Indian Peacock genome sequence, its comparative analysis and demographic history

It has become customary for me to put any manuscript on the biorxiv way before it gets published. My first manuscript to land on the pre-print server was the killer whale culture manuscript way back in Feb 2016. The date is actually very important as this  was when biorxiv really became main stream in biology with the number of monthly submission going from 60 to 200 per month. Subsequently, the bird comparative population genomics manuscript was on biorxiv before getting published.

Now, very recently the genome of the Indian Peacock was sequenced by Dr. Vineet Sharma from IISER Bhopal. The amount of press coverage was considerable. The Hindu, Mongabay and The times of India all had something to say about this genome. Being part of the team, pushing for posting of the peacock genome manuscript on biorxiv seemed the most obvious thing to do. The manuscript has now been accepted by the journal Frontiers in Genetics after two rounds of interactive review. Screenshot of the provisionally accepted abstract is given below. 

Interestingly, it seems that the Peacock genome is the first bird genome to come out of India. The International Chicken Genome Sequencing Consortium published the first bird genome in 2004. Almost one and half decades later, we have managed to claim a bird genome sequence, even if it is based on paired-end sequencing only. Great effort has been made on the data analysis front to make up for the lack of mate-pair, nanopore, pacbio, optical mapping, genetic map, BAC and other fancy forms of data. Yet, one has to remember that this goes to suggest that perhaps we lag behind rest of the world by almost 15 years atleast in this field.

SLR's whose function does not involve taking photographs

SLR's are a type of camera that let the person using it to see through the lens and actually see the image that is being captured based on a clever use of a mirror and prism system. However, we are not talking about these SLR's in this post. Rather, we come up with a new expansion for SLR's in the form of ssDNA binding protein-like receptors. After being on bioRxiv for a fairly short period, this manuscript has been published by the Immunobiology journal. It has to be noted that the wait times for editorial decisions were reasonable and reviewer comments were well thought. The initial submission was in Feb 2018 and the first revision was already resubmitted in June 2018. Hence, this journal is definitely a good avenue for publishing immunology research.

This paper is a moderately straightforward bioinformatic exercise.  However, the amount of domain knowledge that comes into play is extraordinary for an immunology novice. Interferon induction, innate immune sensors, host range breadth, Baltimore classification are just some of the concepts that all had to be weaved together to make this hypothesis come to life. Without a doubt, the bachelor course "Flow of Genetic Information" that I taught last semester was an important connecting link that made this paper possible. The fact that the title "A hypothetical new role for single-stranded DNA binding proteins in the immune system" itself has the word hypothetical in it makes this a very different paper than the large dataset based papers that have been my forte.  

Unfortunately, we don't go beyond some preliminary testing of our hypothesis. Hopefully, this paper will stimulate debate and fuel a more sophisticated search for much more single-stranded DNA sensors. At the very least, stronger and unequivocal evidence in favor of TLR9 and IFI16 would be a step in the correct direction. Fine-scale dissection of the abilities of these innate immune sensors to distinguish between very similar yet distinct molecules is without any doubt challenging to validate experimentally. An exceedingly clever experimental paper that does this would be the ideal outcome that we would like to see as a result of this brief bioinformatic venture.

So long and thanks for all the fish : Does the bottlenose dolphin demographic history have a message?

Bottlenose dolphins have enthralled human beings by their amazing performances in dolphinariums and have been part of popular culture becoming the most popular of all dolphin species, while also stimulating public concern over the welfare of display animals. The song "So Long, and Thanks for All the Fish" has established a cult following for this species. 

The genome of the common bottlenose dolphin Tursiops truncatus was sequenced during the boom days of the genomics era when assembling a genome was still considered cool. This initial effort was part of the 29 mammals project. However, we have long since passed that point. So, by the time Yim et al., sequenced the genome of the Minke whale, it was standard practice to look at aquatic adaptation in numerous related species. In addition to looking at coding level changes, they cleverly "Estimated whale population size history". Existing cetacean genomes were also roped into this analysis of effective population size history.

Of the four genomes analyzed in the Yim et al., paper the most surprising result was seen for the bottlenose dolphin that showed an increase in Ne that started at the beginning of the ice age. If this pattern were true it could have interesting implications for understanding the effect of climate change on the demographic history of species. In our preprint titled "Population genomic analysis reveals contrasting demographic changes of two closely related dolphin species in the last glacial", we delve into bottlenose demographic history. 

