scholarly journals Exome sequences of toque macaques (Macaca sinica) of Sri Lanka reveal many amino acid changes

2019 ◽  
Author(s):  
Nilmini Hettiarachchi ◽  
Naoki Osada ◽  
Hirofumi Nakaoka ◽  
Takashi Hayakawa ◽  
Ituro Inoue ◽  
...  
Keyword(s):  
Sri Lanka ◽  
Macaca Mulatta ◽  
Reference Genome ◽  
Psychological Disorder ◽  
Model Organisms ◽  
Evolutionary Relationships ◽  
Island Population ◽  
Macaca Sinica ◽  
First Time ◽  
Geographical Locations

AbstractMacaques are one of the most widely used model organisms in biomedical research. Macaca mulatta and M. fascicularis are currently being used for toxicology, HIV, diabetes, neuroscience and psychiatric and psychological disorder researches. Many studies have been conducted on M. mulatta and M. fascicularis genomes for this purpose in order to understand the genomic properties of these species. Several M. fascicularis individuals from different geographical locations and also M. mulatta genomes have been sequenced and studied in depth for the purpose of understanding the phylogenetic and evolutionary relationships between various macaque populations. But still a gap in knowledge remains for other macaque populations such as the Sinica group. In this study for the very first time, we sequenced the exome of toque macaques (M. sinica), an endemic island population of Sri Lanka. Here we confirmed that M. sinica and M. thibetana cluster together and are closely related, also the three distinct phylogenetic groupings of fascicularis and sinica. We also found that M. sinica has less number of polymorphisms with respect to the reference genome M. mulatta signifying the smaller and restricted population size of this species.

scholarly journals Genome Assembly of the Canadian Two-row Malting Barley Cultivar AAC Synergy

2021 ◽  
Author(s):  
Wayne Xu ◽  
James R Tucker ◽  
Wubishet A Bekele ◽  
Frank M You ◽  
Yong-Bi Fu ◽  
...  
Keyword(s):  
Reference Genome ◽  
Single Copy ◽  
Barley Cultivar ◽  
Malting Barley ◽  
Orthologous Genes ◽  
Hordeum Vulgare L ◽  
Chromosome Conformation ◽  
Mate Pair ◽  
Genome Assemblies ◽  
First Time

Abstract Barley (Hordeum vulgare L.) is one of the most important global crops. The six-row barley cultivar Morex reference genome has been used by the barley research community worldwide. However, this reference genome can have limitations when used for genomic and genetic diversity analysis studies, gene discovery, and marker development when working in two-row germplasm that is more common to Canadian barley. Here we assembled, for the first time, the genome sequence of a Canadian two-row malting barley, cultivar AAC Synergy. We applied deep Illumina paired-end reads, long mate-pair reads, PacBio sequences, 10X chromium linked read libraries, and chromosome conformation capture sequencing (Hi-C) to generate a contiguous assembly. The genome assembled from super-scaffolds had a size of 4.85 Gb, N50 of 2.32 Mb and an estimated 93.9% of complete genes from a plant database (BUSCO, benchmarking universal single-copy orthologous genes). After removal of small scaffolds (< 300 Kb), the assembly was arranged into pseudomolecules of 4.14 Gb in size with seven chromosomes plus unanchored scaffolds. The completeness and annotation of the assembly were assessed by comparing it with the updated version of six-row Morex and recently released two-row Golden Promise genome assemblies.

scholarly journals In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Bison bonasus))—Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2226
Author(s):  
Sazia Kunvar ◽  
Sylwia Czarnomska ◽  
Cino Pertoldi ◽  
Małgorzata Tokarska
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Bos Taurus ◽  
Model Organism ◽  
Genotyping By Sequencing ◽  
Model Organisms ◽  
European Bison ◽  
Model Animal ◽  
Pcr Duplicates ◽  
Species Specific

The European bison is a non-model organism; thus, most of its genetic and genomic analyses have been performed using cattle-specific resources, such as BovineSNP50 BeadChip or Illumina Bovine 800 K HD Bead Chip. The problem with non-specific tools is the potential loss of evolutionary diversified information (ascertainment bias) and species-specific markers. Here, we have used a genotyping-by-sequencing (GBS) approach for genotyping 256 samples from the European bison population in Bialowieza Forest (Poland) and performed an analysis using two integrated pipelines of the STACKS software: one is de novo (without reference genome) and the other is a reference pipeline (with reference genome). Moreover, we used a reference pipeline with two different genomes, i.e., Bos taurus and European bison. Genotyping by sequencing (GBS) is a useful tool for SNP genotyping in non-model organisms due to its cost effectiveness. Our results support GBS with a reference pipeline without PCR duplicates as a powerful approach for studying the population structure and genotyping data of non-model organisms. We found more polymorphic markers in the reference pipeline in comparison to the de novo pipeline. The decreased number of SNPs from the de novo pipeline could be due to the extremely low level of heterozygosity in European bison. It has been confirmed that all the de novo/Bos taurus and Bos taurus reference pipeline obtained SNPs were unique and not included in 800 K BovineHD BeadChip.

