Exploring the unmapped DNA and RNA reads in a songbird genome

Mapping Intimacies ◽

10.1101/371963 ◽

2018 ◽

Cited By ~ 1

Author(s):

Veronika N. Laine ◽

Toni I. Gossmann ◽

Kees van Oers ◽

Marcel E. Visser ◽

Martien A.M. Groenen

Keyword(s):

Reference Genome ◽

De Novo ◽

Sequence Similarity ◽

Bird Species ◽

Parus Major ◽

Great Tit ◽

Biological Information ◽

Blood Parasites ◽

Sequence Contigs ◽

Unmapped Reads

AbstractBackgroundA widely used approach in next-generation sequencing projects is the alignment of reads to a reference genome. A significant percentage of reads, however, frequently remain unmapped despite improvements in the methods and hardware, which have enhanced the efficiency and accuracy of alignments. Usually unmapped reads are discarded from the analysis process, but significant biological information and insights can be uncovered from this data. We explored the unmapped DNA (normal and bisulfite treated) and RNA sequence reads of the great tit (Parus major) reference genome individual. From the unmapped reads we generated de novo assemblies. The generated sequence contigs were then aligned to the NCBI non-redundant nucleotide database using BLAST, identifying the closest known matching sequence.ResultsMany of the aligned contigs showed sequence similarity to sequences from different bird species and genes that were absent in the great tit reference assembly. Furthermore, there were also contigs that represented known P. major pathogenic species. Most interesting were several species of blood parasites such as Plasmodium and Trypanosoma.ConclusionsOur analyses revealed that meaningful biological information can be found when further exploring unmapped reads. It is possible to discover sequences that are either absent or misassembled in the reference genome and sequences that indicate infection or sample contamination. In this study we also propose strategies to aid the capture and interpretation of this information from unmapped reads.

A comparison of methodological approaches to the study of young sex chromosomes: A case study in Poecilia

10.1101/2021.11.29.470452 ◽

2021 ◽

Author(s):

Iulia Darolti ◽

Pedro Almeida ◽

Alison E Wright ◽

Judith E Mank

Keyword(s):

Sex Chromosomes ◽

Reference Genome ◽

Sex Chromosome ◽

De Novo ◽

Sequence Similarity ◽

Sequence Evolution ◽

Structural Variations ◽

Recombination Suppression ◽

Custom Made ◽

Methodological Approaches

Studies of sex chromosome systems at early stages of divergence are key to understanding the initial process and underlying causes of recombination suppression. However, identifying signatures of divergence in homomorphic sex chromosomes can be challenging due to high levels of sequence similarity between the X and the Y. Variations in methodological precision and underlying data can make all the difference between detecting subtle divergence patterns or missing them entirely. Recent efforts to test for X-Y sequence differentiation in the guppy have led to contradictory results. Here we apply different analytical methodologies to the same dataset to test for the accuracy of different approaches in identifying patterns of sex chromosome divergence in the guppy. Our comparative analysis reveals that the most substantial source of variation in the results of the different analyses lies in the reference genome used. Analyses using custom-made de novo genome assemblies for the focal species successfully recover a signal of divergence across different methodological approaches. By contrast, using the distantly related Xiphophorus reference genome results in variable patterns, due to both sequence evolution and structural variations on the sex chromosomes between the guppy and Xiphophorus. Changes in mapping and filtering parameters can additionally introduce noise and obscure the signal. Our results illustrate how analytical differences can alter perceived results and we highlight best practices for the study of nascent sex chromosomes.

Naseljavanje velike sjenice (Parus major L.) u mlade bjelogorične sastojine pomoću škrinjica za gniježđenje

Šumarski list ◽

10.31298/sl.143.7-8.6 ◽

2019 ◽

Vol 143 (7-8) ◽

pp. 352-352

Author(s):

Zdravko Dolenec

Keyword(s):

