scholarly journals Diversity of Meloidogyne exigua (Tylenchida: Meloidogynidae) populations from coffee and rubber tree

Nematology ◽  
2008 ◽  
Vol 10 (6) ◽  
pp. 897-910 ◽  
Author(s):  
Maria de Fátima Muniz ◽  
Regina Carneiro ◽  
Maria Ritta Almeida ◽  
Vicente Paulo Campos ◽  
Philippe Castagnone-Sereno ◽  
...  
Keyword(s):  
Genetic Polymorphism ◽  
Malate Dehydrogenase ◽  
Phylogenetic Analyses ◽  
Rubber Tree ◽  
Tree Plantations ◽  
Bootstrap Support ◽  
Intraspecific Polymorphism ◽  
Rapd Pcr ◽  
Scar Primers ◽  
Esterase Phenotypes

AbstractIsozymes (esterase and malate dehydrogenase), SCAR and RAPD-PCR were studied in 15 populations of three races of Meloidogyne exigua collected in coffee-producing areas in Brazil, Bolivia and Costa Rica and one population from rubber tree plantations in Brazil. This study revealed four esterase phenotypes (E1, E2, E2a, E3) and three malate dehydrogenase phenotypes (N1, N1a, N2) for M. exigua populations. The most common multi-enzyme phenotype was E2N1. The enzymatic phenotypes do not separate M. exigua races. Sixteen populations of M. exigua were tested in Multiplex PCR using SCAR primers ex-D15F/R that allowed the identification of all M. exigua populations. Phylogenetic analyses showed high intraspecific polymorphism (25.9-59.6%) for all M. exigua studied. However, all populations clustered together with 100% bootstrap support, thereby demonstrating the consistency of species identification. In general, no correlation was found between enzymatic profile, race and genetic polymorphism of the studied populations.

Morphology and multi-gene phylogeny reveal a new fungal genus and species from Hevea brasiliensis latex in Yunnan, China

Phytotaxa ◽  
2022 ◽  
Vol 530 (1) ◽  
pp. 65-76
Author(s):  
RUIFANG XU ◽  
KEVIN D. HYDE ◽  
SAMANTHA C. KARUNARATHNA ◽  
JIAN-CHU XU ◽  
PETER E. MORTIMER ◽  
...  
Keyword(s):  
Yunnan Province ◽  
Phylogenetic Analyses ◽  
Rubber Tree ◽  
Natural Rubber Latex ◽  
Tree Plantations ◽  
Bayesian Analyses ◽  
Distinct Genus ◽  
Statistical Support ◽  
Brown Band ◽  
High Statistical Support

During a survey of rubber tree plantations in Yunnan Province, China, a fungus growing on natural rubber latex was collected and isolated. Maximum likelihood and Bayesian analyses of combined ITS, LSU, SSU, tef-α and rpb2 genes showed the isolated taxon belongs to Wiesneriomycetaceae and was well separated from closely related genera with high statistical support. It can be differentiated from other genera in Wiesneriomycetaceae by synnemata with catenate conidia that are cylindrical, 0–4 to multi-septate, often with a dark brown band at the septa. Morphology, phylogenetic analyses and pairwise homoplasy index (PHI) tests provide evidence that the new isolate is a distinct genus. The genus Heveicola is introduced, with H. xishuangbannaensis as the type species. A key to the genera in Wiesneriomycetaceae is also provided.

scholarly journals Genomic Characteristics and Comparative Genomics Analysis of Two Chinese Corynespora cassiicola Strains Causing Corynespora Leaf Fall (CLF) Disease

2021 ◽  
Vol 7 (6) ◽  
pp. 485
Author(s):  
Boxun Li ◽  
Yang Yang ◽  
Jimiao Cai ◽  
Xianbao Liu ◽  
Tao Shi ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Single Molecule ◽  
Rubber Tree ◽  
Gene Families ◽  
Gene Clusters ◽  
The Philippines ◽  
Tree Plantations ◽  
Comparative Genomic ◽  
Corynespora Cassiicola ◽  
Leaf Fall