New record of Hipposideros speoris (Chiroptera: Hipposideridae) from Myanmar hidden in the National Zoological Collections of the Zoological Survey of India

Mammalia ◽  
2019 ◽  
Vol 83 (5) ◽  
pp. 515-517
Author(s):  
Tauseef Hamid Dar ◽  
Manokaran Kamalakannan ◽  
Chinnadurai Venkatraman ◽  
Kailash Chandra
Keyword(s):  
Sri Lanka ◽  
New Record ◽  
Zoological Survey ◽  
Museum Specimen ◽  
First Time

Abstract Hipposideros speoris is a small-sized leaf-nosed bat and was thought to be restricted to India and Sri Lanka. Based on a single museum specimen preserved in alcohol housed in the National Zoological Collections of the Zoological Survey of India, we report and confirm the presence of H. speoris for the first time in Pyay, Myanmar.

AStrap: identification of alternative splicing from transcript sequences without a reference genome

2018 ◽  
Vol 35 (15) ◽  
pp. 2654-2656 ◽  
Author(s):  
Guoli Ji ◽  
Wenbin Ye ◽  
Yaru Su ◽  
Moliang Chen ◽  
Guangzao Huang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Alternative Splicing ◽  
Single Molecule ◽  
Reference Genome ◽  
De Novo ◽  
Supplementary Information ◽  
Model Organisms ◽  
Sequencing Data ◽  
Extensive Evaluation ◽  
Reference Genomes

Abstract Summary Alternative splicing (AS) is a well-established mechanism for increasing transcriptome and proteome diversity, however, detecting AS events and distinguishing among AS types in organisms without available reference genomes remains challenging. We developed a de novo approach called AStrap for AS analysis without using a reference genome. AStrap identifies AS events by extensive pair-wise alignments of transcript sequences and predicts AS types by a machine-learning model integrating more than 500 assembled features. We evaluated AStrap using collected AS events from reference genomes of rice and human as well as single-molecule real-time sequencing data from Amborella trichopoda. Results show that AStrap can identify much more AS events with comparable or higher accuracy than the competing method. AStrap also possesses a unique feature of predicting AS types, which achieves an overall accuracy of ∼0.87 for different species. Extensive evaluation of AStrap using different parameters, sample sizes and machine-learning models on different species also demonstrates the robustness and flexibility of AStrap. AStrap could be a valuable addition to the community for the study of AS in non-model organisms with limited genetic resources. Availability and implementation AStrap is available for download at https://github.com/BMILAB/AStrap. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Rapture-ready darters: choice of reference genome and genotyping method (whole-genome or sequence capture) influence population genomic inference in Etheostoma

2020 ◽  
Author(s):  
Brendan N. Reid ◽  
Rachel L. Moran ◽  
Christopher J. Kopack ◽  
Sarah W. Fitzpatrick
Keyword(s):  
Reference Genome ◽  
Sequence Data ◽  
Low Cost ◽  
Read Depth ◽  
Model Organisms ◽  
Whole Genome ◽  
Reduced Representation ◽  
Sequence Capture ◽  
Population Genomic ◽  
The Impact

AbstractResearchers studying non-model organisms have an increasing number of methods available for generating genomic data. However, the applicability of different methods across species, as well as the effect of reference genome choice on population genomic inference, are still difficult to predict in many cases. We evaluated the impact of data type (whole-genome vs. reduced representation) and reference genome choice on data quality and on population genomic and phylogenomic inference across several species of darters (subfamily Etheostomatinae), a highly diverse radiation of freshwater fish. We generated a high-quality reference genome and developed a hybrid RADseq/sequence capture (Rapture) protocol for the Arkansas darter (Etheostoma cragini). Rapture data from 1900 individuals spanning four darter species showed recovery of most loci across darter species at high depth and consistent estimates of heterozygosity regardless of reference genome choice. Loci with baits spanning both sides of the restriction enzyme cut site performed especially well across species. For low-coverage whole-genome data, choice of reference genome affected read depth and inferred heterozygosity. For similar amounts of sequence data, Rapture performed better at identifying fine-scale genetic structure compared to whole-genome sequencing. Rapture loci also recovered an accurate phylogeny for the study species and demonstrated high phylogenetic informativeness across the evolutionary history of the genus Etheostoma. Low cost and high cross-species effectiveness regardless of reference genome suggest that Rapture and similar sequence capture methods may be worthwhile choices for studies of diverse species radiations.