Bird Species ◽

Parus Major ◽

Wood Decay ◽

Great Tit ◽

Bird Diversity ◽

Cyanistes Caeruleus ◽

High Position ◽

Cavity Nesters ◽

Exotic Tree ◽

Tree Cavity

Conservation of the biodiversity of the forest ecosystems is becoming one of the priority issues in the forest management. Birds play an important role in the overall life of the forest ecosystem, for instance, as an important component of the trophic chains. Recent studies worldwide suggest decline in the population size and richness of the forest bird species, especially those nesting in the cavity of the forest trees. Special emphasis is placed on the secondary cavity nesters. In contrast to the primary cavity excavators, which are making a tree cavity by themselves, secondary cavity nesters for their nesting use cavities made by the primary cavity excavators or natural cavities formed by gradual wood decay process. In order to maintain bird diversity in the forests with a lack of nesting cavities, installation of the nestboxes is an important strategy in many countries. This applies mainly to young deciduous, coniferous stands, and monocultural plantations and areas afforested with exotic tree species. In this paper, occupation of the nestboxes in the young deciduous stands was investigated. According to some researchers, the colour of the nestbox and its height above the ground could be important factors of the nestbox occupation in some bird species. In this study, a total of 120 standard wooden nestboxes were used (60 green and 60 brown). Nestboxes were installed in pairs on a single tree, at a height of 4.0 to 4.5 m (“high” position) and 2.0 to 2.5 m (“low” position). On the first tree, the green nestbox was in the “high” position, on the next tree in the “low” position and so on. The aim of this study was to determine the degree of occupancy of the nestboxes with a respect to the colour and the position on the tree. Because of the intra- and interspecific competition, only one of the nestbox pair was inhabited. Of the total 60 nestbox pairs, 44 (73.3%) nestboxes were occupied; 35 (79, 5%) by a Great Tit (Parus major) and 9 (20.5%) by a Blue Tit (Cyanistes caeruleus). Great Tits occupied mainly “green” nestboxes (88.6%), with no significant differences in the height position of the chosen nestbox. In conclusion, the colour of the nestboxes is more important factor than the height position on the tree during the occupation of the nestboxes by a Great Tit.

Using nest-boxes in pine stands of the Augustów Forest

Forest Research Papers ◽

10.2478/frp-2019-0012 ◽

2019 ◽

Vol 80 (2) ◽

pp. 137-143

Author(s):

Grzegorz Zawadzki ◽

Jerzy Zawadzki ◽

Dorota Zawadzka ◽

Anna Sołtys

Keyword(s):

Breeding Success ◽

Bird Species ◽

Parus Major ◽

Great Tit ◽

Nest Boxes ◽

Coal Tit ◽

Constant Rate ◽

North Eastern ◽

Pine Stands ◽

Dendrocopos Major

Abstract In 2011–2014, the occupancy of nest-boxes by secondary hole-nesting birds and their breeding success was investigated in pine stands of the Augustów Forest (North-Eastern Poland). In the studied area of 12600 ha, the share of Scots Pine Pinus sylvestris L. in the stands was 92%. On average, birds occupied 54% and bats 3% of the 224–317 nest boxes controlled yearly. Nest boxes were also used by the Pygmy Owl Glaucidium passerinum L. as food caches. In total, broods of nine secondary hole-nesting species were observed, but only four bird species nested in each year of study. The most numerous species, occupying 53–60% of all boxes each year was the Pied Flycatcher Ficedula hypoleuca Pall. The Great Tit Parus major L. occupied 15–24% and the Coal Tit Periparus ater L. 10–12% of available nest-boxes, while the Redstart Phoenicurus phoenicurus L. used 2–7% of nest boxes. The yearly breeding success was highest for tits (Great Tit – 52–84%, Coal Tit – 50–72%) and strongly variable for the Pied Flycatchers – 38–78%. Broods were lost due to predation by martens Martes sp. (38%) and great spotted woodpeckers Dendrocopos major L. (6%) as well as nest competition (2%). The nest-boxes were occupied at a constant rate during the following four years after their exposition. Over 67% of the new nest-boxes were occupied annually which means new nest-boxes (up to 4 years) were occupied significantly more often than boxes older than 4 years.

