scholarly journals A Challenge to Integrate Bioinformatics and Biodiversity Informatics Data as Museomics

2018 ◽  
Vol 2 ◽  
pp. e26102 ◽  
Author(s):  
Takeru Nakazato
Keyword(s):  
Gene Expression ◽  
Phylogenetic Analysis ◽  
Molecular Biology ◽  
Life Science ◽  
Sequence Data ◽  
Molecular Data ◽  
Biodiversity Informatics ◽  
Science Data ◽  
Dna Sequence Data ◽  
Ngs Data

Museum-preserved samples are attracting attention as a rich resource for DNA studies. Museomics aims to link DNA sequence data back to the museum collection. Molecular biologists are interested in morphological information including body size, pattern, and colors, and sequence data have also become essential for biodiversity research as evidence for species identification and phylogenetic analysis. For more than 30 years, molecular data, such as DNA and protein sequences, have been captured by the DNA Data Bank of Japan (DDBJ), the European Bioinformatics Institute (EBI, UK), and the National Center for Biotechnology Information (NCBI, US) under the International Nucleotide Sequence Database Collaboration (INSDC). INSDC provides collected molecular data to researchers as public databases including GenBank for DNA sequences and Gene Expression Omnibus (GEO) for gene expression. These three institutes synchronize archived data and publish all data on an FTP (File Transfer Protocol) site so that it is available for big data analysis. In recent years, high-throughput sequencing technology, also called next-generation sequencing (NGS) technology, has been widely utilized for molecular biology including genomics, transcriptomics, and metagenomics. Biodiversity researchers also focus on NGS data for DNA barcoding and phylogenetic analysis as well as molecular biology. Additionally, a portable NGS platform, MinION (Oxford Nanopore Technologies), has been launched, enabling biodiversity researchers to perform DNA sequencing in the field. Along with GenBank and GEO data, INSDC accepts NGS data and provides a public primary database, called the Sequence Read Archive (SRA). As of March 2018, 6.4 Peta Bases of NGS data is freely available under more than 130,000 projects in SRA. The Database Center for Life Science (DBCLS) provides a search engine for public NGS data, called DBCLS SRA (http://sra.dbcls.jp/) in collaboration with DDBJ. SRA contains not only raw sequence reads or processed data mapped to genome, but also information on the experimental design, including project types, sequencing platforms, and sample species. Researchers can use this data to refine their search results. We also linked publications referring to NGS data to the corresponding SRA entries. The mission of DBCLS is to accelerate the accessibility of life science data. Collected data used to be described in the Excel-readable tabular format, but these formats are difficult to merge with other databases because of the ambiguity of labels. To overcome this difficulty, we recently integrated life science data with Semantic Web technology. We held annual meetings to integrate life science data, called BioHackathons, in which researchers from all over the world participated. UniProt and Ensembl databases currently provide an RDF (Resource Description Framework) version of curated genome and protein data, respectively. In the biodiversity domain, there are many databases such as GBIF (The Global Biodiversity Information Facility) for species occurrence records, EoL (The Encyclopedia of Life) as a knowledge base of all species, and BoL (The Barcode of Life) for DNA barcoding data. RDF is utilized to describe Darwin Core based data so that bioinformatics and biodiversity informatics researchers can technically merge both types of data. Currently, specimen data and DNA sequence data are not linked. Museomics starts with cross-referencing specimen and sequence IDs and by making data sources comply with an existing standard.

