Revisiting Y-chromosome detection methods: R-CQ and KAMY efficiently identify Y chromosome sequences in Tephritidae insect pests DOI Creative Commons
Dimitris Rallis, Konstantina T. Tsoumani, Flávia Krsticevic

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Ноя. 1, 2023

Abstract The detection and characterization of sex chromosome sequences is particularly important for major pest families, like the Tephritidae, whereas alternative management approaches, mainly involving male-only release programs, rely on ability to target manipulate sex-specific genomic regions, those Y chromosome. However, resolving detecting X at level requires careful consideration algorithmic outputs, especially in species where extensive markers are not available. Here, we present R-CQ KAMY, two computational methods developed chromosome-linked sequences. We evaluate their performance newly generated chromosome-level assemblies four Tephritid species: Ceratitis capitata, Bactrocera dorsalis, zonata Anastrepha ludens . By combining predictions with a manual curation process, assess strengths limitations each method provide robust dataset curated X- Y-linked Overall, our results establish framework studying poorly characterized lineages identifying supporting broader development chromosome-based managements systems.

Язык: Английский

Viral metagenomics of 100-year-old museum specimens highlights the long-term stability of RNA DOI Creative Commons
Alexandra Keene, Mark D. Stenglein

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Окт. 3, 2024

ABSTRACT Recovery of virus sequences from old samples provides an opportunity to study evolution and reconstruct historic virus-host interactions. Studies have mainly relied on DNA or RNA fixed frozen samples. The millions specimens in natural history museums represent a potential treasure trove sequences, but it is not clear how well survives We experimentally assessed the stability insects stored dry at room temperature over 72 weeks. Although molecules grew fragmented, yields remained surprisingly constant. RT-qPCR host showed minimal differences between dried specimens. To assess survival much older we acquired Drosophila North American entomological collections. recovered known novel viruses including several coding complete genomes fly collected 1908. found that virome D. melanogaster has changed little past century. Galbut virus, most prevalent infection contemporary , was also common Finally, investigated genomic physical features surviving RNA. survived chemically damaged, preferentially double stranded contained ribonucleoprotein complexes. This - especially certain types – can survive biological extended periods absence fixation freezing confirms utility provide clearer understanding evolution.

Язык: Английский

Процитировано

1
Genomics of a sexually selected sperm ornament and female preference in Drosophila DOI
Zeeshan Ali Syed, R. Antonio Gómez, Kirill Borziak

и другие.

Nature Ecology & Evolution, Год журнала: 2024, Номер unknown

Опубликована: Ноя. 22, 2024

Язык: Английский

Процитировано

1
The genome sequence of a drosophilid fruit fly, Drosophila histrio (Meigen, 1830) DOI Creative Commons
Darren J. Obbard

Wellcome Open Research, Год журнала: 2024, Номер 9, С. 56 - 56

Опубликована: Фев. 19, 2024

We present a genome assembly from an individual female Drosophila histrio (the drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The sequence is 189.2 megabases in span. Most of the scaffolded into 5 chromosomal pseudomolecules, including X sex chromosome. mitochondrial has also been assembled and 16.02 kilobases length.

Язык: Английский

Процитировано

0
FlaHMM: unistrand flamenco-like piRNA cluster prediction in Drosophila species using hidden Markov models DOI Creative Commons
Maria‐Anna Trapotsi, Jasper van Lopik, Gregory J. Hannon

и другие.

NAR Genomics and Bioinformatics, Год журнала: 2024, Номер 6(3)

Опубликована: Июль 2, 2024

PIWI-interacting RNAs (piRNAs) are a class of small non-coding that essential for transposon control in animal gonads. In

Язык: Английский

Процитировано

0
Temperature affects conspecific and heterospecific mating rates inDrosophila DOI Creative Commons
Jonathan A. Rader, Daniel R. Matute

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Окт. 28, 2024

ABSTRACT Behavioral mating choices and success are important factors in the development of reproductive isolation during speciation. Environmental conditions, especially temperature, can affect these key traits. conditions vary across, frequently delimit species’ geographic ranges. Pairing suboptimal with relative rarity conspecifics at range margins may set stage for hybridization. Despite importance behaviors as a barrier, general understanding interaction between behavioral environment is lacking, part because systematic studies rare. With this report, we begin to bridge that gap by providing evidence temperature has significant - but not consistent influence on success, thus Drosophila . We studied propensity four different temperatures among 14 species non-choice conspecific trials heterospecific two triads known regularly hybridize wild. show frequency varies significantly across 10°C (from 18ºC 28ºC), both 1:1 high-density en-masse trials, effect highly species-specific. also consistently low moderate some crosses. As decreases outside optimal thermal range, while matings remain constant, proportion relatively high. This result indicates modulate impose barriers rate More broadly, our results demonstrate truly understand how choice occur nature, they need be an environmental context.

Язык: Английский

Процитировано

0
PLOS Biology and the life sciences in 2024 DOI Creative Commons
Daniel Routledge

PLoS Biology, Год журнала: 2024, Номер 22(12), С. e3002985 - e3002985

Опубликована: Дек. 18, 2024

As we reach the end of 2024, celebrate an amazing year science for PLOS Biology and life sciences more broadly, thank everyone who continues to support journal.

Язык: Английский

Процитировано

0
Phylogenetic and functional diversity amongDrosophila-associated metagenome-assembled genomes DOI Creative Commons
Aaron A. Comeault, Alberto H. Orta,

David P. Fidler

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Дек. 22, 2024

Abstract Host-associated microbial communities can mediate interactions between their hosts and biotic abiotic environments. While much work has been done to document how microbiomes vary across species environments, less is known about the functional consequences of this variation. Here, we test for variation among drosophilid-associated bacteria by conducting Oxford Nanopore long-read sequencing generating metagenome-assembled genomes (MAGs) from six drosophilid fly collected in association with ‘anthropogenic’ environments North America, Europe, Africa. Using phylogenetic analyses, find that flies harbor a diverse microbiome includes core members closely related genera Gilliamella , Orbus Entomomonas Dysgonomonas others. Comparisons publicly available bacterial show many these are associated phylogenetically insect gut microbiomes. annotations predicted secondary metabolite biosynthetic gene clusters, MAGs belonging different orders content functions including metabolic capacity they respond environmental stressors. Our results provide evidence wild functionally communities. These findings highlight need quantify abundance function insect-associated others on performance

Язык: Английский

Процитировано

0
Revisiting Y-chromosome detection methods: R-CQ and KAMY efficiently identify Y chromosome sequences in Tephritidae insect pests DOI Creative Commons
Dimitris Rallis, Konstantina T. Tsoumani, Flávia Krsticevic

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Ноя. 1, 2023

Abstract The detection and characterization of sex chromosome sequences is particularly important for major pest families, like the Tephritidae, whereas alternative management approaches, mainly involving male-only release programs, rely on ability to target manipulate sex-specific genomic regions, those Y chromosome. However, resolving detecting X at level requires careful consideration algorithmic outputs, especially in species where extensive markers are not available. Here, we present R-CQ KAMY, two computational methods developed chromosome-linked sequences. We evaluate their performance newly generated chromosome-level assemblies four Tephritid species: Ceratitis capitata, Bactrocera dorsalis, zonata Anastrepha ludens . By combining predictions with a manual curation process, assess strengths limitations each method provide robust dataset curated X- Y-linked Overall, our results establish framework studying poorly characterized lineages identifying supporting broader development chromosome-based managements systems.

Язык: Английский

Процитировано

0