Volume 19, issue 1, December 2018

895 articles in this issue

Female-specific SNP markers provide insights into a WZ/ZZ sex determination system for mud crabs Scylla paramamosain, S. tranquebarica and S. serrata with a rapid method for genetic sex identification

Authors (first, second and last of 15)
- Xi Shi
- Khor Waiho
- Hongyu Ma
- Content type: Research article
- Open Access
- Published: 29 December 2018
- Article: 981
This is part of 1 collection:
Multicellular invertebrate genomics
Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes

Authors
- Boas Pucker
- Samuel F. Brockington
- Content type: Research article
- Open Access
- Published: 29 December 2018
- Article: 980
This is part of 1 collection:
Plant genomics
Multiple interspecific hybridization and microsatellite mutations provide clonal diversity in the parthenogenetic rock lizard Darevskia armeniaca

Authors (first, second and last of 9)
- Anastasiya E. Girnyk
- Andrey A. Vergun
- Alexey P. Ryskov
- Content type: Research article
- Open Access
- Published: 29 December 2018
- Article: 979
This is part of 1 collection:
Comparative and evolutionary genomics
Analysis of Dendrobium huoshanense transcriptome unveils putative genes associated with active ingredients synthesis

Authors (first, second and last of 6)
- Yingdan Yuan
- Maoyun Yu
- Jinchi Zhang
- Content type: Research article
- Open Access
- Published: 29 December 2018
- Article: 978
This is part of 1 collection:
Plant genomics
Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

Authors (first, second and last of 6)
- Weiwen Wang
- Miriam Schalamun
- Robert Lanfear
- Content type: Methodology article
- Open Access
- Published: 29 December 2018
- Article: 977
This is part of 1 collection:
Plant genomics
Evolutionary, structural and functional analysis of the caleosin/peroxygenase gene family in the Fungi

Authors (first, second and last of 6)
- Farzana Rahman
- Mehedi Hassan
- Denis J. Murphy
- Content type: Research article
- Open Access
- Published: 28 December 2018
- Article: 976
This is part of 1 collection:
Comparative and evolutionary genomics
Characterization of miRNA profiles in the mammary tissue of dairy cattle in response to heat stress

Authors (first, second and last of 10)
- Qiuling Li
- Chunhong Yang
- Jifeng Zhong
- Content type: Research article
- Open Access
- Published: 28 December 2018
- Article: 975
This is part of 1 collection:
Transcriptomic methods
Systematics for types and effects of DNA variations

Authors
- Mauno Vihinen
- Content type: Review
- Open Access
- Published: 28 December 2018
- Article: 974
This is part of 1 collection:
Comparative and evolutionary genomics
Genome rearrangements in Escherichia coli during de novo acquisition of resistance to a single antibiotic or two antibiotics successively

Authors (first, second and last of 5)
- Marloes Hoeksema
- Martijs J. Jonker
- Benno H. ter Kuile
- Content type: Research article
- Open Access
- Published: 27 December 2018
- Article: 973
This is part of 1 collection:
Prokaryote microbial genomics
Genome-wide association study of Mycobacterium avium subspecies Paratuberculosis infection in Chinese Holstein

Authors (first, second and last of 13)
- Yahui Gao
- Jianping Jiang
- Dongxiao Sun
- Content type: Research article
- Open Access
- Published: 27 December 2018
- Article: 972
This is part of 1 collection:
Non-human and non-rodent vertebrate genomics
Discerning novel splice junctions derived from RNA-seq alignment: a deep learning approach

Authors (first, second and last of 4)
- Yi Zhang
- Xinan Liu
- Jinze Liu
- Content type: Research article
- Open Access
- Published: 27 December 2018
- Article: 971
This is part of 1 collection:
Transcriptomic methods
Identification of putative fecundity-related gustatory receptor genes in the brown planthopper Nilaparvata lugens

Authors (first, second and last of 8)
- Kui Kang
- Pan Yang
- Wen-Qing Zhang
- Content type: Research article
- Open Access
- Published: 27 December 2018
- Article: 970
This is part of 1 collection:
Multicellular invertebrate genomics
Changes in H3K27ac following lipopolysaccharide stimulation of nasopharyngeal epithelial cells