On the identity of Lophostoma silvicolum occidentalis (Davis & Carter, 1978) (Chiroptera: Phyllostomidae)

Zootaxa ◽  
2011 ◽  
Vol 2962 (1) ◽  
pp. 1 ◽  
Author(s):  
PAÚL M. VELAZCO ◽  
RICHARD CADENILLAS
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Data ◽  
Molecular Data ◽  
Dorsal Side ◽  
Valid Species ◽  
Mastoid Process ◽  
Molecular Variation ◽  
Lateral Projection ◽  
Dna Sequence Data ◽  
The Andes

The Neotropical bat genus Lophostoma (Phyllostomidae: Phyllostominae) currently includes seven species. Two taxa, Lophostoma aequatorialis and Lophostoma silvicolum occidentalis, occur west of the Andes in Ecuador and Peru. In the description of L. aequatorialis, these two taxa were compared solely on the basis of morphology because DNA sequence data could not be obtained from the type series of L. s. occidentalis. Here, comparisons are based on molecular data and extensive morphological comparisons. The congruence between the morphological and molecular variation in our analyses support the recognition of L. occidentalis as a valid species and the consideration of L. aequatorialis as a junior synonym of L. occidentalis. Phylogenetic analysis of Lophostoma based on cytochrome-b sequences indicates that L. occidentalis is closely related to L. schulzi. L. occidentalis can be recognized by its white to pale post-auricular patches; dorsal side of the forearm naked; well-developed lateral projection of mastoid process; wide basioccipital; shallow basisphenoid pits weakly separated by a septum; P3 and P4 distal accessory cusp present; M1 ectocingulum strongly developed; M1 mesostyle absent; M1 mesostylar crest present; M1 anterior ectoflexus deep and posterior ectoflexus shallow; M1 lingual cingulum present; M2 mesostyle absent; and M2 mesostylar crest present.

Revised circumscription of Nothofagus and recognition of the segregate genera Fuscospora, Lophozonia, and Trisyngyne (Nothofagaceae)

Phytotaxa ◽  
2013 ◽  
Vol 146 (1) ◽  
pp. 1 ◽  
Author(s):  
PETER B. HEENAN ◽  
ROB D. SMISSEN
Keyword(s):  
Phylogenetic Analysis ◽  
South America ◽  
Papua New Guinea ◽  
New Genus ◽  
New Caledonia ◽  
Sequence Data ◽  
Morphological Characters ◽  
New Combinations ◽  
Southern South America ◽  
Dna Sequence Data

The generic taxonomy of the Nothofagaceae is revised. We present a new phylogenetic analysis of morphological characters and map these characters onto a recently published phylogenetic tree obtained from DNA sequence data. Results of these and previous analyses strongly support the monophyly of four clades of Nothofagaceae that are currently treated as subgenera of Nothofagus. The four clades of Nothofagaceae are robust and well-supported, with deep stem divergences, have evolutionary equivalence with other genera of Fagales, and can be circumscribed with morphological characters. We argue that these morphological and molecular differences are sufficient for the four clades of Nothofagaceae to be recognised at the primary rank of genus, and that this classification will be more informative and efficient than the currently circumscribed Nothofagus with four subgenera.        Nothofagus is recircumscribed to include five species from southern South America, Lophozonia and Trisyngyne are reinstated, and the new genus Fuscospora is described. Fuscospora and Lophozonia, with six and seven species respectively, occur in New Zealand, southern South America and Australia. Trisyngyne comprises 25 species from New Caledonia, Papua New Guinea and Indonesia. New combinations are provided where necessary in each of these genera.

Molecular and Ultrastructural Analysis of a Porocephalus sp. (Arthropoda: Pentastomida) Removed from a Rattlesnake

2021 ◽  
Vol Vol 66 (1) (January (1)) ◽  
pp. 1-5
Author(s):  
Jerome Goddard ◽  
Gerald Baker ◽  
Petra Jericke ◽  
Lawrence Birchman ◽  
Ethan Woodward ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Adult Female ◽  
Sequence Data ◽  
Molecular Data ◽  
Ultrastructural Analysis ◽  
Oxidase Subunit ◽  
Data Support ◽  
Partial 18S