Within and between population variations of incubation rhythm of great tits Parus major

Behaviour ◽

10.1163/1568539x-00003218 ◽

2014 ◽

Vol 151 (12-13) ◽

pp. 1827-1845 ◽

Cited By ~ 8

Author(s):

Elena Álvarez ◽

Emilio Barba

Keyword(s):

Latitudinal Gradient ◽

Bird Species ◽

Parus Major ◽

Great Tit ◽

Central European ◽

The North ◽

Trade Offs ◽

First Time ◽

Incubation Rhythm

Uniparental incubation frequently means that eggs remain unattended for periods where the incubating bird is foraging out of the nest. The determination of incubation rhythms (i.e., the length and temporal pattern of incubation sessions) and the factors which affect them are therefore important to understand life-history trade-offs. We described the incubation rhythm and its temporal variation of a southern European great tit Parus major population, and review previous studies to check for latitudinal trends. In the studied population, females were active (from first exit in the morning to last entrance in the evening) 12.5 h per day, performing incubation sessions (on-bouts) of 26 min and recesses (off-bouts) of 12 min. Thus, they were incubating around 67% of their active day, or 83% of the whole day. Attentiveness (% of time incubating) increased throughout the incubation period, due to shorter off-bouts. The active day was longer as the number of daylight hours increased. We show for the first time in a bird species that attentiveness was constant along a latitudinal gradient ranging from Norway to Spain. Females spend a higher proportion of the daylight hours out of the nest as latitude decreases, compensating incubation time during the longer nights. Off-bouts were shorter in central European populations, increasing towards the north and the south, while on-bouts showed no latitudinal variation.

Dawn Singing in the Great Tit (Parus Major): Mate Attraction, Mate Guarding, or Territorial Defence?

Behaviour ◽

10.1163/156853994x00244 ◽

1994 ◽

Vol 131 (1-2) ◽

pp. 115-138 ◽

Cited By ~ 76

Author(s):

Tore Slagsvold ◽

Glenn-Peter SÆTRE ◽

Svein Dale

Keyword(s):

Bird Species ◽

Parus Major ◽

Mate Guarding ◽

Passerine Bird ◽

Early Morning ◽

Great Tit ◽

Egg Laying ◽

Territorial Defence ◽

Resident Male ◽

Conflicting Demands

AbstractIn a number of passerine bird species, mated males sing at dawn and this song activity peaks in the fertile period of the mate. We present the hypothesis that an important function of such dawn singing is to maintain the territory. We suggest that mate guarding and territorial defence are demanding and often mutually exclusive activities. Losing paternity is so costly that males give priority to mate guarding. Males therefore use the early morning period, before their mate emerges from the roost, to claim territory ownership. We report some preliminary tests of this hypothesis from a study of great tits (Parus major). Simulating male intrusion by a playback experiment showed that the resident male was more often absent from central parts of the territory, following the mate, during the periods of nest building and egg laying than during incubation. This supports the assumption of conflicting demands between mate following and territorial defence. From the hypothesis we expected males to spend effort in defending their territory as soon as they were free to do so. Consistent with this prediction, we found that male song activity was high before the mate left the nest at dawn, when she temporarily visited the nest during the day, and when she entered the nest to roost at night. A female removal experiment showed that unmated males, having no mate to guard, sang as much at dawn as mated males. Only one of the eight widowed males succeeded to replace their mate. We discuss some alternative functions of dawn singing in the great tit, such as attraction of own mate, a replacement mate, and extra-pair mates. We conclude that the hypotheses are not mutually exclusive, and song may serve multiple purposes.

Uncovering missed indels by leveraging unmapped reads

10.1101/488601 ◽

2018 ◽

Author(s):

Mohammad Shabbir Hasan ◽

Xiaowei Wu ◽

Liqing Zhang

Keyword(s):

