Chromosome genome assembly and annotation of Artocarpus Nanchuanensis with Nanopore and Hi-C sequencing data

The A.nanchuanensis (Artocarpus Nanchuanensis, Moraceae) is an evergreen Artocarpus genus representative tree species in the northernmost natural distribution and one of the extremely endangered tree species in China. In this study, we obtained a high-quality chromosome-scale genome assembly and annotation for A.nanchuanensis using inter-grated approaches, including Illumina, Nanopore sequencing platform as well as Hi-C. A total of 128.71 gigabases (Gb) raw Nanopore Sequel reads were generated from 20 kb libraries. After filtering, 123.38 Gb clean reads were obtained, giving 160.34x coverage depth. The final assembled A.nanchuanensis genome was 769.44 Mb with a contig N50 of 2.09 Mb, and 99.62% (766.50 Mb) of the assembly data was assigned to 28 pseudochromosomes. Gene modelling predicted 41,636 protein-coding genes, of which 95.10% were annotated. The gene annotation completeness was evaluated by BUSCO, and 94.44% conserved genes could be found in the assembly data. The disclosure of A.nanchuanensis genome sequence information provides an important resource to expand our understanding of the molecular mechanism in its unique biological processes and nutritional, medicinal benefits.

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Floristic Variation of Tree Communities and Their Association with Soil Properties in Pulau Jerejak, Penang, Peninsular Malaysia

Science Letters ◽

10.24191/sl.v14i1.7899 ◽

2020 ◽

Vol 14 (1) ◽

pp. 34

Author(s):

Faezah Pardi

Keyword(s):

Tree Species ◽

Diversity Index ◽

Basal Area ◽

Peninsular Malaysia ◽

Importance Value ◽

Conservation Action ◽

Endangered Tree ◽

Endangered Tree Species ◽

Tree Communities ◽

Floristic Variation

This study was conducted at Pulau Jerejak, Penang to determine the floristic variation of its tree communities. A 0.5-hectare study plot was established and divided into 11 subplots. A total of 587 trees with diameter at breast height (DBH) of 5 cm and above were measured, identified and recorded. The tree communities comprised of 84 species, 63 genera and 32 families. The Myrtaceae was the most speciose family with 10 recorded species while Syzgium glaucum (Myrtaceae) was the most frequent species. The Myrtaceae recorded the highest density of 306 individuals while Syzgium glaucum (Myrtaceae) had the highest species density of 182 individuals. Total tree basal area (BA) was 21.47 m2/ha and family with the highest BA was Myrtaceae with 5.81 m2/ha while at species level, Syzgium glaucum (Myrtaceae) was the species with the highest total BA in the plot with value of 4.95 m2/ha. The Shannon˗Weiner Diversity Index of tree communities showed a value of 3.60 (H'max = 4.43) and Evenness Index of 0.81 which indicates high uniformity of tree species. The Margalef Richness Index (R') revealed that the tree species richness was 13.02. Myrtaceae had the highest Importance Value of 20.4%. The Canonical Correspondence Analysis (CCA) showed that Diospyros buxifolia (Ebenaceae) and Pouteria malaccensis (Sapotaceae) were strongly correlated to low pH. Dysoxylum cauliflorum (Meliaceae) and Eriobotrya bengalensis (Rosaceae) were correlated to phosphorus (P) and calcium ion (Ca2+), respectively. Therefore, the trees species composition at Pulau Jerejak showed that the biodiversity is high and conservation action should be implemented to protect endangered tree species. Keywords: Floristic variation; Tree communities; Trees composition; Pulau Jerejak; Species diversity

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Genetic diversity of central and peripheral populations of Toona ciliata var. pubescens, an endangered tree species endemic to China

Chinese Journal of Plant Ecology ◽

10.3724/sp.j.1258.2013.00006 ◽

2013 ◽

Vol 37 (1) ◽

pp. 52-60 ◽

Cited By ~ 2

Author(s):

Jun LIU ◽

Jing-Min JIANG ◽

Jun ZOU ◽

Jin-Liang XU ◽

Han SHEN ◽

...

