Genome complexity: de novo or orphan genes (Introduction)

by David Turell , Saturday, February 23, 2019, 19:57 (2100 days ago) @ David Turell

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https://www.cambridge.org/core/books/next-generation-systematics/next-generation-apomor...

"Shortly after the publication of the first whole genome in 1995, it became clear that species possessed many more taxonomically unique, or restricted, gene sequences than expected. When seven whole genomes had been published, R. F. Doolittle, a molecular biologist of many decades’ experience, commented: ‘I am surprised that so many open reading frames remain as unidentified [i.e. unique] reading frames’. Five years later, when 60 whole genomes had been sequenced, he called taxonomically unique sequences ‘the biggest surprise in genome sequencing’.

" Today, with whole-genome sequencing further facilitated by next generation technologies, these taxonomically restricted genes, also known as orphan genes, or ‘ORFans’) continue to be discovered in every newly sequenced species genome. These genes represent one of the most intriguing aspects of systematics, lying at the intersection of genomics, genetics, comparative and structural biology, phylogenetics and evolution. Yet, by their very nature, they are difficult to study using conventional comparative approaches and attract little research funding.

My comment: They are part of 'so-called junk' DNA and definitely appear to have functionality. As orphans they do not come from preceding organisms in evolution. This is not what Darwin expected:

"'a chapter on orphan and taxonomically restricted genes in Next Generation Systematics (Cambridge University Press 2016) by Richard Buggs and Paul Nelson. There they ventured a prediction: “We suspect that if one’s model system or species of study does something unique and interesting, TRGs [taxonomically restricted genes, aka orphans] will be at least partially responsible, and worth seeking out.'”

https://uncommondescent.com/evolution/id-predictions-on-orphan-genes-and-symbiosis/

"…the ANG [accessory nidimental gland] of E. scolopes is highly derived and shows an elevated evolutionary accumulation in both its coding (novel gene formation) and noncoding (turnover of the regulatory sequence) complements. The ANG is a secretory organ within the female reproductive system containing a bacterial consortium that is deposited into the egg capsule and is believed to play a role in defense from fouling and/or pathogens during embryogenesis (7, 8, 15, 16). Taxonomically restricted (i.e., orphan) genes have contributed to the evolution of unique tissues and organs in a number of animals."