Breast Cancer ◽

Reference Genome ◽

Biological Information ◽

Breast Cancer Patients ◽

Short Reads ◽

Alignment Procedure ◽

Mutation Database ◽

Protein Functions ◽

Next Generation Sequencing Ngs ◽

Unmapped Reads

AbstractIn current practice, Next Generation Sequencing (NGS) applications start with mapping/aligning short reads to the reference genome, with the aim of identifying genetic mutations. While most short reads can be mapped to the reference genome accurately by existing alignment tools, a significant number remain unmapped and excluded from downstream analyses thus potentially discarding important biological information hidden in the unmapped reads. This paper describes Genesis-indel, a computational pipeline that explores the unmapped reads to identify novel indels that are initially missed in the alignment procedure. Genesis-indel is applied to the unmapped reads of 30 Breast Cancer patients from TCGA. Results show that the unmapped reads are conserved between the two subtypes of breast cancer investigated in this study and might contribute to the divergence between the subtypes. Genesis-indel is able to leverage the unmapped reads to identify 72,997 small to large novel high-quality indels previously not found in the original alignments and among them, 16,141 have not been annotated in the widely used mutation database. Statistical analysis shows that these new indels mostly altered the oncogenes and tumor suppressor genes. Functional annotation further reveals that these indels are strongly correlated to pathways of cancer and can have high to moderate impact on protein functions. Additionally, these indels overlap with the genes that are missed in the indels from the originally mapped reads and contribute to the tumorigenesis in multiple carcinomas.

Bird ringing report for Slovenia in 2017 and short overview of colour ringing in the period of 2012–2017

Acrocephalus ◽

10.1515/acro-2018-0010 ◽

2018 ◽

Vol 39 (178-179) ◽

pp. 129-163

Author(s):

Al Vrezec ◽

Dare Fekonja

Keyword(s):

Rare Species ◽

Bird Species ◽

Parus Major ◽

Great Tit ◽

Sterna Hirundo ◽

Barn Swallow ◽

Sylvia Atricapilla ◽

Cygnus Olor ◽

Mute Swans ◽

Ljubljansko Barje

Abstract In 2017, the Slovenian bird ringing scheme concluded 90 years of continuous ringing in the country. In 2017, we collected data on 176 bird species. We ringed 79,886 birds of 164 species, recorded 177 recoveries of birds ringed in Slovenia and found abroad, 295 foreign recoveries in Slovenia and 2,209 local recoveries. The most ringed species were the Blackcap Sylvia atricapilla and Great Tit Parus major and, among pulli in the nest, the Great Tit, White Stork Ciconia ciconia and Barn Swallow Hirundo rustica. In 2017, 12 colour ringing schemes were active in Slovenia. In the 2012-2017 period, the number of recoveries of birds ringed in Slovenia and found abroad increased significantly due to colour ringing, especially regarding the waterbirds. With colour ringing, the likelihood of recoveries is considerably greater (75.20 ± 91.36 recoveries per 100 ringed birds) than with metal ringing only (0.11 ± 0.08 recoveries per 100 ringed birds). Among local recoveries, the most frequent were the Mute Swans Cygnus olor and Common Terns Sterna hirundo, and among foreign recoveries the Black-headed Gulls Chroicocephalus ridibundus predominated. In 2017, the first Broad-billed Sandpiper Calidris falcinellus was ringed in Slovenia (Sečovlje salinas), and additional three rare species were ringed as well: the Yellow-browed Warbler Phylloscopus inornatus (Ljubljansko barje), Paddyfield Warbler Acrocephalus agricola (Ljubljansko barje) and Little Bunting Emberiza pusilla (Šentrupert).

A higher incidence of moult–breeding overlap in great tits across time is linked to an increased frequency of second clutches: a possible effect of global warming?

Animal Biodiversity and Conservation ◽

10.32800/abc.2021.44.0303 ◽

2021 ◽

pp. 303-315

Author(s):

I. Solís ◽

J. J. Sanz ◽

L. Imba ◽

E. Álvarez ◽

E. Barba

Keyword(s):

Global Warming ◽

Breeding Season ◽

Temporal Trend ◽

Bird Species ◽

Parus Major ◽

Great Tit ◽

Breeding Birds ◽

The Other ◽

First Year ◽

Start Date

The rise of temperatures due to global warming is related to a lengthening of the breeding season in many bird species. This allows more pairs to attempt two clutches within the breeding season, thus finishing their breeding activity later in the season and therefore potentially overlapping these with post–breeding moult. We tested whether this occurred in two Spanish great tit Parus major populations. The proportion of pairs laying second clutches increased from 1 % to 32 % over the study period in one of the populations (Sagunto, 1995–2019), while it did not change in the other (Quintos, 2006–2019; mean 5 %). We did not find any temporal trend for moult start date of late–breeding birds in any population. The proportion of individuals of both sexes that overlapped moult and breeding increased in Sagunto. For this latter population, sex and age, but not clutch type, contributed to the variability in the probability of overlapping in late–breeding individuals, this being higher for first–year males and lower for older females.