Rubber tree Corynespora leaf fall (CLF) disease, caused by the fungus Corynespora cassiicola, is one of the most damaging diseases in rubber tree plantations in Asia and Africa, and this disease also threatens rubber nurseries and young rubber plantations in China. C. cassiicola isolates display high genetic diversity, and virulence profiles vary significantly depending on cultivar. Although one phytotoxin (cassicolin) has been identified, it cannot fully explain the diversity in pathogenicity between C. cassiicola species, and some virulent C. cassiicola strains do not contain the cassiicolin gene. In the present study, we report high-quality gapless genome sequences, obtained using short-read sequencing and single-molecule long-read sequencing, of two Chinese C. cassiicola virulent strains. Comparative genomics of gene families in these two stains and a virulent CPP strain from the Philippines showed that all three strains experienced different selective pressures, and metabolism-related gene families vary between the strains. Secreted protein analysis indicated that the quantities of secreted cell wall-degrading enzymes were correlated with pathogenesis, and the most aggressive CCP strain (cassiicolin toxin type 1) encoded 27.34% and 39.74% more secreted carbohydrate-active enzymes (CAZymes) than Chinese strains YN49 and CC01, respectively, both of which can only infect rubber tree saplings. The results of antiSMASH analysis showed that all three strains encode ~60 secondary metabolite biosynthesis gene clusters (SM BGCs). Phylogenomic and domain structure analyses of core synthesis genes, together with synteny analysis of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) gene clusters, revealed diversity in the distribution of SM BGCs between strains, as well as SM polymorphisms, which may play an important role in pathogenic progress. The results expand our understanding of the C. cassiicola genome. Further comparative genomic analysis indicates that secreted CAZymes and SMs may influence pathogenicity in rubber tree plantations. The findings facilitate future exploration of the molecular pathogenic mechanism of C. cassiicola.

scholarly journals The first mitochondrial genome of the genus Exhippolysmata (Decapoda: Caridea: Lysmatidae), with gene rearrangements and phylogenetic associations in Caridea

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ying-ying Ye ◽  
Jing Miao ◽  
Ya-hong Guo ◽  
Li Gong ◽  
Li-hua Jiang ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Bootstrap Support ◽  
Trna Genes ◽  
Gene Rearrangements ◽  
Phylogenetic Studies ◽  
Gc Skew ◽  
Strong Bootstrap Support

AbstractThe complete mitochondrial genome (mitogenome) of animals can provide useful information for evolutionary and phylogenetic analyses. The mitogenome of the genus Exhippolysmata (i.e., Exhippolysmata ensirostris) was sequenced and annotated for the first time, its phylogenetic relationship with selected members from the infraorder Caridea was investigated. The 16,350 bp mitogenome contains the entire set of 37 common genes. The mitogenome composition was highly A + T biased at 64.43% with positive AT skew (0.009) and negative GC skew (− 0.199). All tRNA genes in the E. ensirostris mitogenome had a typical cloverleaf secondary structure, except for trnS1 (AGN), which appeared to lack the dihydrouridine arm. The gene order in the E. ensirostris mitogenome was rearranged compared with those of ancestral decapod taxa, the gene order of trnL2-cox2 changed to cox2-trnL2. The tandem duplication-random loss model is the most likely mechanism for the observed gene rearrangement of E. ensirostris. The ML and BI phylogenetic analyses place all Caridea species into one group with strong bootstrap support. The family Lysmatidae is most closely related to Alpheidae and Palaemonidae. These results will help to better understand the gene rearrangements and evolutionary position of E. ensirostris and lay a foundation for further phylogenetic studies of Caridea.