Authors
- Lisa Borghini
- Martin Hibberd
- Sonia Davila
- Content type: Research article
- Open Access
- Published: 27 December 2018
- Article: 969
This is part of 1 collection:
Human and rodent genomics
Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn’s disease discovered using metagenomic and genomic analyses

Authors (first, second and last of 28)
- Alexander V. Tyakht
- Alexander I. Manolov
- Vadim M. Govorun
- Content type: Research article
- Open Access
- Published: 27 December 2018
- Article: 968
This is part of 1 collection:
Prokaryote microbial genomics
Important cardiac transcription factor genes are accompanied by bidirectional long non-coding RNAs

Authors (first, second and last of 6)
- Yutaro Hori
- Yoko Tanimoto
- Jun K. Takeuchi
- Content type: Research article
- Open Access
- Published: 27 December 2018
- Article: 967
This is part of 1 collection:
Human and rodent genomics
Plant stress RNA-seq Nexus: a stress-specific transcriptome database in plant cells

Authors (first, second and last of 4)
- Jian-Rong Li
- Chun-Chi Liu
- Yu-Ting Chen
- Content type: Database
- Open Access
- Published: 27 December 2018
- Article: 966
This is part of 1 collection:
Plant genomics
Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.

Authors (first, second and last of 4)
- Olga O. Bochkareva
- Elena V. Moroz
- Mikhail S. Gelfand
- Content type: Research article
- Open Access
- Published: 27 December 2018
- Article: 965
This is part of 1 collection:
Comparative and evolutionary genomics
ACES: a machine learning toolbox for clustering analysis and visualization

Authors (first, second and last of 5)
- Jiangning Gao
- Görel Sundström
- Manfred G. Grabherr
- Content type: Software
- Open Access
- Published: 27 December 2018
- Article: 964
This is part of 1 collection:
Human and rodent genomics
Genome-wide analysis of consistently RNA edited sites in human blood reveals interactions with mRNA processing genes and suggests correlations with cell types and biological variables

Authors (first, second and last of 7)
- Edoardo Giacopuzzi
- Massimo Gennarelli
- Alessandro Barbon
- Content type: Research article
- Open Access
- Published: 27 December 2018
- Article: 963
This is part of 1 collection:
Human and rodent genomics
Genome-wide identification of SERK genes in apple and analyses of their role in stress responses and growth

Authors (first, second and last of 8)
- Liwei Zheng
- Juanjuan Ma
- Mingyu Han
- Content type: Research article
- Open Access
- Published: 27 December 2018
- Article: 962
This is part of 1 collection:
Plant genomics
Comparative analysis of the mitochondrial genomes of oriental spittlebug trible Cosmoscartini: insights into the relationships among closely related taxa

Authors (first, second and last of 4)
- Tianjuan Su
- Bo He
- Aiping Liang
- Content type: Research article
- Open Access
- Published: 27 December 2018
- Article: 961
This is part of 1 collection:
Comparative and evolutionary genomics
ddSeeker: a tool for processing Bio-Rad ddSEQ single cell RNA-seq data

Authors (first, second and last of 11)
- Dario Romagnoli
- Giulia Boccalini
- Matteo Benelli
- Content type: Software
- Open Access
- Published: 24 December 2018
- Article: 960
This is part of 1 collection:
Transcriptomic methods
Comparison of reprogramming factor targets reveals both species-specific and conserved mechanisms in early iPSC reprogramming

Authors (first, second and last of 9)
- Kai Fu
- Constantinos Chronis
- Matteo Pellegrini
- Content type: Research article
- Open Access
- Published: 22 December 2018
- Article: 956
This is part of 1 collection:
Comparative and evolutionary genomics
High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing

Authors (first, second and last of 6)
- Li-Yi Xu
- Li-Yuan Wang
- Hao Cheng
- Content type: Research article
- Open Access
- Published: 22 December 2018
- Article: 955
This is part of 1 collection:
Plant genomics
Kinetics of the chromosome 14 microRNA cluster ortholog and its potential role during placental development in the pregnant mare

Authors (first, second and last of 7)
- Pouya Dini
- Peter Daels
- Barry A. Ball
- Content type: Research article
- Open Access
- Published: 20 December 2018
- Article: 954
This is part of 1 collection:
Non-human and non-rodent vertebrate genomics
Power in pairs: assessing the statistical value of paired samples in tests for differential expression