scholarly journals Report on first certificate course on applied physiology of pain, analgesia, anesthesia, and euthanasia for laboratory animals held in Sri Lanka

2018 ◽  
Vol 42 (2) ◽  
pp. 263-266
Author(s):  
Mangala Gunatilake
Keyword(s):  
Sri Lanka ◽  
Laboratory Animal ◽  
Pain Perception ◽  
Anesthesia Machine ◽  
Laboratory Animals ◽  
Comparative Biology ◽  
Human Beings ◽  
Unpleasant Sensation ◽  
Applied Physiology ◽  
First Time

Similar to human beings, pain is an unpleasant sensation experienced by animals as well. There is no exception when the animals are subjected to experimental procedures. Our duty as researchers/scientists is to prevent or minimize the pain in animals so as to lessen their suffering and distress during experimental procedures. The basics of the physiology of pain and pain perception, analgesia, anesthesia, and euthanasia of laboratory animals were included to complete the program, before the practical part was attempted and before advanced topics, such as comparison of anesthetic combinations, were discussed. Therefore, this course was organized in Sri Lanka for the first time in collaboration with the Comparative Biology Centre of Newcastle University, UK. During this course, we were able to demonstrate how an anesthesia machine could be used in laboratory animal anesthesia for the first time in the country. None of the animal houses in the country were equipped with an anesthesia machine at the time of conducting the course.

Clonal propagation through stem cuttings and air layering in Syzygium caryophyllatum (L.) Alston an endemic tree Species of the Western Ghats and Sri Lanka

2016 ◽  
Vol 23 (2) ◽  
pp. 85-87
Author(s):  
Abdul Hussain ◽  
C. Anilkumar
Keyword(s):  
Sri Lanka ◽  
Tree Species ◽  
Western Ghats ◽  
Clonal Propagation ◽  
Stem Cuttings ◽  
Resource Base ◽  
Natural Habitats ◽  
Ideal Tool ◽  
First Time ◽  
The Western Ghats

Rooting trials conducted with stem cuttings and air layering in Syzygium caryophyllatum (L.) Alston, an important medicinal and fruit plant gave promising results after treatment with auxins such as IAA, IBA and NAA in different concentrations. Both stem cuttings and air layering from 10 year old plants have resulted a maximum rooting of 80% and 70% respectively through the application of IBA-1000ppm, in their natural habitats. The plants developed from stem cuttings and air layering was also survived with 90% success. Thus the standardized clonal propagation method in S. caryophyllatum through stem cutting and air layering reported for the first time can be taken as an ideal tool for the multiplication and subsequent resource base utilization of the species since the populations are prone to endangerment in its habitats.

The effect of biologically active supplements on blood hematological parameters of male rhesus macaques

2020 ◽  
Author(s):  
Н.В. Гапонов ◽  
Г.Л. Яговенко ◽  
А.Н. Степанова
Keyword(s):  
Macaca Mulatta ◽  
Rhesus Macaques ◽  
Hematological Parameters ◽  
Biologically Active ◽  
Model Organisms ◽  
Blood Morphology ◽  
Platelet Concentration ◽  
Deuterium Depleted Water ◽  
In The Beginning ◽  
Male Rhesus