Keyword(s):

Genetic Diversity ◽

Tree Species ◽

Peripheral Populations ◽

Endangered Tree ◽

Endangered Tree Species ◽

Toona Ciliata

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Nucleotide variation at the methionine synthase locus in an endangered tree species, Fokienia hodginsii (Cupressaceae) in Vietnam

AFRICAN JOURNAL OF BIOTECHNOLOGY ◽

10.5897/ajb12.1166 ◽

2012 ◽

Vol 11 (88) ◽

pp. 15398-15404 ◽

Cited By ~ 1

Author(s):

Duc Quang Nguyen ◽

Thi Phuong Hoa Phan ◽

Van Tan Dao ◽

Van Thang Nguyen

Keyword(s):

Tree Species ◽

Methionine Synthase ◽

Nucleotide Variation ◽

Endangered Tree ◽

Endangered Tree Species

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Somatic embryogenesis and plantlet formation from a rare and endangered tree species,Oplopanax elatus

Journal of Plant Biology ◽

10.1007/bf03031163 ◽

2006 ◽

Vol 49 (4) ◽

pp. 320-325 ◽

Cited By ~ 16

Author(s):

Heung Kyu Moon ◽

Ji Ah Kim ◽

So Young Park ◽

Yong Wook Kim ◽

Ho Duck Kang

Keyword(s):

Somatic Embryogenesis ◽

Tree Species ◽

Endangered Tree ◽

Endangered Tree Species ◽

Plantlet Formation ◽

Rare And Endangered ◽

Oplopanax Elatus

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The genome sequence of the European peacock butterfly, Aglais io (Linnaeus, 1758)

Wellcome Open Research ◽

10.12688/wellcomeopenres.17204.1 ◽

2021 ◽

Vol 6 ◽

pp. 258

Author(s):

Konrad Lohse ◽

Alexander Mackintosh ◽

Roger Vila ◽

◽

...

Keyword(s):

Genome Sequence ◽

Genome Assembly ◽

Sex Chromosome ◽

Gene Annotation ◽

Protein Coding ◽

Individual Male ◽

Protein Coding Genes ◽

A Genome ◽

Inachis Io

We present a genome assembly from an individual male Aglais io (also known as Inachis io and Nymphalis io) (the European peacock; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 384 megabases in span. The majority (99.91%) of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled. Gene annotation of this assembly on Ensembl has identified 11,420 protein coding genes.

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TrancriptomeReconstructoR, A Data-Driven Annotation of Complex Transcriptomes

10.21203/rs.3.rs-131404/v1 ◽

2020 ◽

Author(s):

Maxim Ivanov ◽

Albin Sandelin ◽

Sebastian Marquardt

Keyword(s):

De Novo ◽

Gene Annotation ◽

R Package ◽

Sequence Information ◽

Rna Seq ◽

Sequencing Data ◽

Gene Model ◽

Preparation Methods ◽

Downstream Analysis

Abstract Background: The quality of gene annotation determines the interpretation of results obtained in transcriptomic studies. The growing number of genome sequence information calls for experimental and computational pipelines for de novo transcriptome annotation. Ideally, gene and transcript models should be called from a limited set of key experimental data. Results: We developed TranscriptomeReconstructoR, an R package which implements a pipeline for automated transcriptome annotation. It relies on integrating features from independent and complementary datasets: i) full-length RNA-seq for detection of splicing patterns and ii) high-throughput 5' and 3' tag sequencing data for accurate definition of gene borders. The pipeline can also take a nascent RNA-seq dataset to supplement the called gene model with transient transcripts.We reconstructed de novo the transcriptional landscape of wild type Arabidopsis thaliana seedlings as a proof-of-principle. A comparison to the existing transcriptome annotations revealed that our gene model is more accurate and comprehensive than the two most commonly used community gene models, TAIR10 and Araport11. In particular, we identify thousands of transient transcripts missing from the existing annotations. Our new annotation promises to improve the quality of A.thaliana genome research.Conclusions: Our proof-of-concept data suggest a cost-efficient strategy for rapid and accurate annotation of complex eukaryotic transcriptomes. We combine the choice of library preparation methods and sequencing platforms with the dedicated computational pipeline implemented in the TranscriptomeReconstructoR package. The pipeline only requires prior knowledge on the reference genomic DNA sequence, but not the transcriptome. The package seamlessly integrates with Bioconductor packages for downstream analysis.

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Indopiptadenia Oudhensis (Brandis) Brenan an Endangered Tree Species: Measures for the Coservation

Indian Journal of Forestry ◽

10.54207/bsmps1000-2014-b49y96 ◽

2014 ◽

Vol 37 (1) ◽

pp. 69-72

Author(s):

Giriraj Panwar ◽

Kumar Ambrish ◽

S. Srivastava

Keyword(s):

Seed Germination ◽

Tree Species ◽

Seed Viability ◽

Habitat Destruction ◽

Anthropogenic Pressure ◽

Endangered Tree ◽

Endangered Tree Species ◽

Poor Seed ◽

Over Exploitation

Indopiptadenia oudhensis (Brandis) Brenan is an endangered tree species of family Mimosaceae. Species is mainly distributed at Indo-Nepal border and facing threats such as anthropogenic pressure, habitat destruction, over exploitation, low seed viability and poor seed germination.

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