Ultrastructural and molecular data are provided from a single adult female pentastomid opportunistically collected from a road-killed rattlesnake in Russell, KS. Ultrastructural data consisted of light and SEM microscopy of the pentastomid and its eggs, while molecular data consisted of partial 18S and 28S ribosomal sequences and a partial cytochrome c oxidase subunit 1 sequence from the same specimen used for SEM. Ultrastructural and molecular data support generic identification of the pentastomid as Porocephalus sp. These molecular data were also used with previously published pentastomid sequence data for a concatenated phylogenetic analysis, which support the current, morphology-based taxonomic placement of the genus.

scholarly journals Phylogenetic Analysis of a ‘Jewel Orchid’ Genus Goodyera (Orchidaceae) Based on DNA Sequence Data from Nuclear and Plastid Regions

PLoS ONE ◽  
2016 ◽  
Vol 11 (2) ◽  
pp. e0150366 ◽  
Author(s):  
Chao Hu ◽  
Huaizhen Tian ◽  
Hongqing Li ◽  
Aiqun Hu ◽  
Fuwu Xing ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequence ◽  
Sequence Data ◽  
Dna Sequence Data ◽  
Jewel Orchid

Generic Delimitations and Relationships of the Cape Genera Capnophyllum, Dasispermum, and Sonderina, the North African Genera Krubera and Stoibrax, and a New Monotypic Genus of the Subfamily Apioideae (Apiaceae)

2009 ◽  
Vol 34 (3) ◽  
pp. 580-594 ◽  
Author(s):  
Anthony R. Magee ◽  
Ben-Erik van Wyk ◽  
Patricia M. Tilney ◽  
Stephen R. Downie
Keyword(s):  
Sequence Data ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Sets ◽  
Monotypic Genus ◽  
North African ◽  
African Species ◽  
Dna Sequence Data ◽  
The North ◽  
Relationship Of

Generic circumscriptions and phylogenetic relationships of the Cape genera Capnophyllum, Dasispermum, and Sonderina are explored through parsimony and Bayesian inference analyses of nrDNA ITS and cpDNA rps16 intron sequences, morphology, and combined molecular and morphological data. The relationship of these genera with the North African genera Krubera and Stoibrax is also assessed. Analyses of both molecular data sets place Capnophyllum, Dasispermum, Sonderina, and the only southern African species of Stoibrax (S. capense) within the newly recognized Lefebvrea clade of tribe Tordylieae. Capnophyllum is strongly supported as monophyletic and is distantly related to Krubera. The monotypic genus Dasispermum and Stoibrax capense are embedded within a paraphyletic Sonderina. This complex is distantly related to the North African species of Stoibrax in tribe Apieae, in which the type species, Stoibrax dichotomum, occurs. Consequently, Dasispermum is expanded to include both Sonderina and Stoibrax capense. New combinations are formalized for Dasispermum capense, D. hispidum, D. humile, and D. tenue. An undescribed species from the Tanqua Karoo in South Africa is also closely related to Capnophyllum and the Dasispermum–Sonderina complex. The genus Scaraboides is described herein to accommodate the new species, S. manningii. This monotypic genus shares the dorsally compressed fruit and involute marginal wings with Capnophyllum, but is easily distinguished by its erect branching habit, green leaves, scabrous umbels, and fruit with indistinct median and lateral ribs, additional solitary vittae in each marginal wing, and parallel, closely spaced commissural vittae. Despite the marked fruit similarities with Capnophyllum, analyses of DNA sequence data place Scaraboides closer to the Dasispermum–Sonderina complex, with which it shares the erect habit, green (nonglaucous) leaves, and scabrous umbels.

scholarly journals Introducing Chaetothyriothecium, a new genus of Microthyriales

Phytotaxa ◽  
2014 ◽  
Vol 161 (2) ◽  
pp. 157 ◽  
Author(s):  
Sinang Hongsanan ◽  
Putarak Chomnunti ◽  
Pedro W. Crous ◽  
Ekachai Chukeatirote ◽  
Kevin D. Hyde
Keyword(s):  
New Genus ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Plant Host ◽  
Dna Sequence Data ◽  
Limited Sampling ◽  
Black Spots ◽  
Gene Data ◽  
Central Thailand

