Extrachromosomal mobile genetic elements (eMGEs), including phages and plasmids, that can move across different microbes, play important roles in genome evolution and shaping the structure of microbial communities. However, we still know very little about eMGEs, especially their abundances, distributions and putative functions in microbiomes. Thus, a comprehensive description of eMGEs is of great utility. Here we present mMGE, a comprehensive catalog of 517 251 non-redundant eMGEs, including 92 492 plasmids and 424 759 phages, derived from diverse body sites of 66 425 human metagenomic samples. About half the eMGEs could be further grouped into 70 074 clusters using relaxed criteria (referred as to eMGE clusters below). We provide extensive annotations of the identified eMGEs including sequence characteristics, taxonomy affiliation, gene contents and their prokaryotic hosts. We also calculate the prevalence, both within and across samples for each eMGE and eMGE cluster, enabling users to see putative associations of eMGEs with human phenotypes or their distribution preferences. All eMGE records can be browsed or queried in multiple ways, such as eMGE clusters, metagenomic samples and associated hosts. The mMGE is equipped with a user-friendly interface and a BLAST server, facilitating easy access/queries to all its contents easily. mMGE is freely available for academic use at: https://mgedb.comp-sysbio.org.

Haploids and doubled haploids are critical components of plant breeding. This review is focused on studies on haploids and double haploids inducted in cucurbits through in vitro pollination with irradiated pollen, unfertilized ovule/ovary culture, and anther/microspore culture during the last 30 years, as well as comprehensive analysis of the main factors of each process and comparison between chromosome doubling and ploidy identification methods, with special focus on the application of double haploids in plant breeding and genetics. This review identifies existing problems affecting the efficiency of androgenesis, gynogenesis, and parthenogenesis in cucurbit species. Donor plant genotypes and surrounding environments, developmental stages of explants, culture media, stress factors, and chromosome doubling and ploidy identification are compared at length and discussed as methodologies and protocols for androgenesis, gynogenesis, and parthenogenesis in haploid and double haploid production technologies.

Known gut virus diversity is currently skewed by challenges in fecal virus-like particles (VLPs) enrichment and towards active viruses detectable in shotgun metagenomic sequencing. Here, we apply a virus detection procedure, including vigorous enrichment to harvest large quantity of VLPs, and combined Illumina and PacBio sequencing, to fecal samples of 180 Chinese volunteers. Integrated assembly of the short- and long-reads generate more and longer viral genomes compared to existing methods. The resulting viral genome dataset, referred as to the Human Gut Virome collection (HGV), covers the full spectrum of the gut virome, i.e., an HGV-trained machine-learning algorithm recognizes most (81~97%) public gut viruses; meanwhile, it contains 71.50% novel genomes, including 20% that cannot be recognized by machine-learning models trained on public viruses. Further analysis of the HGV reveals a substantially higher diversity of the human gut virome. For example, we identify thousands of viral genomes that are more prevalent than crAssphages and Gubaphages, the two most diverse phages in the human gut, and several viral clades that are more diverse than the two. Tother, our results indicate a vastly enlarged gut viral diversity that significantly broadens our knowledge on the viral dark matter of the human gut microbial ecology.