((C. koraiensis, C. sinensis), C. tetrandra), C. julianae), C. cerasifera) clade. These findings and the genetic resources developed here will be conducive to further studies on the genus Celtis involving phylogeny, population genetics, and conservation biology.
    Molecular and morphological evidence for a new species of Isodon (Lamiaceae) from southern China
    Ya-Ping Chen, Cun-Zhong Huang, Yue Zhao, Chun-Lei Xiang
    2021, 43(01):  54-62.  doi:10.1016/j.pld.2020.06.004
    Abstract ( 122 )   HTML ( )   PDF (7660KB) ( 40 )   Save
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    Isodon brevipedunculatus, a new species from southern China, is described and illustrated. The phylogenetic position of the new species within the genus was analyzed based on two nuclear ribosomal DNA regions and an ingroup sampling of about 80% of Asian species of Isodon. The results show that I. brevipedunculatus is recovered in a clade that consists of species mainly with glandular mericarps and that are distributed in the Sino-Japanese region. Combining molecular and geographical evidence, our study reveals that I. brevipedunculatus is most closely related to Isodon amethystoides and Isodon bifidocalyx, but differs from the former in lamina shape, number of flowers per cyme, and peduncle length, and from the latter in lamina indumentum, calyx morphology, and corolla length.
    Characterization of an algal phosphomannose isomerase gene and its application as a selectable marker for genetic manipulation of tomato
    Yuanyuan Lin, Junchao Huang
    2021, 43(01):  63-70.  doi:10.1016/j.pld.2020.06.001
    Abstract ( 140 )   HTML ( )   PDF (16265KB) ( 9 )   Save
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    Establishing a transgenic plant largely relies on a selectable marker gene that can confer antibiotic or herbicide resistance to plant cells. The existence of such selectable marker genes in genetically modified foods has long been criticized. Plant cells generally exhibit too low an activity of phosphomannose isomerase (PMI) to grow with mannose as a sole carbon source. In this study, we characterized PMI from the green microalga Chlorococcum sp. and assessed its feasibility as a selectable marker for plant biotechnology. Chlorococcum sp. PMI (ChlPMI) was shown to be closely related to higher plants but more distant to bacterial counterparts. Overexpression of ChlPMI in tomato induced callus and shoot formation in media containing mannose (6 g/L) and had an average transformation rate of 3.9%. Based on this transformation system, a polycistronic gene cluster containing crtB, HpBHY, CrBKT and SlLCYB (BBBB) was co-expressed in a different tomato cultivar. Six putative transformants were achieved with a transformation rate of 1.4%, which produced significant amounts of astaxanthin due to the expression of the BBBB genes. Taken together, these findings indicate that we have established an additional tool for plant biotechnology that may be suitable for genetically modifying foods safely.
    Functional characterization of the Arabidopsis SERRATE under salt stress
    Minghui Mou, Qijuan Wang, Yanli Chen, Diqiu Yu, Ligang Chen
    2021, 43(01):  71-77.  doi:10.1016/j.pld.2020.06.010
    Abstract ( 93 )   HTML ( )   PDF (7663KB) ( 27 )   Save
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    SERRATE (SE) plays critical roles in RNA metabolism and plant growth regulation. However, its function in stresseresponse processes remains largely unknown. Here, we examined the regulatory role of SE using the se-1 mutant and its complementation line under saline conditions. The expression of SE was repressed by salt treatment at both mRNA and protein levels. After treatment with different NaCl concentrations, the se-1 mutants showed increased sensitivity to salinity. This heightened sensitivity was evidenced by decreased germination, reduced root growth, more serious chlorosis, and increased conductivity of the mutants compared with the wild type. Further analysis revealed that SE regulates the pre-mRNA splicing of several well-characterized marker genes associated with salt stress tolerance. Our data thus imply that SE may function as a key component in plant response to salt stress by modulating the splicing of salt stress-associated genes.
    Accession-specific flowering time variation in response to nitrate fluctuation in Arabidopsis thaliana
    Fei-Hong Yan, Li-Ping Zhang, Fang Cheng, Dong-Mei Yu, Jin-Yong Hu
    2021, 43(01):  78-85.  doi:10.1016/j.pld.2020.05.004
    Abstract ( 104 )   HTML ( )   PDF (5318KB) ( 40 )   Save
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    Flowering time, a key transition point from vegetative to reproductive growth, is regulated by an intrinsic complex of endogenous and exogenous signals including nutrient status. For hundreds of years, nitrogen has been well known to modulate flowering time, but the molecular genetic basis on how plants adapt to ever-changing nitrogen availability remains not fully explored. Here we explore how Arabidopsis natural variation in flowering time responds to nitrate fluctuation. Upon nitrate availability change, we detect accession- and photoperiod-specific flowering responses, which also feature a accession-specific dependency on growth traits. The flowering time variation correlates well with the expression of floral integrators, SOC1 and FT, in an accession-specific manner. We find that gene expression variation of key hub genes in the photoperiod-circadian-clock (GI), aging (SPLs) and autonomous (FLC) pathways associates with the expression change of these integrators, hence flowering time variation. Our results thus shed light on the molecular genetic mechanisms on regulation of accession- and photoperiod-specific flowering time variation in response to nitrate availability.
    Diversity in seed oil content and fatty acid composition in Acer species with potential as sources of nervonic acid
    Xing He, De-Zhu Li, Bo Tian
    2021, 43(01):  86-92.  doi:10.1016/j.pld.2020.10.003
    Abstract ( 83 )   HTML ( )   PDF (1897KB) ( 19 )   Save
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    Nervonic acid (NA, cis-15-tetracosenoic acid) is a very long-chain monounsaturated fatty acid that has been shown to be a core component of nerve fibers and nerve cells. It can be used to treat and prevent many neurological diseases. At present, commercially available NA is mainly derived from Acer truncatum seeds, which contain about 5%-6% NA in their seed oil. The aim of this study were to identify and analyze NA-containing Acer species that could be used as NA resource plants. For this purpose, 46 Acer species seeds were collected in China and in some or all of the seed oils from these species 15 fatty acids were detected, including linoleic acid, oleic acid (C18:1△9, C18:1△11), erucic acid, palmitic acid, NA, linolenic acid (C18:3△6,9,12, C18:3△9,12,15), eicosenoic acid (C20:1△11, C20:1△13), stearic acid, behenic acid, tetracosanoic acid, arachidic acid, and docosadienoic acid. Nervonic acid was detected in all samples, but the content was highly variable among species. NA content over 9% was detected in eleven species, of which Acer elegantulum had the highest levels (13.90%). The seed oil content, seed weight, and fatty acid profiles varied among species, but the comprehensive evaluation value (W) showed that A. coriaceifolium could be a new potential NA resources plant. The results also showed that NA was significantly negatively correlated with palmitic acid, oleic acid, and eicosenoic acid, but positively correlated with eicosadienoic acid, behenic acid, erucic acid, and tetracosanoic acid, which indicate the probable pathway for NA biosynthesis in Acer plants. This study has identified Acer species that may serve as NA resources and will help guide subsequent species breeding programs.