About MPS

PacBio HiFiLong, accurate reads Oxford NanoporeONT ultra-long reads Hi-CChromatin contacts v3jf13 pseudochromosomes

Raw sequencing data

  • PacBio HiFi33.0 Gbp · read N50 18.2 kb · ≈32×
  • Oxford Nanopore (ONT)30.1 Gbp · mean read 51.6 kb · ≈29×
  • Hi-C83.3 Gbp · PE150 · ≈81×

The organism: a mulberry psyllid

Paurocephala sauteri is a jumping plant louse (Hemiptera: Sternorrhyncha: Psylloidea) that feeds on the phloem of mulberry (Morus). Nymphs and adults gather on young leaves and shoots; heavy infestations curl and yellow the foliage and coat it with honeydew, which lowers the quality of the leaves harvested for silkworm rearing.

The assembly: chromosome-level

The 1.03 Gb genome was assembled from PacBio HiFi and Oxford Nanopore (ONT) long reads together with Hi-C chromatin-contact data into 13 pseudochromosomes spanning 886.0 Mb (85.7% of the assembly); the remaining 147.3 Mb is placed on 2,448 unanchored sequences. BUSCO completeness of the assembly is 94.9% against the Hemiptera set (n = 2,510).

The annotation: integrated evidence

20,591 protein-coding genes with 22,977 transcripts and 126,222 exons. Functional evidence covers 12,970 genes by GO, 14,904 by InterPro and 11,430 by eggNOG; 3,164 tRNAs, 606 rRNAs, 240 other non-coding RNAs and 471 pseudogenes complete the annotation. BUSCO completeness of these annotated proteins is 92.2% against the Hemiptera set (n = 2,510).

Length of the 13 pseudochromosomesBar chart of chromosome length in megabases: Chr01 98.2 Mb, Chr02 90.5 Mb, Chr03 86.1 Mb, Chr04 82.7 Mb, Chr05 81.8 Mb, Chr06 76.5 Mb, Chr07 66.5 Mb, Chr08 61.2 Mb, Chr09 55.0 Mb, Chr10 53.2 Mb, Chr11 51.2 Mb, Chr12 49.8 Mb, Chr13 33.4 Mb.025507510098.2Chr0190.5Chr0286.1Chr0382.7Chr0481.8Chr0576.5Chr0666.5Chr0761.2Chr0855.0Chr0953.2Chr1051.2Chr1149.8Chr1233.4Chr13Length (Mb)Total 886.0 Mb
13 pseudochromosomes — length of each chromosome in Mb, summing to 886.0 Mb. Chr01 is the largest (98.2 Mb) and Chr13 the smallest (33.4 Mb).
Functional annotation coverage of the protein-coding genesHorizontal bars out of 20,591 protein-coding genes: GO 12,970 genes (63.0%); InterPro 14,904 genes (72.4%); eggNOG 11,430 genes (55.5%).GO12,970 (63.0%)InterPro14,904 (72.4%)eggNOG11,430 (55.5%)010,29520,591Genes with at least one hit20,591 protein-coding genes
Functional annotation coverage — number of the 20,591 protein-coding genes with at least one GO term (12,970), InterPro signature (14,904) or eggNOG orthologous group (11,430).

Genome Overview

A chromosome-level, HiFi-based assembly of the mulberry psyllid with integrated functional annotation.

Tool Center

Browse, align and search the Psauteri_v3jf genome. Each tool opens with a link back to this page; data downloads are available from the top navigation.

Gene Search
MPS Annotation API
Look up genes by ID or functional keyword (description / GO / InterPro / KEGG) and inspect their annotation.
Open tool
BLAST
SequenceServer
Run sequence similarity searches against the P. sauteri genome, CDS and protein sets, with nucleotide and protein query types.
Open tool
Genome Browser
JBrowse 2
Interactively browse the 13 pseudochromosomes, the gene models and the annotated repeats of Psauteri_v3jf.
Open tool
HMMER Search
HMMER 3.4 · Pfam-A
Search homologs (phmmer), annotate domains (hmmscan) or mine family members (hmmsearch) with HMMER 3 — against the psyllid proteome and Pfam-A.
Open tool
Expression Atlas
RNA-seq TPM matrix
Browse gene-level TPM across the female adult (FA), male adult (MA) and nymph (N5) transcriptomes — 6 samples, 3 biological groups.
Open the atlas
Planned
Synteny & Orthologs
Cross-species comparison
Compare the P. sauteri chromosomes with other Sternorrhyncha genomes and trace conserved gene order.
In development

Research Team

The research group of Prof. Fuping Lu, Institute of Environment and Plant Protection, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, Hainan.

* Correspondence: fuping_36@163.com

Data Downloads

The complete Psauteri_v3jf v1.0 release package: assembly, gene models, sequence sets and the annotation tables used by this database. Files are served directly; verify them against md5sum.txt.