Poročilo o obročkanju ptic v Sloveniji v letu 2016 in pojavljanje mušje listnice Phylloscopus inornatus v 25 letih v Sloveniji

Acrocephalus ◽

10.1515/acro-2017-0011 ◽

2017 ◽

Vol 38 (174-175) ◽

pp. 171-202

Author(s):

Al Vrezec ◽

Dare Fekonja

Keyword(s):

Rare Species ◽

Bird Species ◽

Parus Major ◽

Great Tit ◽

Sylvia Atricapilla ◽

Passer Montanus ◽

Cygnus Olor ◽

White Storks ◽

Emberiza Melanocephala ◽

Mute Swans

Abstract In 2016, data on 176 bird species were gathered during bird ringing activities in Slovenia. A total of 65,711 birds of 165 different species were ringed. Furthermore, 148 recoveries of birds ringed in Slovenia and found abroad, 245 foreign recoveries in Slovenia and 1840 local recoveries were made. The most frequently ringed species was the Blackcap Sylvia atricapilla. Among the ringed nestlings, Great Tits Parus major, Tree Sparrows Passer montanus and White Storks Ciconia ciconia predominated. Considering recoveries of birds ringed or found abroad, the most frequent were finds based on colour rings, especially of Black-headed Gulls Chroicocephalus ridibundus, Mute Swans Cygnus olor and Common Terns Sterna hirundo. As far as local recoveries are concerned, most data were collected for Great Tit and Siskin Spinus spinus. Among rare species, two Yellow-browed Warblers Phylloscopus inornatus were ringed, one Paddyfield Warbler Acrocephalus agricola, one Little Emberiza pusilla and one Black-headed Bunting Emberiza melanocephala, the latter as a singing male, which probably also bred in 2016. The catch frequency of the Yellow-browed Warblers has indeed been increasing in Slovenia in the last 25 years, but this is still a rare and irregular vagrant on autumn migration.

Evaluating the role of reference-genome phylogenetic distance on evolutionary inference

10.1101/2021.03.03.433733 ◽

2021 ◽

Author(s):

Aparna Prasad ◽

Eline D Lorenzen ◽

Michael V Westbury

Keyword(s):

Genetic Diversity ◽

Reference Genome ◽

De Novo ◽

Bird Species ◽

Phylogenetic Distance ◽

Runs Of Homozygosity ◽

Target Species ◽

Genome Wide ◽

Evolutionary Inference

AbstractWhen a high-quality genome assembly of a target species is unavailable, an option to avoid the costly de novo assembly process is a mapping-based assembly. However, mapping shotgun data to a distant relative may lead to biased or erroneous evolutionary inference. Here, we used short-read data from a mammal and a bird species (beluga and rowi kiwi) to evaluate whether reference genome phylogenetic distance can impact downstream demographic (PSMC) and genetic diversity (heterozygosity, runs of homozygosity) analyses. We mapped to assemblies of species of varying phylogenetic distance (conspecific to genome-wide divergence of >7%), and de novo assemblies created using cross-species scaffolding. We show that while reference genome phylogenetic distance has an impact on demographic analyses, it is not pronounced until using a reference genome with >3% divergence from the target species. When mapping to cross-species scaffolded assemblies, we are unable to replicate the original beluga demographic analyses, but can with the rowi kiwi, presumably reflecting the more fragmented nature of the beluga assemblies. As for genetic diversity estimates, we find that increased phylogenetic distance has a pronounced impact; heterozygosity estimates deviate incrementally as phylogenetic distance increases. Moreover, runs of homozygosity are removed when mapping to any non-conspecific assembly. However, these biases can be reduced when mapping to a cross-species scaffolded assembly. Taken together, our results show that caution should be exercised when selecting the reference genome for mapping assemblies. Cross-species scaffolding may offer a way to avoid a costly, traditional de novo assembly, while still producing robust, evolutionary inference.