Database Update Completed

Despite my expectation included at the end of my previous database update notification, many of us are still in the midst of lasting anxiety caused by the COVID19 pandemic, I guess. To be honest, I did not imagine that it would last so long.

In this update, the database has adopted Ensembl release 104 and Ensembl Genome release 51. The subset of the database derived from NCBI has also been updated.

In total, 39 species based on recently released genome sequences have been newly covered, which are marked with '*' in the Species page.  

I mostly enjoy adding new species to this page (based largely on manual steps) and memorizing their names, while it can be a pain if I have little time for the work. The species that attracted me the most in the today's work was this species - superb fairywren (ルリオーストラリアムシクイ), which lives in Eastern Australia and is famous for sexual dimorphism.

Because of my new appointment at National Institute of Genetics in Mishima, I need to make some decisions about the continuation of this and other web servers. Still, nothing will change for an upcoming year, I believe.

Shigehiro Kuraku

Update in April 2020, in the midst of the COVID-19 threat

After a very long interval (ca.2 years), I have updated the sequence database for aLeaves. This update does not only incorporate an increment in NCBI but also encompasses some of the species in Ensembl and Ensembl Metazoa introduced after the last update in 2018 (Ensembl release 93 and Ensembl Metazoa release 38). In total, 10 sauropsids (reptiles and birds), 6 actinopterygian fishes, and 1 invertebrate deuterostome have been newly included (marked with '*' in this Species page) which are listed below:

Sauropsids
Dromaius novaehollandiae (emu)  
Struthio camelus australis (African ostrich)   
Strigops habroptila  (owl parrot or kakapo) 
Crocodylus porosus (Australian saltwater crocodile)
Pogona vitticeps (central bearded dragon)
Notechis scutatus (Mainland tiger snake)
Chelonoidis abingdonii (Abingdon island giant tortoise)
Sphenodon punctatus (tuatara)   
Salvator merianae (Argentine black and white tegu)    
Gopherus agassizii (Agassiz’s desert tortoise)

Actinopterygian fishes
Esox lucius (northern pike)
Ictalurus punctatus (channel catfish)   
Hippocampus comes (tiger tail seahorse)   
Mola mola (ocean sunfish)   
Paramormyrops kingsleyae (elephant fish or elephant nose fish)   
Scleropages formosus (Asian arowana)

Invertebrate deuterostome
Branchiostoma lanceolatum (European lancelet or Mediterranean amphioxus)

More species (especially, mammals and actinopterygian fishes) have been covered by Ensembl, but I have adopted only the species above, to minimize the manual and computational load of maintenance while maximizing the species diversity.

I truly hope that we will be in a more comfortable world when I commit the next update.

Stay safe and healthy,

Shigehiro Kuraku

Update the database to include approx. 40 species

More than a year after the last update, I have updated all the databases to incorporate Ensembl release 93 and gene models of quite a few species with emerging genome-wide sequence data. The species newly introduced have been marked with a red asterisk ('*') in the species list in this page.

Particularly, I am delighted to announce that they now include three elasmobranch shark species, brownbanded bamboo shark, cloudy catshark, and whale shark, whose genome assemblies and gene models were produced in my lab in Kobe (see our original paper published online today in Nature Ecology and Evolution).

I have also included gene models of the Madagascar ground gecko Paroedura picta for which my lab performed de novo genome sequecing and gene prediction (see our original paper published earlier this year in BMC Biology).

Shigehiro Kuraku

Databases updated to include 10 more invertebrate species

With one week delay, I have updated all the databases for searches at aLeaves. This reflects inclusion of new species at EnsemblMetazoa release 31 listed below.

• Belgica antarctica (Antarctic midge)
• Bombus impatiens (common bumblebee)
• Lepeophtheirus salmonis (salmon louse)
• Lingula anatina (a brachiopod)
• Lucilia cuprina (Australian sheep blowfly)
• Octopus bimaculoides (California two-spot octopus)
• Sarcoptes scabiei (itch mite): gene set SscaA1.1 from VectorBase
• Stegodyphus mimosarum (African social velvet spider)
• Strongyloides ratti (parasitic nematode): from WormBase WS250
• Thelohanellus kitauei (a myxosporean)

To see where these individual species are categorized, please refer to the Species page (marked with '*') at the server.

Please feel free to contact me if you have any question, bug report, or request of adding more species.

S. Kuraku

aLeaves Databases Update Scheduled

Let me announce to you that I plan to update the aLeaves databases next Monday on the 27th - it has been more than a year since the last update.