scholarly journals Nutrient cycling in a RRIM 600 clone rubber plantation

2003 ◽  
Vol 60 (2) ◽  
pp. 353-357 ◽  
Author(s):  
Marcos Roberto Murbach ◽  
Antonio Enedi Boaretto ◽  
Takashi Muraoka ◽  
Euclides Caxambu Alexandrino de Souza
Keyword(s):  
Nutrient Cycling ◽  
Rubber Tree ◽  
Nutrient Content ◽  
Nutrient Loss ◽  
Tree Plantations ◽  
Rubber Plantation ◽  
Rubber Latex ◽  
Nutrient Retranslocation ◽  
One Year ◽  
K Fertilization

Few reports have been presented on nutrient cycling in rubber tree plantations (Hevea brasiliensis Muell. Arg.). This experiment was carried out to evaluate: the effect of K rates on the amount of nutrients transfered to the soil in a 13-year old Hevea brasilensis RRIM 600 clone plantation, nutrient retranslocation from the leaves before falling to the soil, and nutrient loss by dry rubber export. The experiment started in 1998 and potassium was applied at the rates of 0, 40, 80 and 160 kg ha-1 of K2O under the crowns of 40 rubber trees of each plot. Literfall collectors, five per plot, were randomly distributed within the plots under the trees. The accumulated literfall was collected monthly during one year. The coagulated rubber latex from each plot was weighed, and samples were analyzed for nutrient content. Increasing K fertilization rates also increased the K content in leaf literfall. Calcium and N were the most recycled leaf nutrients to the soil via litterfall. Potassium, followed by P were the nutrients with the highest retranslocation rates. Potassium was the most exported nutrient by the harvested rubber, and this amount was higher than that transfered to the soil by the leaf literfall.

scholarly journals RAPD-ANALYSIS OF CYCLAMEN SPP. GENOME POLYMORPHISM

2019 ◽  
Vol 7 ◽  
pp. 949-953
Author(s):  
Elza Makaradze ◽  
Galina Meparishvili ◽  
Natela Varshanidze ◽  
Inga Diasamidze ◽  
Ketevan Dolidze ◽  
...  
Keyword(s):  
Genetic Polymorphism ◽  
Species Diversity ◽  
Rapd Markers ◽  
Biological Diversity ◽  
Molecular Genetic ◽  
Wild Plants ◽  
Large Species ◽  
Genetic Studies ◽  
Rapd Pcr ◽  
Rare Endemic

Wild plants form the basis of biological resources both for Georgia and the whole world. A strategic task of any country is to preserve the biological diversity of plants. In the territory of Ajara, a large species diversity of plants grows, among which there are rare, endemic and relict plants. In particular, Cyclamen adzharicum. Modern systematics of wild plants in Georgia is based on classical methods of botany. In this regard, it is relevant to conduct genetic studies of species diversity and genetic polymorphism of species and populations using molecular genetic markers, in particular RAPD-PCR methods. The purpose of this study was to identify genetic polymorphism in Cyclamen L species using RAPD methods. As a result of the conducted research the 65 RAPD-markers in length from 150 to 1500 BP have been revealed. The number of the amplified fragments DNA varied depending on the primer from 6 (OPA-2) to 11 (OPB-4). The results of grouping Cyclamen adzharicum and C. coum samples allowed two clusters to be identified. In the first cluster were samples of three populations Cyclamen adzharicum and showed a low stubble in the intra-species variability. Cyclamen coum was attributed to the second cluster. The used primers gave the opportunity to identify polymorphism between the tested types of cyclamen.

