PROJECTS

1KITE

The 1000 Insect Transcriptome Evolution (1KITE) (1KITE wiki, 1KITE database) project aims to reconstruct deep-level phylogenies for insects using core orthologs found in transcriptomes of 1,000 insect species encompassing all recognized insect orders. The project was initiated in early 2011. Xin Zhou is a co-founder and one of the two speakers (Bernhard Misof) of the project. 1KITE has brought together more than 100 internationally recognized experts in molecular biology, morphology, paleontology, embryology, bioinformatics, and scientific computing in a yet unparalleled way. In 2014, 1KITE published the first robust insect phylogeny using the largest phylogenomic dataset ever (1,478 single copy genes for 144 taxa), as the cover story of Science. Since then, progresses have been made for multiple sub-lineages of insects, including Hymenoptera, Trichoptera, Coleoptera, Lepidoptera, etc. In addition to improving our understanding of insect phylogenies, the 1KITE has also contributed to the development and optimization of a series of analytical pipelines/methods, e.g., de novo transcriptome assembly, gene ortholog prediction, hybrid enrichment design, etc. At last, a large gene repertoire is built for the insects, providing an exciting opportunity to study gene diversity and evolution within this diverse group.

Phylogenies:

Phylogenomics toolbox:

Gene evolution in insects:

Gene repertoire:

Biodiversity Genomics

Recent developments in high-throughput sequencing technologies are rapidly changing the way people conduct biodiversity research and practice in programs involving biodiversity assessment, e.g., biomonitoring. My team has focused on developing and optimizing genomic approaches to characterizing insect communities, which typically involves sequencing of bulk samples composed of a large variety of insect groups, a.k.a. "insect soup". In particular, we advocate a new strategy called PCR-free mitochondrial-metagenomics (a.k.a. mitochondrial genome skimming), where bulk DNA is directly sequenced without target gene amplification and then compared with reference barcode genes or mito-genomes. This approach allows us to understand insect diversity both qualitatively and quantitatively.

Trichoptera Barcode of Life

DNA barcoding, the use of standard, short DNA fragments for species identification, provides an alternative approach in characterizing biodiversity. The International Barcode of Life (iBOL) project has constructed comprehensive DNA barcode libraries for many organismal groups. In 2007, Xin Zhou initiated the Trichoptera Barcode of Life project, which now has barcode coverages for nearly 1/3 of known caddisfly species (15,000 globally), covering all extant families and 2/3 genera. This collaborative project contains barcode references for many common caddisfly species of the world, facilitating species identification where morphology approves difficult (immature, female). As part of integrative evidence, DNA barcodes have revealed many cases of cryptic diversity in Trichoptera and accelerated larval identification and description. A summary of the Trichoptera barcoding project was recently published in Philosophical Transactions of the Royal Society B: Biology Science.

Trichoptera Barcode of Life
Larval caddisflies of Churchill
Barcoding Trichoptera of Great Smoky Mountains
Ephemeroptera, Plecoptera, and Trichoptera of Churchill
Larval association using DNA sequences
Full-length barcodes for 1$
Larvae of Chinese Hydropsychidae: I, II, III

Pollination diversity of Chinese honeybee

The Chinese honeybee (Apis cerana) is mainly distributed in east Asia including a large portion of China, pollinating many native floras. These endemic pollinators are facing a critical risk of population drop due to habitat loss, insecticide, disease, and the introduction of the western honeybees (Apis mellifera). As local bee farms are encouraged to increase bee populations by importing hives from other regions of China, the chances of losing endemic genomic traits of many local populations are very high. Similarly, we know very little about the pollination diversity (i.e. eco-services to local floras) of the Chinese honeybees. These gaps of knowledge are major roadblocks for bee conservation and management. Work is being scheduled to understand what flowering plants are A. cerana visiting in time and space. Genomic techniques, such as DNA metabarcoding and mitochondrial genome skimming, will be applied in this research.

Honeybee gut microbiota

Although the gut-microbiota composition of A. cerana is generally similar to that of A. mellifera in terms of core bacteria, distinct differences have been observed between these two species. Given interesting variations in biology, ecology, as well as threats faced by these two closely related bees, it would be crucial to understand how is microbiota involved in the survival of A. cerana, and how that might differ from A. mellifera. We are currently surveying the diversity of gut-microbes for geographic populations of A. cerana.