Review on the computational genome annotation of sequences obtained by next-generation sequencing

GF Ejigu, J Jung - Biology, 2020 - mdpi.com
Simple Summary Due to the development of high-throughput sequencing technologies,
computational genome annotation of sequences has become one of the principal research …

Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions

B Pucker, I Irisarri, J de Vries, B Xu - Quantitative Plant Biology, 2022 - cambridge.org
Third-generation long-read sequencing is transforming plant genomics. Oxford Nanopore
Technologies and Pacific Biosciences are offering competing long-read sequencing …

Ancient gene linkages support ctenophores as sister to other animals

DT Schultz, SHD Haddock, JV Bredeson, RE Green… - Nature, 2023 - nature.com
A central question in evolutionary biology is whether sponges or ctenophores (comb jellies)
are the sister group to all other animals. These alternative phylogenetic hypotheses imply …

Graph pangenome captures missing heritability and empowers tomato breeding

Y Zhou, Z Zhang, Z Bao, H Li, Y Lyu, Y Zan, Y Wu… - Nature, 2022 - nature.com
Missing heritability in genome-wide association studies defines a major problem in genetic
analyses of complex biological traits,. The solution to this problem is to identify all causal …

Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics

T Yang, R Liu, Y Luo, S Hu, D Wang, C Wang… - Nature …, 2022 - nature.com
Complete and accurate reference genomes and annotations provide fundamental resources
for functional genomics and crop breeding. Here we report a de novo assembly and …

Construction of a chromosome-scale long-read reference genome assembly for potato

GM Pham, JP Hamilton, JC Wood, JT Burke… - …, 2020 - academic.oup.com
Background Worldwide, the cultivated potato, Solanum tuberosum L., is the No. 1 vegetable
crop and a critical food security crop. The genome sequence of DM1–3 516 R44, a doubled …

The complete and fully-phased diploid genome of a male Han Chinese

C Yang, Y Zhou, Y Song, D Wu, Y Zeng, L Nie, P Liu… - Cell Research, 2023 - nature.com
Since the release of the complete human genome, the priority of human genomic study has
now been shifting towards closing gaps in ethnic diversity. Here, we present a fully phased …

InsectBase 2.0: a comprehensive gene resource for insects

Y Mei, D **g, S Tang, X Chen, H Chen… - Nucleic acids …, 2022 - academic.oup.com
Insects are the largest group of animals on the planet and have a huge impact on human life
by providing resources, transmitting diseases, and damaging agricultural crop production …

Origins and evolution of extreme life span in Pacific Ocean rockfishes

SRR Kolora, GL Owens, JM Vazquez, A Stubbs… - Science, 2021 - science.org
Pacific Ocean rockfishes (genus Sebastes) exhibit extreme variation in life span, with some
species being among the most long-lived extant vertebrates. We de novo assembled the …

TSEBRA: transcript selector for BRAKER

L Gabriel, KJ Hoff, T Brůna, M Borodovsky, M Stanke - Bmc Bioinformatics, 2021 - Springer
Background BRAKER is a suite of automatic pipelines, BRAKER1 and BRAKER2, for the
accurate annotation of protein-coding genes in eukaryotic genomes. Each pipeline trains …