Carbon stock in rubber tree plantations in Western Ghana and Mato Grosso (Brazil)

2008 ◽  
Vol 255 (7) ◽  
pp. 2347-2361 ◽  
Author(s):  
J.B. Wauters ◽  
S. Coudert ◽  
E. Grallien ◽  
M. Jonard ◽  
Q. Ponette
Keyword(s):  
Carbon Stock ◽  
Rubber Tree ◽  
Tree Plantations ◽  
Mato Grosso

scholarly journals Genetic polymorphism and phylogenetic analyses of 21 non‐CODIS STR loci in a Chinese Han population from Shanghai

2019 ◽  
Vol 8 (2) ◽  
Author(s):  
Zhihan Zhou ◽  
Chengchen Shao ◽  
Jianhui Xie ◽  
Hongmei Xu ◽  
Yidong Liu ◽  
...  
Keyword(s):  
Genetic Polymorphism ◽  
Phylogenetic Analyses ◽  
Chinese Han Population ◽  
Chinese Han ◽  
Han Population ◽  
Str Loci

Phaeosphaeria chinensis sp. nov. (Phaeosphaeriaceae) with an asexual/sexual morph connection from GuangDong Province, China

Phytotaxa ◽  
2019 ◽  
Vol 419 (1) ◽  
pp. 28-38 ◽  
Author(s):  
KE-KE ZHANG ◽  
SINANG HONGSANAN ◽  
DANUSHKA S. TENNAKOON ◽  
SHENG-LI TIAN ◽  
NING XIE
Keyword(s):  
New Species ◽  
Bayesian Inference ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Guangdong Province ◽  
Distinct Species ◽  
Bootstrap Support ◽  
Comprehensive Description ◽  
High Bootstrap ◽  
Asexual Morphs

Phaeosphaeria chinensis sp. nov. was found on dead leaves, collected from Guangdong Province, China. Morphology of the new species was compared with other Phaeosphaeria species and related genera of Phaeosphaeriaceae. Phylogenetic analyses of combined ITS, LSU, SSU and TEF-1 sequence data based on maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) revealed that P. chinensis as a distinct species within the Phaeosphaeria with high bootstrap support. The comparison of the new species with other Phaeosphaeria species and a comprehensive description and micrographs are provided. The linkage of sexual and asexual morphs of the new species is also showed.

scholarly journals Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction

2020 ◽  
Author(s):  
Matthew H Van Dam ◽  
James B Henderson ◽  
Lauren Esposito ◽  
Michelle Trautwein
Keyword(s):  
Marine Invertebrates ◽  
Phylogenetic Analyses ◽  
Single Gene ◽  
Gene Tree ◽  
Single Copy ◽  
Species Tree ◽  
Bootstrap Support ◽  
Gene Trees ◽  
Species Trees ◽  
Tree Reconstruction

Abstract Ultraconserved genomic elements (UCEs) are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes does not require prior knowledge of genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here, we characterized UCEs from 11 phylogenomic studies across the animal tree of life, from birds to marine invertebrates. We found that within vertebrate lineages, UCEs are mostly intronic and intergenic, while in invertebrates, the majority are in exons. We then curated four different sets of UCE markers by genomic category from five different studies including: birds, mammals, fish, Hymenoptera (ants, wasps, and bees), and Coleoptera (beetles). Of genes captured by UCEs, we find that many are represented by two or more UCEs, corresponding to nonoverlapping segments of a single gene. We considered these UCEs to be nonindependent, merged all UCEs that belonged to a particular gene, constructed gene and species trees, and then evaluated the subsequent effect of merging cogenic UCEs on gene and species tree reconstruction. Average bootstrap support for merged UCE gene trees was significantly improved across all data sets apparently driven by the increase in loci length. Additionally, we conducted simulations and found that gene trees generated from merged UCEs were more accurate than those generated by unmerged UCEs. As loci length improves gene tree accuracy, this modest degree of UCE characterization and curation impacts downstream analyses and demonstrates the advantages of incorporating basic genomic characterizations into phylogenomic analyses. [Anchored hybrid enrichment; ants; ASTRAL; bait capture; carangimorph; Coleoptera; conserved nonexonic elements; exon capture; gene tree; Hymenoptera; mammal; phylogenomic markers; songbird; species tree; ultraconserved elements; weevils.]

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