The order Microthyriales comprises foliar biotrophs, epiphytes, pathogens or saprobes that occur on plant leaves and stems. The order is relatively poorly known due to limited sampling and few in-depth studies. There is also a lack of phylogenetic data for these fungi, which form small black spots on plant host surfaces, but rarely cause any damage to the host. A "Microthyriaceae"-like fungus collected in central Thailand is described as a new genus, Chaetothyriothecium (type species Chaetothyriothecium elegans sp. nov.). Phylogenetic analyses of LSU gene data showed this species to cluster with other members of Microthyriales, where it is related to Microthyrium microscopicum the type of the order. The description of the new species is supplemented by DNA sequence data, which resolves its placement in the order. Little molecular data is available for this order, stressing the need for further collections and molecular data.

scholarly journals Liparis wenshanensis, a new orchid species from China: Evidence from morphological and molecular analyses

Phytotaxa ◽  
2015 ◽  
Vol 204 (4) ◽  
pp. 253 ◽  
Author(s):  
YONG-YU SU ◽  
YI-LANG HUANG ◽  
LI-JUN CHEN ◽  
PEI-WEN ZHANG ◽  
Zhong-Jian Liu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequence ◽  
Sequence Data ◽  
Detailed Comparison ◽  
Distinct Species ◽  
Systematic Position ◽  
Orchid Species ◽  
Molecular Analyses ◽  
Dna Sequence Data

A new orchid species, Liparis wenshanensis, discovered in Yunnan, China is described and illustrated in this study based on morphological and molecular analyses. A detailed comparison between the newly discovered orchid and other members of the genus, Liparis, was conducted. The new plant is characterized by the combination of the following features: a long rachis with 45 to 55 flowers; white sepals, petals and column; a greenish lip with a purplish center; strongly recurved and revolute dorsal sepals and petals; strongly recurved, oblong lateral sepals; a cordate lip that is strongly deflexed below the middle, with a two-lobed apex and a two-lobed callus at the base; an arcuate column with a lamella extending along the center almost to the stigma, and with a pair of broad wings toward the apex. These features distinguish the new orchid from all other known species of Liparis. We proceeded to a phylogenetic analysis to ascertain the systematic position of this enigmatic species. Molecular analyses based on nuclear ribosomal ITS and plastid matK DNA sequence data supports the recognition of L. wenshanensis as a distinct species.

Molecular data allow to elucidate the taxonomic placement of some Umbelliferae from Middle Asia and Afghanistan (Pinacantha, Ladyginia, Peucedanum mogoltavicum)

Phytotaxa ◽  
2018 ◽  
Vol 350 (1) ◽  
pp. 42 ◽  
Author(s):  
GALINA V. DEGTJAREVA ◽  
MICHAEL G. PIMENOV ◽  
TAHIR H. SAMIGULLIN
Keyword(s):  
Phylogenetic Tree ◽  
Dna Sequence ◽  
Sequence Data ◽  
Molecular Data ◽  
Systematic Position ◽  
New Combination ◽  
Dna Sequence Data ◽  
Middle Asia ◽  
Molecular Phylogenetic Tree ◽  
Molecular Phylogenetic

The systematic position of three Apiaceae-Apioideae taxa, Pinacantha porandica, Ladyginia bucharica and Peucedanum mogoltavicum, from Middle Asia and Afghanistan, is clarified based on nrITS DNA sequence data. In the molecular phylogenetic tree, the monotypic Pinacantha is placed in unresolved position within the Ferulinae. Although there is no morphological information on essential characters, we propose a new position of Pinacantha porandica within the genus Ferula. As a result a new combination Ferula porandica is proposed, with a new section Pinacantha to accommodate it. The attribution of Peucedanum mogoltavicum to Ferula has been confirmed, its correct name being Ferula lithophila. The genus Ladyginia should not be included in Ferula, its closest relatives being Mozaffariania and Glaucosciadium from the Glaucosciadium Clade.

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