Few key highlights of our manuscript:

1. In addition to analyzing the genomes of four common bottlenose dolphin individuals from the public sequencing repository (SRA), we also sequenced four genomes of Indian bottlenose dolphin individuals. The comparison of these 8 genomes shows contrasting demographic changes in the two sister species. 
2. We use 3 different programs (PSMC, MSMC & SMC++) to reconstruct the demographic history of both dolphin species.
3. After reconstructing the changes in effective population size, we use the pseudo-diploid analysis of all pairs of these 8 genomes to analyze 28 pseudo-diploid genomes. Based on this we estimate the split times between species as well as between populations within species.
4. For all our analysis we perform quality control to ensure robustness of our results. Repeat regions are identified using repeat masker program and masked out. Coverage of each individual genome is considered to rule out the possibility of coverage dependent biases in results. Although mutation rate and generation times are fairly well-known for cetaceans, we looked at the combinations of 4 mutation rate estimates and 4 generation time estimates. We find that the main conclusions remain unaltered even after varying all these parameters.
5. Considerable effort is spent on optimizing the settings of the PSMC program. First, the bootstrap analysis is done with 100 bootstraps for each individual to look at within genome heterogeneity. Next various setting for the -p parameter was tried out to have sufficient resolution in the PSMC results while also having a sufficient number of recombination events after 20 iterations of the program.

It is worth noting that the field of population size history estimation has matured well. New methods that are able to estimate Ne in more recent times have helped answer many questions that were not possible to answer with older methods. For example, the recent analysis of the Tibetan frog (Nanorana parkeri) genome using both G-PhoCS and PSMC brings traditional demographic analysis together with PSMC which had made its way into genomic papers all by itself.

A truly new direction for the use of effective population size histories is presented in a preprint posted on biorxiv titled  "Comparative demography elucidates the longevity of parasitic and symbiotic relationships.". Despite the immense potential in using comparative demography to answer questions in studying parasitic and symbiotic relationships, it will be interesting to see how robust these inferences are and whether they can be supported by independent sources of evidence. Our study on dolphins also explores this aspect of the contribution of predator and prey abundance on population size. After sitting on biorxiv for over a year, it is finally out as a letter in MBE.

Anandi Gopal Joshi - Google Doodle - This year will probably see one for Janaki Ammal

It has been a while since I have written about JA. A lot has happened in that time. The most significant new thing is the Janaki Ammal Scholarships instituted by the John Innes Centre. I am very curious to know if students have joined a Ph.D. position availing this fellowship.  

Closer to home, today is the 153rd birthday of Anandi Gopal Joshi (one of the earliest Indian female physician). Google in its infinite wisdom decided to honor her with a doodle (see below). She has a degree certificate in one hand and appears to be wearing a stethoscope.  The image behind her is also split into two halves, one half is what could be her native country which had a scarcity of multi-storied houses during her time and the other half seems to be a townhouse in rural US of A. The trees also change accordingly.

For JA, they would need to have 3 continents, some sugar cane, brinjal and most definitely have karyotypes with various ploidy levels.

Now all I can hope for is that the folks at Google put two and two together and make a doodle for Janaki Ammal this year. Her birthday is on 4th of November and it will be 121 years. But then again it might take 32 more years. 

Getting creative with molecular biology

Creating something new using concepts you have learned leads to a better understanding of the subject.  Instead of simply remembering the ideas of somebody else, one can actually remember how one used those ideas to create something new. Yet, it is not easy to convince educators about the utility of using visual arts to teach science. A recent review titled "The Role of the Visual Arts in Enhancing the Learning Process" tries to make a case for visual arts in enhancing the learning process.

The class on "Flow of genetic information" that i am currently teaching got a chance to get creative this week. They were given 3 activities to do in the class.

Task 1: Compare DNA replication, Transcription & Translation and create an easy to understand diagram/table.

Task 2: Compare different information flow processes considering as many examples as you can think of

Task 3: Show the hierarchical organization of DNA

• Use color chalk if needed.
• Pay special attention to differences between prokaryotes & eukaryotes

Here are the end results:
Task 1

Task 2

Task 3

Does the central dogma paper have hidden Masonic iconography?

A lot has been written about Freemasonry in recent times. One of the most prominent features of the iconography associated with free masons is the Eye of Providence. The traditional depiction of this involves a triangle or pyramid shape.

If you have read the paper Central Dogma of Molecular Biology by Francis Crick, you might have noticed that the paper is filled with figures that look like above screen grab. It is a triangle and has some circles. This would actually be a very smart way to sneak in Masonic iconography. Was Francis Crick a free mason? It is actually possible, as it has been argued that some of the most powerful and intellectually gifted people have been part of free masonry.

A beetle to be proud of

June is almost over. It has already started raining here in Bhopal. The weather is now at that pleasant optima when it's neither too hot nor too rainy. Wish it could stay like this forever. Humidity is another thing altogether. It is really a pleasure to go out walking in the campus.

You have the frogs making their calls in one place and the beetles roaming in another. See below picture of a beetle we managed to capture.