Authors (first, second and last of 4)
- John R. Stevens
- Jennifer S. Herrick
- Martha L. Slattery
- Content type: Methodology article
- Open Access
- Published: 20 December 2018
- Article: 953
This is part of 1 collection:
Transcriptomic methods
Genome sequence of walking catfish (Clarias batrachus) provides insights into terrestrial adaptation

Authors (first, second and last of 19)
- Ning Li
- Lisui Bao
- Zhanjiang Liu
- Content type: Research article
- Open Access
- Published: 20 December 2018
- Article: 952
This is part of 1 collection:
Non-human and non-rodent vertebrate genomics
Identification and characterization of SSR, SNP and InDel molecular markers from RNA-Seq data of guar (Cyamopsis tetragonoloba, L. Taub.) roots

Authors
- Omika Thakur
- Gursharn Singh Randhawa
- Content type: Research article
- Open Access
- Published: 20 December 2018
- Article: 951
This is part of 1 collection:
Plant genomics
Complete chloroplast genome sequence of Betula platyphylla: gene organization, RNA editing, and comparative and phylogenetic analyses

Authors (first, second and last of 5)
- Sui Wang
- Chuanping Yang
- Guan-Zheng Qu
- Content type: Research article
- Open Access
- Published: 20 December 2018
- Article: 950
This is part of 1 collection:
Plant genomics
Comparative transcriptomic analysis of bovine papillomatosis

Authors (first, second and last of 5)
- Débora M. Barreto
- Gerlane S. Barros
- Marcus V. A. Batista
- Content type: Research article
- Open Access
- Published: 19 December 2018
- Article: 949
This is part of 1 collection:
Non-human and non-rodent vertebrate genomics
Combining multiple functional annotation tools increases coverage of metabolic annotation

Authors (first, second and last of 5)
- Marc Griesemer
- Jeffrey A. Kimbrel
- Patrik D’haeseleer
- Content type: Research article
- Open Access
- Published: 19 December 2018
- Article: 948
This is part of 1 collection:
Prokaryote microbial genomics
Dichotomy in redundant enhancers points to presence of initiators of gene regulation

Authors
- Wei Song
- Ivan Ovcharenko
- Content type: Research article
- Open Access
- Published: 18 December 2018
- Article: 947
This is part of 1 collection:
Human and rodent genomics
Accuracy of genomic selection for growth and wood quality traits in two control-pollinated progeny trials using exome capture as the genotyping platform in Norway spruce

Authors (first, second and last of 8)
- Zhi-Qiang Chen
- John Baison
- Harry X. Wu
- Content type: Research article
- Open Access
- Published: 18 December 2018
- Article: 946
This is part of 1 collection:
Plant genomics
Multiple trans QTL and one cis-regulatory deletion are associated with the differential expression of cone opsins in African cichlids

Authors
- Sri Pratima Nandamuri
- Matthew A. Conte
- Karen L. Carleton
- Content type: Research article
- Open Access
- Published: 18 December 2018
- Article: 945
This is part of 1 collection:
Comparative and evolutionary genomics
iMGEins: detecting novel mobile genetic elements inserted in individual genomes

Authors (first, second and last of 6)
- Junwoo Bae
- Kyeong Won Lee
- Mina Rho
- Content type: Software
- Open Access
- Published: 18 December 2018
- Article: 944
This is part of 1 collection:
Comparative and evolutionary genomics
Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

Authors (first, second and last of 9)
- Clémence Medina
- Martine da Rocha
- Stéphanie Jaubert-Possamai
- Content type: Research article
- Open Access
- Published: 18 December 2018
- Article: 943
This is part of 1 collection:
Plant genomics
A catalog of annotated high-confidence SNPs from exome capture and sequencing reveals highly polymorphic genes in Norway spruce (Picea abies)

Authors (first, second and last of 9)
- Aïda Azaiez
- Nathalie Pavy
- Jean Bousquet
- Content type: Research article
- Open Access
- Published: 17 December 2018
- Article: 942
This is part of 1 collection:
Plant genomics
DAWN: a resource for yielding insights into the diversity among wheat genomes

Authors (first, second and last of 5)
- Nathan S. Watson-Haigh
- Radosław Suchecki
- Ute Baumann
- Content type: Software
- Open Access
- Published: 17 December 2018
- Article: 941
This is part of 1 collection:
Plant genomics
Identification and characterisation of microRNAs and their target genes in phosphate-starved Nicotiana benthamiana by small RNA deep sequencing and 5’RACE analysis

Authors
- Amanda Huen
- Julia Bally
- Penelope Smith
- Content type: Research article
- Open Access
- Published: 17 December 2018
- Article: 940
This is part of 1 collection:
Plant genomics
Chromosome map of the Siamese cobra: did partial synteny of sex chromosomes in the amniote represent “a hypothetical ancestral super-sex chromosome” or random distribution?

