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What is Tsumugi's gender? I know that she is created from Hoshijiro's placenta and shares the same seiyuu, but does that also means that they are of the same gender? Was there any evidence that shows that Tsumugi is a female?

I know that Nagate is in love with Tsumugi as Tsumugi was born from placenta Hoshijiro, but since IRL same gender relationship do exist, I don't think this can be used to prove that Tsumugi is a female.

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Shiraui Tsumugi is a 融合個体 (yuugou kotai, meaning "fusion individual organism") created with the intent of serving as a biological weapon (生体兵器 = seitaiheiki). As such, Ochiai's intent as to whether Tsumugi has a sex and/or gender is unknown.

“Sex” and “gender” bear disparate meanings (though many people accidentally conflate these words). In the technical distinction, “sex” is a neutral word referring solely to physiology including differences in reproductive organs, brain chemistry, and hormones, whereas “gender” refers to cultural constructions/assumptions about what personality traits and behaviors best suit (or are innately connected to) a particular biological anatomy. It is not clear whether or not Tsumugi subscribes to a belief in gender essentialism or what "her" specific concept of "female gender" would include and not include. Tsumugi does not seem to have any focus on or concerns regarding gender identity. However, the creators have implied that Tsumugi identifies as female through the following aspects:

  • Tsumugi was given a female seiyuu (voice actor) and speaks in feminine Japanese rather than masculine Japanese (more details on Japanese gendered language can be found here at Tofugu)
  • Tsumugi's mannerisms culturally align closer to the gender norms of Japanese girls and women than to 1) Japanese men or to 2) Shinatose Izana's mannerisms which were intentionally written as gender-ambiguous (since Izana is intersex)
  • Tsumugi's bodily form features what looks like the shape of a very fluttery dress
  • Tsumugi likes Nagate from the get-go, which could imply that Tsumugi possesses memories of Hoshijiro, who was both biologically female and mentally identified as female

Tsumugi's sex is unknown (whether or not the body has any female anatomy and could reproduce in kind). Gauna are not understood to bear distinct bodily organs, but on the other hand, Gauna placenta are able to replicate a functioning human uterus. In real life, even plants can reproduce and are labeled in science as “male” or “female,” or even “male” and “female” parts on the very same individual plant, without needing to reproduce by sexual intercourse of the human kind (using the words “male” and “female” for these plant parts makes their reproduction easier to describe). On the other hand, some humans cannot naturally reproduce (infertile, or use in vitro fertilization), but no one is unwilling to call them “male” or “female” due to that limitation alone, since that is not what verifies whether or not they are indeed male or female (biologically and in identity). So even without organs it is possible that Tsumugi could be biologically female in addition to identifying as female in gender. Interestingly, Tsumugi's tentacle (触手 = shokushu) arguably looks rather phallic, but it does not seem to be perceived this way by the other characters.

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According to the Knights of Sidonia wiki page, Tsumugi's gender is female.

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