Как показали многочисленные исследования, морфологический состав крови зависит от многих факторов, в частности таких, как условия кормления и содержания, возраст подопытных объектов. Однако отсутствуют данные о влиянии биологически активных добавок, таких как хлорелла, «Бактистатин», вода со сниженной концентрацией дейтерия, на гематологические показатели. Приматы обладают высоким анатомо-физиологическим сходством с человеком, поэтому являются незаменимой моделью для воспроизведения различных патологических и токсических состояний человека. Приматы вида макака-резус (Macaca mulatta) являются наиболее удобными и востребованными в работе, широко используются в медико-биологических исследованиях. Для корректной оценки воздействия биологически активных добавок (БАД) на организмы приматов необходимы достоверные сведения о функционировании их кроветворной системы. По результатам нашего исследования в начале опыта количество эритроцитов в крови самцов макак-резусов во всех исследуемых группах было незначительно увеличено относительно физиологической нормы (5–6,2 млн в 1 мм3). Эта закономерность может быть связана со значительным увеличением температуры окружающей среды к моменту начала постановки опыта и не связано с влиянием БАД. Подобная закономерность наблюдалась и по остальным показателям. Так, уровень тромбоцитов в начале эксперимента находился в пределах референтных показателей — от 200 до 400 млрд/л, за исключением самцов 2-й опытной группы. В этой группе наблюдалось незначительное увеличение тромбоцитов — на 17,60 млрд/л, или на 4,40% от максимально допустимых значений референтных показателей. Результаты анализов крови в конце эксперимента показали, что у всех самцов макак-резусов в опытных группах в результате применения БАД количество тромбоцитов приблизилось к физиологической норме. На основании чего можно сделать вывод, что применение суспензии хлореллы, сухой хлореллы, «Бактистатина» и воды с пониженным содержанием дейтерия не приводило к критическому отклонению морфологических показателей крови, что, в свою очередь, даёт возможность применять БАД в рационах кормления обезьян. Blood morphology depends on many factors, particularly feeding, welfare and age of animals. The influence of biologically active supplements (BAS) such as chlorella, “Baktistatin”, and deuterium-depleted water on blood hematological parameters remains open to question. Primates are quite similar to humans in anatomy and physiology and hence are perfect model organisms when testing various pathological and toxic processes. Macaca mulatta is commonly used in research. To analyze the effect of BAS on primate organism the blood test is required. In the beginning of the experiment the concentration of red blood cells (RBC) exceeded slightly physiologically normal state in all the groups (5–6.2 million/mm3). This could possibly be a result of hot conditions. Same was true for other parameters. Platelet concentration was normal and varied within 200–400 billion/l in the beginning, except for the males of the second group. The second group showed insignificant increase in platelet concentration — by 17.60 billion/l, or 4.40%. Feeding male rhesus macaques with BAS optimized platelet concentration. Chlorella suspension, dry chlorella, “Baktistatin”, and deuterium-depleted water had no critical influence on blood morphology and, therefore, could be used in primate diet.

scholarly journals Vertical profiles of sub-micron aerosol single scattering albedo over Indian region immediately before monsoon onset and during its development: Research from the SWAAMI field campaign

2019 ◽  
Author(s):  
Mohanan R. Manoj ◽  
Sreedharan K. Satheesh ◽  
Krishnaswamy K. Moorthy ◽  
Hugh Coe
Keyword(s):  
Active Phase ◽  
Single Scattering ◽  
Single Scattering Albedo ◽  
Development Research ◽  
Aerosol Absorption ◽  
South West ◽  
Aerosol Scattering ◽  
First Time ◽  
Geographical Locations

Abstract. Vertical structures of aerosol single scattering albedo (SSA), from near the surface through the free troposphere, have been estimated for the first time at distinct geographical locations over the Indian mainland and adjoining oceans, using in-situ measurements of aerosol scattering and absorption coefficients aboard the FAAM BAe-146 aircraft during the South West Asian Aerosol Monsoon Interactions (SWAAMI) campaign from June to July 2016. These are used to examine the spatial variation of SSA profiles and also to characterize its transformation from just prior to the onset of Indian Summer Monsoon (June 2016) to its active phase (July 2016). Very strong aerosol absorption, with SSA values as low as 0.7, persisted in the lower altitudes (

Clidicus minilankanus sp. n., with notes on remaining Sri Lankan Clidicus species (Coleoptera, Staphylinidae, Scydmaeninae)

Zootaxa ◽  
2020 ◽  
Vol 4718 (1) ◽  
pp. 87-94
Author(s):  
PAWEŁ JAŁOSZYŃSKI
Keyword(s):  
Phylogenetic Analysis ◽  
Sri Lanka ◽  
Junior Synonym ◽  
Monophyletic Group ◽  
Evolutionary Relationships ◽  
Sri Lankan

Until now, four species of Clidicus Laporte were found in Sri Lanka, three known from female specimens only. Clidicus minilankanus sp. n., is described, and compared to all remaining sympatric congeners. The Sri Lankan species may form a monophyletic group characterized by several morphological oddities: the head only slightly impressed posteromedially, with a large portion of vertex and frons not divided longitudinally; the pronotum quadrangular and flattened, with vestigial or absent posterior ‘collar’, and the transverse groove that demarcates it from the disc lacking pits or even entirely or partly obliterated; and the metaventrite strongly shortened, so that meso- and metacoxae are nearly adjacent. These characters may justify resurrecting Erineus Walker, a junior synonym of Clidicus (proposed for the first described Sri Lankan species, C. monstrosus (Walker)), as a valid name for a subgenus. This problem must be addressed by a phylogenetic analysis of all Clidicus species, to establish evolutionary relationships within this interesting genus. 

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