Authors (first, second and last of 12)
- Worapong Singchat
- Rebecca E. O’Connor
- Kornsorn Srikulnath
- Content type: Research article
- Open Access
- Published: 17 December 2018
- Article: 939
This is part of 1 collection:
Comparative and evolutionary genomics
Comparative transcriptome analysis revealed key factors for differential cadmium transport and retention in roots of two contrasting peanut cultivars

Authors (first, second and last of 7)
- Rugang Yu
- Yuanyuan Ma
- Gangrong Shi
- Content type: Research article
- Open Access
- Published: 17 December 2018
- Article: 938
This is part of 1 collection:
Transcriptomic methods
Complex regulation of microRNAs in roots of competitively-grown isogenic Nicotiana attenuata plants with different capacities to interact with arbuscular mycorrhizal fungi

Authors (first, second and last of 5)
- Priyanka Pandey
- Ming Wang
- Karin Groten
- Content type: Research article
- Open Access
- Published: 17 December 2018
- Article: 937
This is part of 1 collection:
Plant genomics
Epigenetic modifications acetylation and deacetylation play important roles in juvenile hormone action

Authors
- Amit Roy
- Subba Reddy Palli
- Content type: Research article
- Open Access
- Published: 14 December 2018
- Article: 934
This is part of 1 collection:
Multicellular invertebrate genomics
Integrated microRNA and mRNA analysis in the pathogenic filamentous fungus Trichophyton rubrum

Authors (first, second and last of 7)
- Lingling Wang
- Xingye Xu
- Qi Jin
- Content type: Research article
- Open Access
- Published: 14 December 2018
- Article: 933
This is part of 1 collection:
Eukaryote microbial genomics
Daphnia galeata responds to the exposure to an ichthyosporean gut parasite by down-regulation of immunity and lipid metabolism

Authors (first, second and last of 7)
- Yameng Lu
- Paul R. Johnston
- Justyna Wolinska
- Content type: Research article
- Open Access
- Published: 14 December 2018
- Article: 932
This is part of 1 collection:
Multicellular invertebrate genomics
Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Authors (first, second and last of 7)
- Cormac Brian Fitzgerald
- Andrey N. Shkoporov
- Colin Hill
- Content type: Research article
- Open Access
- Published: 14 December 2018
- Article: 931
This is part of 1 collection:
Prokaryote microbial genomics
RNA sequencing and anthocyanin synthesis-related genes expression analyses in white-fruited Vaccinium uliginosum

Authors (first, second and last of 6)
- Yang Yang
- Baihui Cui
- Chengwen Zong
- Content type: Research article
- Open Access
- Published: 13 December 2018
- Article: 930
This is part of 1 collection:
Plant genomics
Functional genomics of the digestive tract in broilers

Authors (first, second and last of 7)
- Amélie Juanchich
- Christelle Hennequet-Antier
- Agnès Narcy
- Content type: Research article
- Open Access
- Published: 13 December 2018
- Article: 928
This is part of 1 collection:
Non-human and non-rodent vertebrate genomics
Comparative genomic analysis revealed rapid differentiation in the pathogenicity-related gene repertoires between Pyricularia oryzae and Pyricularia penniseti isolated from a Pennisetum grass

Authors (first, second and last of 17)
- Huakun Zheng
- Zhenhui Zhong
- Zonghua Wang
- Content type: Research article
- Open Access
- Published: 13 December 2018
- Article: 927
This is part of 1 collection:
Eukaryote microbial genomics
When pitch adds to volume: coregulation of transcript diversity predicts gene function

Authors
- Alejandro Cáceres
- Juan R. González
- Content type: Research article
- Open Access
- Published: 13 December 2018
- Article: 926
This is part of 1 collection:
Transcriptomic methods

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