This time, ten invertebrate species new to Ensembl Metazoa will be added to the aLeaves species list. In addition, as usual, gene sets for some species will be revised, thanks to new Ensembl gene build, and new sequences in NCBI GenPept will be included in the database 7 and 13.

Shigehiro Kuraku

aLeaves databases based on Ensembl 76

It took more than half a year since the last update. At aLeaves, now you have access to a new set of databases including latest sequences from Ensembl release 76 announced just last week. The species newly included as a result of this update are below:

Papio anubis (Olive baboon) in Database 3 (non-human eutherians)

Alligator sinensis (Chinese alligator) & Poecilia formosa (Amazon molly) in Database 5 (non-mammalian vertebrates)

Onchocerca volvulus in Database 10 (nematodes)

I know that there are many more metazoan speices whose genome sequencing has been conducted, than covered at aLeaves, but basically I include only species whose predicted peptide sequences are available somewhere online, and if not in Ensembl, the products from the genome project should already be published. Still, my knowledge is not enough, so please let me know if you know any speices that fits this criteria.

Next update soon

I will include the sequences from the next Ensembl release (76) in the next update of aLeaves databases.

Previously, I announced that I would update them by the end of July, but please wait for a while for the Ensembl release 76 to be out.

S. Kuraku

Update completed with some new species

To adhere to the latest taxonomic coverage of Ensembl and Ensembl Metazoa, the databases for aLeaves have been updated. The below species have been newly included :

Arthropods
Strigamia maritima
Tetranychus urticae
Megaselia scalaris
Rhodnius prolixus
Anopheles darlingi
 
Nematodes
Pristionchus pacificus
Loa loa
Caenorhabditis japonica
Caenorhabditis brenneri
Caenorhabditis remanei

At the same time, new sequences at NCBI Protein (based on submissions of individual researchers) have also been incorporated into the database 7 and 13.

For some species indicated with '#' in the Species page, the peptide sequence sets are available now at Ensembl or Ensembl Metazoa, although they were available only in other site, such as NCBI Protein. We have newly adopted those new resources at Ensembl or Ensembl Metazoa, but also have basically kept the sequence sets that aLeaves has adopted so far.

Plus, I have included the protein-coding gene set of the sea lamprey (Petromyzon marinus) predicted by the genome annotation consortium (Smith et al., 2013. Nat. Genet.) in the database 6 (for 'Cartilaginous fishes and cyclostomes'), because the gene set available at Ensembl (which aLeaves has adopted so far) is quite different from the consortium dataset and may not be comprehensive enough.

Update of aLeaves database

I plan to update the aLeaves sequence databases by the end of this week.

With this scheduled update, the taxonomic coverage at aLeaves will adhere to that of Ensembl release 72 (for vertebrates) and Ensembl Metazoa release 19 (for invertebrates).

I will announce the date and time of the update at the aLeaves main web site.

Updated !

Details of the update are as follows:

New Ensembl release 70 and EnsemblGenomes Metazoa release 17

Data sets derived from 'Ensembl' and 'EnsemblGenomes Metazoa' have been updated to adhere the latest releases.


New species

Pacific oyster (Crassostrea gigas)

wasp (Nasonia vitripennis)

Southern platyfish (Xiphophorus maculatus) according to Ensembl release 69 and later

Ferret (Mustela putorius furo) according to Ensembl release 69 and later


Altered partitioning between Database 5 & 6

Previously, sequences of the sea lamprey (Petromyzon marinus) were included in Database 5 together with other vertebrates available at Ensembl, while Database 6 has only a single cartilaginous fish, Callorhinchus milii. In the latest setting, sea lamprey sequences are included in Database 6, labelled 'Non-osteichthyan vertebrates'.


'Category ID'

Previously, only sequences from genome-wide resources (also human RefSeq data set) had Species ID (e.g., 'HOMSA' for human) which is recognized at  data set refinement steps the MAFFT server.

To give visual cues for sequences derived from NCBI Protein (Database 7 and 13), I have introduced 'Category ID', which is explained in the table in the 'Species' page .


Additional notes

In parallel with the improvement of the aLeaves server, the interactivity of the MAFFT server is also being improved, in order to better process data sets forwarded from the aLeaves server. Please also try the improved work flow between the two servers by clicking on the link under 'Proceed to tree building' in aLeaves results page.

An update of databases scheduled in mid Feb

I plan to update some aLeaves databases in mid February. The change will include the adoption of the latest Ensembl release.